Starting phenix.real_space_refine on Wed Feb 21 16:09:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwa_10036/02_2024/6rwa_10036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwa_10036/02_2024/6rwa_10036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwa_10036/02_2024/6rwa_10036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwa_10036/02_2024/6rwa_10036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwa_10036/02_2024/6rwa_10036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwa_10036/02_2024/6rwa_10036.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 295 5.16 5 C 59955 2.51 5 N 16070 2.21 5 O 18245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1685": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 94565 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 18913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2361, 18913 Classifications: {'peptide': 2361} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 81, 'TRANS': 2277} Chain: "B" Number of atoms: 18913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2361, 18913 Classifications: {'peptide': 2361} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 81, 'TRANS': 2277} Chain: "C" Number of atoms: 18913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2361, 18913 Classifications: {'peptide': 2361} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 81, 'TRANS': 2277} Chain: "D" Number of atoms: 18913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2361, 18913 Classifications: {'peptide': 2361} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 81, 'TRANS': 2277} Chain: "E" Number of atoms: 18913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2361, 18913 Classifications: {'peptide': 2361} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 81, 'TRANS': 2277} Time building chain proxies: 36.26, per 1000 atoms: 0.38 Number of scatterers: 94565 At special positions: 0 Unit cell: (188.16, 192.64, 269.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 295 16.00 O 18245 8.00 N 16070 7.00 C 59955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.72 Conformation dependent library (CDL) restraints added in 13.3 seconds 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22520 Finding SS restraints... Secondary structure from input PDB file: 450 helices and 100 sheets defined 51.0% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.62 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 removed outlier: 3.507A pdb=" N GLN A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 67 removed outlier: 3.604A pdb=" N GLN A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.776A pdb=" N HIS A 79 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.940A pdb=" N GLU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.742A pdb=" N ALA A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 removed outlier: 4.077A pdb=" N ARG A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 removed outlier: 3.610A pdb=" N SER A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 161 through 176 removed outlier: 4.059A pdb=" N ASN A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 219 through 225 removed outlier: 3.766A pdb=" N SER A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.840A pdb=" N ALA A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.517A pdb=" N LEU A 237 " --> pdb=" O HIS A 233 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 313 through 327 removed outlier: 3.582A pdb=" N ILE A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 removed outlier: 3.742A pdb=" N LEU A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 361 removed outlier: 3.723A pdb=" N LEU A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.715A pdb=" N LEU A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.734A pdb=" N LEU A 423 " --> pdb=" O HIS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.617A pdb=" N HIS A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 removed outlier: 3.937A pdb=" N LEU A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 Processing helix chain 'A' and resid 495 through 517 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 536 through 550 Processing helix chain 'A' and resid 559 through 572 Proline residue: A 566 - end of helix Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.675A pdb=" N LYS A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 Processing helix chain 'A' and resid 620 through 642 removed outlier: 3.887A pdb=" N MET A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 637 " --> pdb=" O GLN A 633 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 673 through 690 removed outlier: 3.581A pdb=" N ILE A 678 " --> pdb=" O PRO A 674 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 702 removed outlier: 3.552A pdb=" N ILE A 696 " --> pdb=" O LYS A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.643A pdb=" N LEU A 710 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 731 removed outlier: 3.902A pdb=" N LEU A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 760 Processing helix chain 'A' and resid 765 through 771 removed outlier: 3.830A pdb=" N LEU A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 797 removed outlier: 3.514A pdb=" N TRP A 787 " --> pdb=" O THR A 783 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 826 removed outlier: 3.653A pdb=" N THR A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 821 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 844 Processing helix chain 'A' and resid 856 through 874 Processing helix chain 'A' and resid 881 through 886 removed outlier: 3.912A pdb=" N ILE A 885 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 881 through 886' Processing helix chain 'A' and resid 887 through 892 Processing helix chain 'A' and resid 892 through 897 Processing helix chain 'A' and resid 899 through 912 removed outlier: 3.782A pdb=" N TRP A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 911 " --> pdb=" O SER A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 916 Processing helix chain 'A' and resid 926 through 936 Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.805A pdb=" N VAL A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 962 " --> pdb=" O GLU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1092 Processing helix chain 'A' and resid 1123 through 1129 Processing helix chain 'A' and resid 1147 through 1158 removed outlier: 4.406A pdb=" N SER A1153 " --> pdb=" O GLU A1149 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A1154 " --> pdb=" O GLN A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1162 removed outlier: 3.685A pdb=" N PHE A1162 " --> pdb=" O TYR A1159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1159 through 1162' Processing helix chain 'A' and resid 1197 through 1201 removed outlier: 3.962A pdb=" N ASN A1200 " --> pdb=" O GLY A1197 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A1201 " --> pdb=" O GLU A1198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1197 through 1201' Processing helix chain 'A' and resid 1237 through 1249 removed outlier: 4.001A pdb=" N ILE A1241 " --> pdb=" O GLY A1237 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1339 removed outlier: 3.540A pdb=" N ASP A1337 " --> pdb=" O LYS A1334 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1387 Processing helix chain 'A' and resid 1478 through 1487 removed outlier: 4.052A pdb=" N VAL A1484 " --> pdb=" O ALA A1480 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU A1485 " --> pdb=" O ARG A1481 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG A1486 " --> pdb=" O GLN A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1495 Processing helix chain 'A' and resid 1496 through 1501 removed outlier: 3.527A pdb=" N GLN A1500 " --> pdb=" O SER A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1526 Processing helix chain 'A' and resid 1635 through 1644 Processing helix chain 'A' and resid 1644 through 1657 Processing helix chain 'A' and resid 1659 through 1668 removed outlier: 3.713A pdb=" N ALA A1663 " --> pdb=" O ASN A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1689 through 1694 removed outlier: 3.582A pdb=" N LEU A1693 " --> pdb=" O VAL A1689 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1705 removed outlier: 3.883A pdb=" N SER A1705 " --> pdb=" O PRO A1702 " (cutoff:3.500A) Processing helix chain 'A' and resid 1707 through 1715 Processing helix chain 'A' and resid 1716 through 1740 Processing helix chain 'A' and resid 1743 through 1762 Processing helix chain 'A' and resid 1777 through 1782 Processing helix chain 'A' and resid 1783 through 1800 removed outlier: 3.603A pdb=" N GLN A1787 " --> pdb=" O ALA A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1816 removed outlier: 4.507A pdb=" N ASP A1816 " --> pdb=" O ASN A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1842 removed outlier: 3.854A pdb=" N TYR A1829 " --> pdb=" O VAL A1825 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP A1830 " --> pdb=" O MET A1826 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A1831 " --> pdb=" O LEU A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1888 through 1975 removed outlier: 3.602A pdb=" N MET A1892 " --> pdb=" O ARG A1888 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1996 removed outlier: 3.626A pdb=" N ARG A1982 " --> pdb=" O ASN A1978 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A1996 " --> pdb=" O GLN A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2009 removed outlier: 3.593A pdb=" N ALA A2005 " --> pdb=" O LEU A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2025 through 2114 removed outlier: 3.596A pdb=" N ALA A2039 " --> pdb=" O GLY A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2154 removed outlier: 3.559A pdb=" N TYR A2121 " --> pdb=" O ASN A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2172 Processing helix chain 'A' and resid 2176 through 2194 Processing helix chain 'A' and resid 2207 through 2213 Processing helix chain 'A' and resid 2220 through 2231 Processing helix chain 'A' and resid 2261 through 2266 removed outlier: 3.578A pdb=" N TYR A2266 " --> pdb=" O LYS A2263 " (cutoff:3.500A) Processing helix chain 'A' and resid 2361 through 2368 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.507A pdb=" N GLN B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 67 removed outlier: 3.603A pdb=" N GLN B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.776A pdb=" N HIS B 79 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.940A pdb=" N GLU B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG B 90 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.742A pdb=" N ALA B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 removed outlier: 4.078A pdb=" N ARG B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.610A pdb=" N SER B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 161 through 176 removed outlier: 4.060A pdb=" N ASN B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 193 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.767A pdb=" N SER B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.840A pdb=" N ALA B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.517A pdb=" N LEU B 237 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 313 through 327 removed outlier: 3.581A pdb=" N ILE B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.742A pdb=" N LEU B 333 " --> pdb=" O PRO B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 361 removed outlier: 3.723A pdb=" N LEU B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.715A pdb=" N LEU B 368 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 391 Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.734A pdb=" N LEU B 423 " --> pdb=" O HIS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 442 removed outlier: 3.617A pdb=" N HIS B 439 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 removed outlier: 3.936A pdb=" N LEU B 457 " --> pdb=" O ASN B 453 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B 467 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 485 Processing helix chain 'B' and resid 495 through 517 Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'B' and resid 536 through 550 Processing helix chain 'B' and resid 559 through 572 Proline residue: B 566 - end of helix Processing helix chain 'B' and resid 577 through 591 removed outlier: 3.675A pdb=" N LYS B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 609 Processing helix chain 'B' and resid 620 through 642 removed outlier: 3.886A pdb=" N MET B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 637 " --> pdb=" O GLN B 633 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 655 through 659 Processing helix chain 'B' and resid 673 through 690 removed outlier: 3.581A pdb=" N ILE B 678 " --> pdb=" O PRO B 674 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 679 " --> pdb=" O THR B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 702 removed outlier: 3.552A pdb=" N ILE B 696 " --> pdb=" O LYS B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.644A pdb=" N LEU B 710 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 713 " --> pdb=" O LYS B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 731 removed outlier: 3.902A pdb=" N LEU B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 760 Processing helix chain 'B' and resid 765 through 771 removed outlier: 3.830A pdb=" N LEU B 769 " --> pdb=" O GLY B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 797 removed outlier: 3.514A pdb=" N TRP B 787 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 826 removed outlier: 3.653A pdb=" N THR B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 820 " --> pdb=" O THR B 816 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 821 " --> pdb=" O ALA B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 844 Processing helix chain 'B' and resid 856 through 874 Processing helix chain 'B' and resid 881 through 886 removed outlier: 3.912A pdb=" N ILE B 885 " --> pdb=" O VAL B 881 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR B 886 " --> pdb=" O SER B 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 881 through 886' Processing helix chain 'B' and resid 887 through 892 Processing helix chain 'B' and resid 892 through 897 Processing helix chain 'B' and resid 899 through 912 removed outlier: 3.781A pdb=" N TRP B 903 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 911 " --> pdb=" O SER B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 916 Processing helix chain 'B' and resid 926 through 936 Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.804A pdb=" N VAL B 960 " --> pdb=" O SER B 956 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 962 " --> pdb=" O GLU B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1092 Processing helix chain 'B' and resid 1123 through 1129 Processing helix chain 'B' and resid 1147 through 1158 removed outlier: 4.405A pdb=" N SER B1153 " --> pdb=" O GLU B1149 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR B1154 " --> pdb=" O GLN B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1162 removed outlier: 3.685A pdb=" N PHE B1162 " --> pdb=" O TYR B1159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1159 through 1162' Processing helix chain 'B' and resid 1197 through 1201 removed outlier: 3.963A pdb=" N ASN B1200 " --> pdb=" O GLY B1197 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B1201 " --> pdb=" O GLU B1198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1197 through 1201' Processing helix chain 'B' and resid 1237 through 1249 removed outlier: 4.001A pdb=" N ILE B1241 " --> pdb=" O GLY B1237 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1334 through 1339 removed outlier: 3.540A pdb=" N ASP B1337 " --> pdb=" O LYS B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1383 through 1387 Processing helix chain 'B' and resid 1478 through 1487 removed outlier: 4.052A pdb=" N VAL B1484 " --> pdb=" O ALA B1480 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU B1485 " --> pdb=" O ARG B1481 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG B1486 " --> pdb=" O GLN B1482 " (cutoff:3.500A) Processing helix chain 'B' and resid 1490 through 1495 Processing helix chain 'B' and resid 1496 through 1501 removed outlier: 3.527A pdb=" N GLN B1500 " --> pdb=" O SER B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1521 through 1526 Processing helix chain 'B' and resid 1635 through 1644 Processing helix chain 'B' and resid 1644 through 1657 Processing helix chain 'B' and resid 1659 through 1668 removed outlier: 3.712A pdb=" N ALA B1663 " --> pdb=" O ASN B1659 " (cutoff:3.500A) Processing helix chain 'B' and resid 1689 through 1694 removed outlier: 3.583A pdb=" N LEU B1693 " --> pdb=" O VAL B1689 " (cutoff:3.500A) Processing helix chain 'B' and resid 1701 through 1705 removed outlier: 3.883A pdb=" N SER B1705 " --> pdb=" O PRO B1702 " (cutoff:3.500A) Processing helix chain 'B' and resid 1707 through 1715 Processing helix chain 'B' and resid 1716 through 1740 Processing helix chain 'B' and resid 1743 through 1762 Processing helix chain 'B' and resid 1777 through 1782 Processing helix chain 'B' and resid 1783 through 1800 removed outlier: 3.604A pdb=" N GLN B1787 " --> pdb=" O ALA B1783 " (cutoff:3.500A) Processing helix chain 'B' and resid 1810 through 1816 removed outlier: 4.507A pdb=" N ASP B1816 " --> pdb=" O ASN B1812 " (cutoff:3.500A) Processing helix chain 'B' and resid 1823 through 1842 removed outlier: 3.854A pdb=" N TYR B1829 " --> pdb=" O VAL B1825 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP B1830 " --> pdb=" O MET B1826 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN B1831 " --> pdb=" O LEU B1827 " (cutoff:3.500A) Processing helix chain 'B' and resid 1888 through 1975 removed outlier: 3.602A pdb=" N MET B1892 " --> pdb=" O ARG B1888 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1996 removed outlier: 3.627A pdb=" N ARG B1982 " --> pdb=" O ASN B1978 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B1996 " --> pdb=" O GLN B1992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1998 through 2009 removed outlier: 3.592A pdb=" N ALA B2005 " --> pdb=" O LEU B2001 " (cutoff:3.500A) Processing helix chain 'B' and resid 2025 through 2114 removed outlier: 3.595A pdb=" N ALA B2039 " --> pdb=" O GLY B2035 " (cutoff:3.500A) Processing helix chain 'B' and resid 2117 through 2154 removed outlier: 3.559A pdb=" N TYR B2121 " --> pdb=" O ASN B2117 " (cutoff:3.500A) Processing helix chain 'B' and resid 2168 through 2172 Processing helix chain 'B' and resid 2176 through 2194 Processing helix chain 'B' and resid 2207 through 2213 Processing helix chain 'B' and resid 2220 through 2231 Processing helix chain 'B' and resid 2261 through 2266 removed outlier: 3.578A pdb=" N TYR B2266 " --> pdb=" O LYS B2263 " (cutoff:3.500A) Processing helix chain 'B' and resid 2361 through 2368 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.507A pdb=" N GLN C 34 " --> pdb=" O ASN C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 67 removed outlier: 3.605A pdb=" N GLN C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.776A pdb=" N HIS C 79 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 95 removed outlier: 3.939A pdb=" N GLU C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG C 90 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.741A pdb=" N ALA C 117 " --> pdb=" O PHE C 113 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 removed outlier: 4.077A pdb=" N ARG C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 148 removed outlier: 3.609A pdb=" N SER C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 161 through 176 removed outlier: 4.060A pdb=" N ASN C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 219 through 225 removed outlier: 3.766A pdb=" N SER C 225 " --> pdb=" O GLN C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.840A pdb=" N ALA C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.518A pdb=" N LEU C 237 " --> pdb=" O HIS C 233 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 254 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 313 through 327 removed outlier: 3.581A pdb=" N ILE C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 removed outlier: 3.742A pdb=" N LEU C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.723A pdb=" N LEU C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.715A pdb=" N LEU C 368 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 391 Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 417 through 428 removed outlier: 3.734A pdb=" N LEU C 423 " --> pdb=" O HIS C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 442 removed outlier: 3.617A pdb=" N HIS C 439 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 469 removed outlier: 3.937A pdb=" N LEU C 457 " --> pdb=" O ASN C 453 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 467 " --> pdb=" O THR C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 485 Processing helix chain 'C' and resid 495 through 517 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 536 through 550 Processing helix chain 'C' and resid 559 through 572 Proline residue: C 566 - end of helix Processing helix chain 'C' and resid 577 through 591 removed outlier: 3.676A pdb=" N LYS C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 609 Processing helix chain 'C' and resid 620 through 642 removed outlier: 3.887A pdb=" N MET C 636 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 637 " --> pdb=" O GLN C 633 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 638 " --> pdb=" O LEU C 634 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 654 Processing helix chain 'C' and resid 655 through 659 Processing helix chain 'C' and resid 673 through 690 removed outlier: 3.582A pdb=" N ILE C 678 " --> pdb=" O PRO C 674 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU C 679 " --> pdb=" O THR C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 702 removed outlier: 3.552A pdb=" N ILE C 696 " --> pdb=" O LYS C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.644A pdb=" N LEU C 710 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 713 " --> pdb=" O LYS C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 731 removed outlier: 3.902A pdb=" N LEU C 721 " --> pdb=" O ASP C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 760 Processing helix chain 'C' and resid 765 through 771 removed outlier: 3.830A pdb=" N LEU C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 797 removed outlier: 3.513A pdb=" N TRP C 787 " --> pdb=" O THR C 783 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 826 removed outlier: 3.654A pdb=" N THR C 816 " --> pdb=" O GLU C 812 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 820 " --> pdb=" O THR C 816 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR C 821 " --> pdb=" O ALA C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 844 Processing helix chain 'C' and resid 856 through 874 Processing helix chain 'C' and resid 881 through 886 removed outlier: 3.912A pdb=" N ILE C 885 " --> pdb=" O VAL C 881 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C 886 " --> pdb=" O SER C 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 881 through 886' Processing helix chain 'C' and resid 887 through 892 Processing helix chain 'C' and resid 892 through 897 Processing helix chain 'C' and resid 899 through 912 removed outlier: 3.781A pdb=" N TRP C 903 " --> pdb=" O ARG C 899 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 911 " --> pdb=" O SER C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 916 Processing helix chain 'C' and resid 926 through 936 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.804A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN C 962 " --> pdb=" O GLU C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1092 Processing helix chain 'C' and resid 1123 through 1129 Processing helix chain 'C' and resid 1147 through 1158 removed outlier: 4.405A pdb=" N SER C1153 " --> pdb=" O GLU C1149 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C1154 " --> pdb=" O GLN C1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1162 removed outlier: 3.684A pdb=" N PHE C1162 " --> pdb=" O TYR C1159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1159 through 1162' Processing helix chain 'C' and resid 1197 through 1201 removed outlier: 3.962A pdb=" N ASN C1200 " --> pdb=" O GLY C1197 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C1201 " --> pdb=" O GLU C1198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1197 through 1201' Processing helix chain 'C' and resid 1237 through 1249 removed outlier: 4.002A pdb=" N ILE C1241 " --> pdb=" O GLY C1237 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) Processing helix chain 'C' and resid 1334 through 1339 removed outlier: 3.540A pdb=" N ASP C1337 " --> pdb=" O LYS C1334 " (cutoff:3.500A) Processing helix chain 'C' and resid 1383 through 1387 Processing helix chain 'C' and resid 1478 through 1487 removed outlier: 4.051A pdb=" N VAL C1484 " --> pdb=" O ALA C1480 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU C1485 " --> pdb=" O ARG C1481 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG C1486 " --> pdb=" O GLN C1482 " (cutoff:3.500A) Processing helix chain 'C' and resid 1490 through 1495 Processing helix chain 'C' and resid 1496 through 1501 removed outlier: 3.527A pdb=" N GLN C1500 " --> pdb=" O SER C1496 " (cutoff:3.500A) Processing helix chain 'C' and resid 1521 through 1526 Processing helix chain 'C' and resid 1635 through 1644 Processing helix chain 'C' and resid 1644 through 1657 Processing helix chain 'C' and resid 1659 through 1668 removed outlier: 3.713A pdb=" N ALA C1663 " --> pdb=" O ASN C1659 " (cutoff:3.500A) Processing helix chain 'C' and resid 1689 through 1694 removed outlier: 3.583A pdb=" N LEU C1693 " --> pdb=" O VAL C1689 " (cutoff:3.500A) Processing helix chain 'C' and resid 1701 through 1705 removed outlier: 3.883A pdb=" N SER C1705 " --> pdb=" O PRO C1702 " (cutoff:3.500A) Processing helix chain 'C' and resid 1707 through 1715 Processing helix chain 'C' and resid 1716 through 1740 Processing helix chain 'C' and resid 1743 through 1762 Processing helix chain 'C' and resid 1777 through 1782 Processing helix chain 'C' and resid 1783 through 1800 removed outlier: 3.603A pdb=" N GLN C1787 " --> pdb=" O ALA C1783 " (cutoff:3.500A) Processing helix chain 'C' and resid 1810 through 1816 removed outlier: 4.508A pdb=" N ASP C1816 " --> pdb=" O ASN C1812 " (cutoff:3.500A) Processing helix chain 'C' and resid 1823 through 1842 removed outlier: 3.853A pdb=" N TYR C1829 " --> pdb=" O VAL C1825 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP C1830 " --> pdb=" O MET C1826 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN C1831 " --> pdb=" O LEU C1827 " (cutoff:3.500A) Processing helix chain 'C' and resid 1888 through 1975 removed outlier: 3.602A pdb=" N MET C1892 " --> pdb=" O ARG C1888 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1996 removed outlier: 3.626A pdb=" N ARG C1982 " --> pdb=" O ASN C1978 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C1996 " --> pdb=" O GLN C1992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1998 through 2009 removed outlier: 3.592A pdb=" N ALA C2005 " --> pdb=" O LEU C2001 " (cutoff:3.500A) Processing helix chain 'C' and resid 2025 through 2114 removed outlier: 3.596A pdb=" N ALA C2039 " --> pdb=" O GLY C2035 " (cutoff:3.500A) Processing helix chain 'C' and resid 2117 through 2154 removed outlier: 3.559A pdb=" N TYR C2121 " --> pdb=" O ASN C2117 " (cutoff:3.500A) Processing helix chain 'C' and resid 2168 through 2172 Processing helix chain 'C' and resid 2176 through 2194 Processing helix chain 'C' and resid 2207 through 2213 Processing helix chain 'C' and resid 2220 through 2231 Processing helix chain 'C' and resid 2261 through 2266 removed outlier: 3.579A pdb=" N TYR C2266 " --> pdb=" O LYS C2263 " (cutoff:3.500A) Processing helix chain 'C' and resid 2361 through 2368 Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.507A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 67 removed outlier: 3.603A pdb=" N GLN D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 80 removed outlier: 3.777A pdb=" N HIS D 79 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 removed outlier: 3.940A pdb=" N GLU D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG D 90 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.742A pdb=" N ALA D 117 " --> pdb=" O PHE D 113 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 141 removed outlier: 4.077A pdb=" N ARG D 141 " --> pdb=" O HIS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 removed outlier: 3.610A pdb=" N SER D 147 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 161 through 176 removed outlier: 4.059A pdb=" N ASN D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 219 through 225 removed outlier: 3.766A pdb=" N SER D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 3.840A pdb=" N ALA D 229 " --> pdb=" O SER D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.517A pdb=" N LEU D 237 " --> pdb=" O HIS D 233 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 254 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 313 through 327 removed outlier: 3.581A pdb=" N ILE D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 336 removed outlier: 3.741A pdb=" N LEU D 333 " --> pdb=" O PRO D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 361 removed outlier: 3.723A pdb=" N LEU D 347 " --> pdb=" O THR D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.715A pdb=" N LEU D 368 " --> pdb=" O THR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 391 Processing helix chain 'D' and resid 395 through 399 Processing helix chain 'D' and resid 417 through 428 removed outlier: 3.734A pdb=" N LEU D 423 " --> pdb=" O HIS D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 removed outlier: 3.617A pdb=" N HIS D 439 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 469 removed outlier: 3.936A pdb=" N LEU D 457 " --> pdb=" O ASN D 453 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA D 467 " --> pdb=" O THR D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 495 through 517 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 536 through 550 Processing helix chain 'D' and resid 559 through 572 Proline residue: D 566 - end of helix Processing helix chain 'D' and resid 577 through 591 removed outlier: 3.676A pdb=" N LYS D 591 " --> pdb=" O ALA D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 609 Processing helix chain 'D' and resid 620 through 642 removed outlier: 3.886A pdb=" N MET D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE D 637 " --> pdb=" O GLN D 633 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR D 638 " --> pdb=" O LEU D 634 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 654 Processing helix chain 'D' and resid 655 through 659 Processing helix chain 'D' and resid 673 through 690 removed outlier: 3.581A pdb=" N ILE D 678 " --> pdb=" O PRO D 674 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU D 679 " --> pdb=" O THR D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 702 removed outlier: 3.552A pdb=" N ILE D 696 " --> pdb=" O LYS D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.644A pdb=" N LEU D 710 " --> pdb=" O THR D 706 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 713 " --> pdb=" O LYS D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 731 removed outlier: 3.903A pdb=" N LEU D 721 " --> pdb=" O ASP D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 760 Processing helix chain 'D' and resid 765 through 771 removed outlier: 3.829A pdb=" N LEU D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 797 removed outlier: 3.513A pdb=" N TRP D 787 " --> pdb=" O THR D 783 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 826 removed outlier: 3.654A pdb=" N THR D 816 " --> pdb=" O GLU D 812 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN D 820 " --> pdb=" O THR D 816 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR D 821 " --> pdb=" O ALA D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 844 Processing helix chain 'D' and resid 856 through 874 Processing helix chain 'D' and resid 881 through 886 removed outlier: 3.912A pdb=" N ILE D 885 " --> pdb=" O VAL D 881 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR D 886 " --> pdb=" O SER D 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 881 through 886' Processing helix chain 'D' and resid 887 through 892 Processing helix chain 'D' and resid 892 through 897 Processing helix chain 'D' and resid 899 through 912 removed outlier: 3.781A pdb=" N TRP D 903 " --> pdb=" O ARG D 899 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 911 " --> pdb=" O SER D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 916 Processing helix chain 'D' and resid 926 through 936 Processing helix chain 'D' and resid 942 through 962 removed outlier: 3.805A pdb=" N VAL D 960 " --> pdb=" O SER D 956 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1092 Processing helix chain 'D' and resid 1123 through 1129 Processing helix chain 'D' and resid 1147 through 1158 removed outlier: 4.406A pdb=" N SER D1153 " --> pdb=" O GLU D1149 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR D1154 " --> pdb=" O GLN D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1159 through 1162 removed outlier: 3.685A pdb=" N PHE D1162 " --> pdb=" O TYR D1159 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1159 through 1162' Processing helix chain 'D' and resid 1197 through 1201 removed outlier: 3.962A pdb=" N ASN D1200 " --> pdb=" O GLY D1197 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D1201 " --> pdb=" O GLU D1198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1197 through 1201' Processing helix chain 'D' and resid 1237 through 1249 removed outlier: 4.002A pdb=" N ILE D1241 " --> pdb=" O GLY D1237 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) Processing helix chain 'D' and resid 1334 through 1339 removed outlier: 3.541A pdb=" N ASP D1337 " --> pdb=" O LYS D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1383 through 1387 Processing helix chain 'D' and resid 1478 through 1487 removed outlier: 4.052A pdb=" N VAL D1484 " --> pdb=" O ALA D1480 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU D1485 " --> pdb=" O ARG D1481 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG D1486 " --> pdb=" O GLN D1482 " (cutoff:3.500A) Processing helix chain 'D' and resid 1490 through 1495 Processing helix chain 'D' and resid 1496 through 1501 removed outlier: 3.527A pdb=" N GLN D1500 " --> pdb=" O SER D1496 " (cutoff:3.500A) Processing helix chain 'D' and resid 1521 through 1526 Processing helix chain 'D' and resid 1635 through 1644 Processing helix chain 'D' and resid 1644 through 1657 Processing helix chain 'D' and resid 1659 through 1668 removed outlier: 3.712A pdb=" N ALA D1663 " --> pdb=" O ASN D1659 " (cutoff:3.500A) Processing helix chain 'D' and resid 1689 through 1694 removed outlier: 3.583A pdb=" N LEU D1693 " --> pdb=" O VAL D1689 " (cutoff:3.500A) Processing helix chain 'D' and resid 1701 through 1705 removed outlier: 3.883A pdb=" N SER D1705 " --> pdb=" O PRO D1702 " (cutoff:3.500A) Processing helix chain 'D' and resid 1707 through 1715 Processing helix chain 'D' and resid 1716 through 1740 Processing helix chain 'D' and resid 1743 through 1762 Processing helix chain 'D' and resid 1777 through 1782 Processing helix chain 'D' and resid 1783 through 1800 removed outlier: 3.604A pdb=" N GLN D1787 " --> pdb=" O ALA D1783 " (cutoff:3.500A) Processing helix chain 'D' and resid 1810 through 1816 removed outlier: 4.507A pdb=" N ASP D1816 " --> pdb=" O ASN D1812 " (cutoff:3.500A) Processing helix chain 'D' and resid 1823 through 1842 removed outlier: 3.854A pdb=" N TYR D1829 " --> pdb=" O VAL D1825 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP D1830 " --> pdb=" O MET D1826 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN D1831 " --> pdb=" O LEU D1827 " (cutoff:3.500A) Processing helix chain 'D' and resid 1888 through 1975 removed outlier: 3.602A pdb=" N MET D1892 " --> pdb=" O ARG D1888 " (cutoff:3.500A) Processing helix chain 'D' and resid 1978 through 1996 removed outlier: 3.625A pdb=" N ARG D1982 " --> pdb=" O ASN D1978 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER D1996 " --> pdb=" O GLN D1992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1998 through 2009 removed outlier: 3.593A pdb=" N ALA D2005 " --> pdb=" O LEU D2001 " (cutoff:3.500A) Processing helix chain 'D' and resid 2025 through 2114 removed outlier: 3.596A pdb=" N ALA D2039 " --> pdb=" O GLY D2035 " (cutoff:3.500A) Processing helix chain 'D' and resid 2117 through 2154 removed outlier: 3.559A pdb=" N TYR D2121 " --> pdb=" O ASN D2117 " (cutoff:3.500A) Processing helix chain 'D' and resid 2168 through 2172 Processing helix chain 'D' and resid 2176 through 2194 Processing helix chain 'D' and resid 2207 through 2213 Processing helix chain 'D' and resid 2220 through 2231 Processing helix chain 'D' and resid 2261 through 2266 removed outlier: 3.578A pdb=" N TYR D2266 " --> pdb=" O LYS D2263 " (cutoff:3.500A) Processing helix chain 'D' and resid 2361 through 2368 Processing helix chain 'E' and resid 29 through 35 removed outlier: 3.506A pdb=" N GLN E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 67 removed outlier: 3.603A pdb=" N GLN E 56 " --> pdb=" O ALA E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 80 removed outlier: 3.775A pdb=" N HIS E 79 " --> pdb=" O ASN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 95 removed outlier: 3.940A pdb=" N GLU E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG E 90 " --> pdb=" O HIS E 86 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 3.741A pdb=" N ALA E 117 " --> pdb=" O PHE E 113 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 141 removed outlier: 4.077A pdb=" N ARG E 141 " --> pdb=" O HIS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 removed outlier: 3.610A pdb=" N SER E 147 " --> pdb=" O PRO E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 157 Processing helix chain 'E' and resid 161 through 176 removed outlier: 4.059A pdb=" N ASN E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 193 Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 219 through 225 removed outlier: 3.767A pdb=" N SER E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 removed outlier: 3.841A pdb=" N ALA E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.518A pdb=" N LEU E 237 " --> pdb=" O HIS E 233 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 254 Processing helix chain 'E' and resid 260 through 270 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 279 through 288 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 313 through 327 removed outlier: 3.581A pdb=" N ILE E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 336 removed outlier: 3.742A pdb=" N LEU E 333 " --> pdb=" O PRO E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 361 removed outlier: 3.724A pdb=" N LEU E 347 " --> pdb=" O THR E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.715A pdb=" N LEU E 368 " --> pdb=" O THR E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 391 Processing helix chain 'E' and resid 395 through 399 Processing helix chain 'E' and resid 417 through 428 removed outlier: 3.733A pdb=" N LEU E 423 " --> pdb=" O HIS E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 442 removed outlier: 3.617A pdb=" N HIS E 439 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 469 removed outlier: 3.937A pdb=" N LEU E 457 " --> pdb=" O ASN E 453 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA E 467 " --> pdb=" O THR E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 485 Processing helix chain 'E' and resid 495 through 517 Processing helix chain 'E' and resid 519 through 528 Processing helix chain 'E' and resid 536 through 550 Processing helix chain 'E' and resid 559 through 572 Proline residue: E 566 - end of helix Processing helix chain 'E' and resid 577 through 591 removed outlier: 3.675A pdb=" N LYS E 591 " --> pdb=" O ALA E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 609 Processing helix chain 'E' and resid 620 through 642 removed outlier: 3.886A pdb=" N MET E 636 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE E 637 " --> pdb=" O GLN E 633 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR E 638 " --> pdb=" O LEU E 634 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 654 Processing helix chain 'E' and resid 655 through 659 Processing helix chain 'E' and resid 673 through 690 removed outlier: 3.581A pdb=" N ILE E 678 " --> pdb=" O PRO E 674 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU E 679 " --> pdb=" O THR E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 702 removed outlier: 3.552A pdb=" N ILE E 696 " --> pdb=" O LYS E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 713 removed outlier: 3.644A pdb=" N LEU E 710 " --> pdb=" O THR E 706 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA E 713 " --> pdb=" O LYS E 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 731 removed outlier: 3.902A pdb=" N LEU E 721 " --> pdb=" O ASP E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 760 Processing helix chain 'E' and resid 765 through 771 removed outlier: 3.830A pdb=" N LEU E 769 " --> pdb=" O GLY E 765 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 797 removed outlier: 3.513A pdb=" N TRP E 787 " --> pdb=" O THR E 783 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY E 797 " --> pdb=" O ALA E 793 " (cutoff:3.500A) Processing helix chain 'E' and resid 799 through 826 removed outlier: 3.654A pdb=" N THR E 816 " --> pdb=" O GLU E 812 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN E 820 " --> pdb=" O THR E 816 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 821 " --> pdb=" O ALA E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 844 Processing helix chain 'E' and resid 856 through 874 Processing helix chain 'E' and resid 881 through 886 removed outlier: 3.913A pdb=" N ILE E 885 " --> pdb=" O VAL E 881 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR E 886 " --> pdb=" O SER E 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 881 through 886' Processing helix chain 'E' and resid 887 through 892 Processing helix chain 'E' and resid 892 through 897 Processing helix chain 'E' and resid 899 through 912 removed outlier: 3.781A pdb=" N TRP E 903 " --> pdb=" O ARG E 899 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR E 911 " --> pdb=" O SER E 907 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 916 Processing helix chain 'E' and resid 926 through 936 Processing helix chain 'E' and resid 942 through 962 removed outlier: 3.805A pdb=" N VAL E 960 " --> pdb=" O SER E 956 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN E 962 " --> pdb=" O GLU E 958 " (cutoff:3.500A) Processing helix chain 'E' and resid 1085 through 1092 Processing helix chain 'E' and resid 1123 through 1129 Processing helix chain 'E' and resid 1147 through 1158 removed outlier: 4.405A pdb=" N SER E1153 " --> pdb=" O GLU E1149 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR E1154 " --> pdb=" O GLN E1150 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1162 removed outlier: 3.685A pdb=" N PHE E1162 " --> pdb=" O TYR E1159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1159 through 1162' Processing helix chain 'E' and resid 1197 through 1201 removed outlier: 3.963A pdb=" N ASN E1200 " --> pdb=" O GLY E1197 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E1201 " --> pdb=" O GLU E1198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1197 through 1201' Processing helix chain 'E' and resid 1237 through 1249 removed outlier: 4.002A pdb=" N ILE E1241 " --> pdb=" O GLY E1237 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR E1249 " --> pdb=" O LEU E1245 " (cutoff:3.500A) Processing helix chain 'E' and resid 1334 through 1339 removed outlier: 3.540A pdb=" N ASP E1337 " --> pdb=" O LYS E1334 " (cutoff:3.500A) Processing helix chain 'E' and resid 1383 through 1387 Processing helix chain 'E' and resid 1478 through 1487 removed outlier: 4.051A pdb=" N VAL E1484 " --> pdb=" O ALA E1480 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU E1485 " --> pdb=" O ARG E1481 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG E1486 " --> pdb=" O GLN E1482 " (cutoff:3.500A) Processing helix chain 'E' and resid 1490 through 1495 Processing helix chain 'E' and resid 1496 through 1501 removed outlier: 3.526A pdb=" N GLN E1500 " --> pdb=" O SER E1496 " (cutoff:3.500A) Processing helix chain 'E' and resid 1521 through 1526 Processing helix chain 'E' and resid 1635 through 1644 Processing helix chain 'E' and resid 1644 through 1657 Processing helix chain 'E' and resid 1659 through 1668 removed outlier: 3.713A pdb=" N ALA E1663 " --> pdb=" O ASN E1659 " (cutoff:3.500A) Processing helix chain 'E' and resid 1689 through 1694 removed outlier: 3.583A pdb=" N LEU E1693 " --> pdb=" O VAL E1689 " (cutoff:3.500A) Processing helix chain 'E' and resid 1701 through 1705 removed outlier: 3.882A pdb=" N SER E1705 " --> pdb=" O PRO E1702 " (cutoff:3.500A) Processing helix chain 'E' and resid 1707 through 1715 Processing helix chain 'E' and resid 1716 through 1740 Processing helix chain 'E' and resid 1743 through 1762 Processing helix chain 'E' and resid 1777 through 1782 Processing helix chain 'E' and resid 1783 through 1800 removed outlier: 3.602A pdb=" N GLN E1787 " --> pdb=" O ALA E1783 " (cutoff:3.500A) Processing helix chain 'E' and resid 1810 through 1816 removed outlier: 4.507A pdb=" N ASP E1816 " --> pdb=" O ASN E1812 " (cutoff:3.500A) Processing helix chain 'E' and resid 1823 through 1842 removed outlier: 3.853A pdb=" N TYR E1829 " --> pdb=" O VAL E1825 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP E1830 " --> pdb=" O MET E1826 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN E1831 " --> pdb=" O LEU E1827 " (cutoff:3.500A) Processing helix chain 'E' and resid 1888 through 1975 removed outlier: 3.602A pdb=" N MET E1892 " --> pdb=" O ARG E1888 " (cutoff:3.500A) Processing helix chain 'E' and resid 1978 through 1996 removed outlier: 3.626A pdb=" N ARG E1982 " --> pdb=" O ASN E1978 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER E1996 " --> pdb=" O GLN E1992 " (cutoff:3.500A) Processing helix chain 'E' and resid 1998 through 2009 removed outlier: 3.593A pdb=" N ALA E2005 " --> pdb=" O LEU E2001 " (cutoff:3.500A) Processing helix chain 'E' and resid 2025 through 2114 removed outlier: 3.595A pdb=" N ALA E2039 " --> pdb=" O GLY E2035 " (cutoff:3.500A) Processing helix chain 'E' and resid 2117 through 2154 removed outlier: 3.559A pdb=" N TYR E2121 " --> pdb=" O ASN E2117 " (cutoff:3.500A) Processing helix chain 'E' and resid 2168 through 2172 Processing helix chain 'E' and resid 2176 through 2194 Processing helix chain 'E' and resid 2207 through 2213 Processing helix chain 'E' and resid 2220 through 2231 Processing helix chain 'E' and resid 2261 through 2266 removed outlier: 3.579A pdb=" N TYR E2266 " --> pdb=" O LYS E2263 " (cutoff:3.500A) Processing helix chain 'E' and resid 2361 through 2368 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 408 through 409 Processing sheet with id=AA3, first strand: chain 'A' and resid 964 through 970 removed outlier: 7.037A pdb=" N ILE A 983 " --> pdb=" O ILE A 966 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA A 968 " --> pdb=" O TYR A 981 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR A 981 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N HIS A 970 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 979 " --> pdb=" O HIS A 970 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 996 " --> pdb=" O PHE A 982 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1003 through 1004 removed outlier: 3.801A pdb=" N ASN A1004 " --> pdb=" O LYS A1007 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1030 through 1035 Processing sheet with id=AA6, first strand: chain 'A' and resid 1101 through 1105 Processing sheet with id=AA7, first strand: chain 'A' and resid 1172 through 1173 removed outlier: 4.286A pdb=" N ILE A1172 " --> pdb=" O LEU A1456 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR A1455 " --> pdb=" O GLN A1467 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1182 through 1183 removed outlier: 3.738A pdb=" N ILE A1445 " --> pdb=" O GLU A1183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1182 through 1183 removed outlier: 3.738A pdb=" N ILE A1445 " --> pdb=" O GLU A1183 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A1436 " --> pdb=" O ALA A1427 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A1427 " --> pdb=" O GLY A1436 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A1422 " --> pdb=" O LYS A1374 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A1372 " --> pdb=" O THR A1424 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A1426 " --> pdb=" O GLN A1370 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A1370 " --> pdb=" O THR A1426 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1187 through 1188 removed outlier: 3.642A pdb=" N ASN A1208 " --> pdb=" O LYS A1227 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A1210 " --> pdb=" O SER A1225 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR A1216 " --> pdb=" O ASP A1219 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A1219 " --> pdb=" O THR A1216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1203 through 1204 removed outlier: 3.735A pdb=" N GLN A1203 " --> pdb=" O ILE A1231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1315 through 1318 removed outlier: 3.583A pdb=" N VAL A1305 " --> pdb=" O ASN A1318 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR A1352 " --> pdb=" O ILE A1264 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A1264 " --> pdb=" O THR A1352 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A1354 " --> pdb=" O LEU A1262 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU A1262 " --> pdb=" O VAL A1354 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A1356 " --> pdb=" O THR A1260 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A1292 " --> pdb=" O GLN A1280 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A1328 " --> pdb=" O LEU A1293 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A1295 " --> pdb=" O ASP A1326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1503 through 1504 Processing sheet with id=AB5, first strand: chain 'A' and resid 1510 through 1516 removed outlier: 3.592A pdb=" N VAL A1560 " --> pdb=" O LEU A1515 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1548 through 1551 removed outlier: 4.149A pdb=" N TYR A1548 " --> pdb=" O ILE A1533 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A1550 " --> pdb=" O PHE A1531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1593 through 1594 Processing sheet with id=AB8, first strand: chain 'A' and resid 1677 through 1678 Processing sheet with id=AB9, first strand: chain 'A' and resid 2014 through 2015 Processing sheet with id=AC1, first strand: chain 'A' and resid 2019 through 2020 Processing sheet with id=AC2, first strand: chain 'A' and resid 2199 through 2206 removed outlier: 5.963A pdb=" N THR A2378 " --> pdb=" O ILE A2278 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE A2278 " --> pdb=" O THR A2378 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A2283 " --> pdb=" O ASP A2323 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2244 through 2246 Processing sheet with id=AC4, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC5, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AC6, first strand: chain 'B' and resid 964 through 970 removed outlier: 7.038A pdb=" N ILE B 983 " --> pdb=" O ILE B 966 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA B 968 " --> pdb=" O TYR B 981 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 981 " --> pdb=" O ALA B 968 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N HIS B 970 " --> pdb=" O LEU B 979 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 979 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 996 " --> pdb=" O PHE B 982 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1003 through 1004 removed outlier: 3.801A pdb=" N ASN B1004 " --> pdb=" O LYS B1007 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1030 through 1035 Processing sheet with id=AC9, first strand: chain 'B' and resid 1101 through 1105 Processing sheet with id=AD1, first strand: chain 'B' and resid 1172 through 1173 removed outlier: 4.286A pdb=" N ILE B1172 " --> pdb=" O LEU B1456 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR B1455 " --> pdb=" O GLN B1467 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1182 through 1183 removed outlier: 3.737A pdb=" N ILE B1445 " --> pdb=" O GLU B1183 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1182 through 1183 removed outlier: 3.737A pdb=" N ILE B1445 " --> pdb=" O GLU B1183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B1436 " --> pdb=" O ALA B1427 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B1427 " --> pdb=" O GLY B1436 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B1422 " --> pdb=" O LYS B1374 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B1372 " --> pdb=" O THR B1424 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B1426 " --> pdb=" O GLN B1370 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B1370 " --> pdb=" O THR B1426 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1187 through 1188 removed outlier: 3.642A pdb=" N ASN B1208 " --> pdb=" O LYS B1227 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B1210 " --> pdb=" O SER B1225 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B1216 " --> pdb=" O ASP B1219 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B1219 " --> pdb=" O THR B1216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1203 through 1204 removed outlier: 3.736A pdb=" N GLN B1203 " --> pdb=" O ILE B1231 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1315 through 1318 removed outlier: 3.581A pdb=" N VAL B1305 " --> pdb=" O ASN B1318 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR B1352 " --> pdb=" O ILE B1264 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B1264 " --> pdb=" O THR B1352 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL B1354 " --> pdb=" O LEU B1262 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B1262 " --> pdb=" O VAL B1354 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY B1356 " --> pdb=" O THR B1260 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B1292 " --> pdb=" O GLN B1280 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B1328 " --> pdb=" O LEU B1293 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B1295 " --> pdb=" O ASP B1326 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1503 through 1504 Processing sheet with id=AD8, first strand: chain 'B' and resid 1510 through 1516 removed outlier: 3.591A pdb=" N VAL B1560 " --> pdb=" O LEU B1515 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1548 through 1551 removed outlier: 4.150A pdb=" N TYR B1548 " --> pdb=" O ILE B1533 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B1550 " --> pdb=" O PHE B1531 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1593 through 1594 Processing sheet with id=AE2, first strand: chain 'B' and resid 1677 through 1678 Processing sheet with id=AE3, first strand: chain 'B' and resid 2019 through 2020 Processing sheet with id=AE4, first strand: chain 'B' and resid 2199 through 2206 removed outlier: 5.963A pdb=" N THR B2378 " --> pdb=" O ILE B2278 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE B2278 " --> pdb=" O THR B2378 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B2283 " --> pdb=" O ASP B2323 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 2244 through 2246 Processing sheet with id=AE6, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AE7, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AE8, first strand: chain 'C' and resid 964 through 970 removed outlier: 7.037A pdb=" N ILE C 983 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA C 968 " --> pdb=" O TYR C 981 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR C 981 " --> pdb=" O ALA C 968 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N HIS C 970 " --> pdb=" O LEU C 979 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU C 979 " --> pdb=" O HIS C 970 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 996 " --> pdb=" O PHE C 982 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1003 through 1004 removed outlier: 3.800A pdb=" N ASN C1004 " --> pdb=" O LYS C1007 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1030 through 1035 Processing sheet with id=AF2, first strand: chain 'C' and resid 1101 through 1105 Processing sheet with id=AF3, first strand: chain 'C' and resid 1172 through 1173 removed outlier: 4.286A pdb=" N ILE C1172 " --> pdb=" O LEU C1456 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR C1455 " --> pdb=" O GLN C1467 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1182 through 1183 removed outlier: 3.736A pdb=" N ILE C1445 " --> pdb=" O GLU C1183 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1182 through 1183 removed outlier: 3.736A pdb=" N ILE C1445 " --> pdb=" O GLU C1183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY C1436 " --> pdb=" O ALA C1427 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C1427 " --> pdb=" O GLY C1436 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP C1422 " --> pdb=" O LYS C1374 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C1372 " --> pdb=" O THR C1424 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C1426 " --> pdb=" O GLN C1370 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C1370 " --> pdb=" O THR C1426 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1187 through 1188 removed outlier: 3.642A pdb=" N ASN C1208 " --> pdb=" O LYS C1227 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL C1210 " --> pdb=" O SER C1225 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C1216 " --> pdb=" O ASP C1219 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP C1219 " --> pdb=" O THR C1216 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1203 through 1204 removed outlier: 3.736A pdb=" N GLN C1203 " --> pdb=" O ILE C1231 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1315 through 1318 removed outlier: 3.583A pdb=" N VAL C1305 " --> pdb=" O ASN C1318 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR C1352 " --> pdb=" O ILE C1264 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C1264 " --> pdb=" O THR C1352 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL C1354 " --> pdb=" O LEU C1262 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU C1262 " --> pdb=" O VAL C1354 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY C1356 " --> pdb=" O THR C1260 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C1292 " --> pdb=" O GLN C1280 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C1328 " --> pdb=" O LEU C1293 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE C1295 " --> pdb=" O ASP C1326 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1503 through 1504 Processing sheet with id=AG1, first strand: chain 'C' and resid 1510 through 1516 removed outlier: 3.592A pdb=" N VAL C1560 " --> pdb=" O LEU C1515 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1548 through 1551 removed outlier: 4.149A pdb=" N TYR C1548 " --> pdb=" O ILE C1533 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY C1550 " --> pdb=" O PHE C1531 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1593 through 1594 Processing sheet with id=AG4, first strand: chain 'C' and resid 1677 through 1678 Processing sheet with id=AG5, first strand: chain 'C' and resid 2019 through 2020 Processing sheet with id=AG6, first strand: chain 'C' and resid 2199 through 2206 removed outlier: 5.963A pdb=" N THR C2378 " --> pdb=" O ILE C2278 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE C2278 " --> pdb=" O THR C2378 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C2283 " --> pdb=" O ASP C2323 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 2244 through 2246 Processing sheet with id=AG8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AG9, first strand: chain 'D' and resid 408 through 409 Processing sheet with id=AH1, first strand: chain 'D' and resid 964 through 970 removed outlier: 7.037A pdb=" N ILE D 983 " --> pdb=" O ILE D 966 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA D 968 " --> pdb=" O TYR D 981 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR D 981 " --> pdb=" O ALA D 968 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N HIS D 970 " --> pdb=" O LEU D 979 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU D 979 " --> pdb=" O HIS D 970 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 996 " --> pdb=" O PHE D 982 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 1003 through 1004 removed outlier: 3.800A pdb=" N ASN D1004 " --> pdb=" O LYS D1007 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 1030 through 1035 Processing sheet with id=AH4, first strand: chain 'D' and resid 1101 through 1105 Processing sheet with id=AH5, first strand: chain 'D' and resid 1172 through 1173 removed outlier: 4.286A pdb=" N ILE D1172 " --> pdb=" O LEU D1456 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR D1455 " --> pdb=" O GLN D1467 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 1182 through 1183 removed outlier: 3.737A pdb=" N ILE D1445 " --> pdb=" O GLU D1183 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 1182 through 1183 removed outlier: 3.737A pdb=" N ILE D1445 " --> pdb=" O GLU D1183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY D1436 " --> pdb=" O ALA D1427 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D1427 " --> pdb=" O GLY D1436 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D1422 " --> pdb=" O LYS D1374 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D1372 " --> pdb=" O THR D1424 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D1426 " --> pdb=" O GLN D1370 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D1370 " --> pdb=" O THR D1426 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 1187 through 1188 removed outlier: 3.643A pdb=" N ASN D1208 " --> pdb=" O LYS D1227 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL D1210 " --> pdb=" O SER D1225 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR D1216 " --> pdb=" O ASP D1219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP D1219 " --> pdb=" O THR D1216 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 1203 through 1204 removed outlier: 3.735A pdb=" N GLN D1203 " --> pdb=" O ILE D1231 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 1315 through 1318 removed outlier: 3.582A pdb=" N VAL D1305 " --> pdb=" O ASN D1318 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR D1352 " --> pdb=" O ILE D1264 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE D1264 " --> pdb=" O THR D1352 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL D1354 " --> pdb=" O LEU D1262 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU D1262 " --> pdb=" O VAL D1354 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY D1356 " --> pdb=" O THR D1260 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG D1292 " --> pdb=" O GLN D1280 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D1328 " --> pdb=" O LEU D1293 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D1295 " --> pdb=" O ASP D1326 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 1503 through 1504 Processing sheet with id=AI3, first strand: chain 'D' and resid 1510 through 1516 removed outlier: 3.592A pdb=" N VAL D1560 " --> pdb=" O LEU D1515 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 1548 through 1551 removed outlier: 4.150A pdb=" N TYR D1548 " --> pdb=" O ILE D1533 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D1550 " --> pdb=" O PHE D1531 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 1593 through 1594 Processing sheet with id=AI6, first strand: chain 'D' and resid 1677 through 1678 Processing sheet with id=AI7, first strand: chain 'D' and resid 2019 through 2020 Processing sheet with id=AI8, first strand: chain 'D' and resid 2199 through 2206 removed outlier: 5.962A pdb=" N THR D2378 " --> pdb=" O ILE D2278 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE D2278 " --> pdb=" O THR D2378 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D2283 " --> pdb=" O ASP D2323 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 2244 through 2246 Processing sheet with id=AJ1, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AJ2, first strand: chain 'E' and resid 408 through 409 Processing sheet with id=AJ3, first strand: chain 'E' and resid 964 through 970 removed outlier: 7.037A pdb=" N ILE E 983 " --> pdb=" O ILE E 966 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA E 968 " --> pdb=" O TYR E 981 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR E 981 " --> pdb=" O ALA E 968 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N HIS E 970 " --> pdb=" O LEU E 979 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU E 979 " --> pdb=" O HIS E 970 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG E 996 " --> pdb=" O PHE E 982 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 1003 through 1004 removed outlier: 3.800A pdb=" N ASN E1004 " --> pdb=" O LYS E1007 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 1030 through 1035 Processing sheet with id=AJ6, first strand: chain 'E' and resid 1101 through 1105 Processing sheet with id=AJ7, first strand: chain 'E' and resid 1172 through 1173 removed outlier: 4.286A pdb=" N ILE E1172 " --> pdb=" O LEU E1456 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR E1455 " --> pdb=" O GLN E1467 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'E' and resid 1182 through 1183 removed outlier: 3.737A pdb=" N ILE E1445 " --> pdb=" O GLU E1183 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'E' and resid 1182 through 1183 removed outlier: 3.737A pdb=" N ILE E1445 " --> pdb=" O GLU E1183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY E1436 " --> pdb=" O ALA E1427 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E1427 " --> pdb=" O GLY E1436 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP E1422 " --> pdb=" O LYS E1374 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E1372 " --> pdb=" O THR E1424 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E1426 " --> pdb=" O GLN E1370 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E1370 " --> pdb=" O THR E1426 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'E' and resid 1187 through 1188 removed outlier: 3.642A pdb=" N ASN E1208 " --> pdb=" O LYS E1227 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL E1210 " --> pdb=" O SER E1225 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR E1216 " --> pdb=" O ASP E1219 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP E1219 " --> pdb=" O THR E1216 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'E' and resid 1203 through 1204 removed outlier: 3.736A pdb=" N GLN E1203 " --> pdb=" O ILE E1231 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 1315 through 1318 removed outlier: 3.582A pdb=" N VAL E1305 " --> pdb=" O ASN E1318 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR E1352 " --> pdb=" O ILE E1264 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE E1264 " --> pdb=" O THR E1352 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL E1354 " --> pdb=" O LEU E1262 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU E1262 " --> pdb=" O VAL E1354 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY E1356 " --> pdb=" O THR E1260 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG E1292 " --> pdb=" O GLN E1280 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA E1328 " --> pdb=" O LEU E1293 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE E1295 " --> pdb=" O ASP E1326 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 1503 through 1504 Processing sheet with id=AK5, first strand: chain 'E' and resid 1510 through 1516 removed outlier: 3.591A pdb=" N VAL E1560 " --> pdb=" O LEU E1515 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'E' and resid 1548 through 1551 removed outlier: 4.150A pdb=" N TYR E1548 " --> pdb=" O ILE E1533 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY E1550 " --> pdb=" O PHE E1531 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'E' and resid 1593 through 1594 Processing sheet with id=AK8, first strand: chain 'E' and resid 1677 through 1678 Processing sheet with id=AK9, first strand: chain 'E' and resid 2199 through 2206 removed outlier: 5.963A pdb=" N THR E2378 " --> pdb=" O ILE E2278 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE E2278 " --> pdb=" O THR E2378 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL E2283 " --> pdb=" O ASP E2323 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'E' and resid 2244 through 2246 4680 hydrogen bonds defined for protein. 13365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 57.30 Time building geometry restraints manager: 30.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 30717 1.34 - 1.46: 19276 1.46 - 1.58: 46022 1.58 - 1.69: 0 1.69 - 1.81: 530 Bond restraints: 96545 Sorted by residual: bond pdb=" C LYS A 776 " pdb=" N PRO A 777 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.99e+00 bond pdb=" C LYS C 776 " pdb=" N PRO C 777 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.93e+00 bond pdb=" C LYS B 776 " pdb=" N PRO B 777 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.92e+00 bond pdb=" C LYS D 776 " pdb=" N PRO D 777 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.89e+00 bond pdb=" C LYS E 776 " pdb=" N PRO E 777 " ideal model delta sigma weight residual 1.334 1.385 -0.052 2.34e-02 1.83e+03 4.86e+00 ... (remaining 96540 not shown) Histogram of bond angle deviations from ideal: 95.47 - 104.98: 1512 104.98 - 114.49: 57848 114.49 - 124.00: 69443 124.00 - 133.50: 2062 133.50 - 143.01: 180 Bond angle restraints: 131045 Sorted by residual: angle pdb=" C ILE B 199 " pdb=" N PRO B 200 " pdb=" CA PRO B 200 " ideal model delta sigma weight residual 127.00 143.01 -16.01 2.40e+00 1.74e-01 4.45e+01 angle pdb=" C ILE C 199 " pdb=" N PRO C 200 " pdb=" CA PRO C 200 " ideal model delta sigma weight residual 127.00 142.97 -15.97 2.40e+00 1.74e-01 4.43e+01 angle pdb=" C ILE A 199 " pdb=" N PRO A 200 " pdb=" CA PRO A 200 " ideal model delta sigma weight residual 127.00 142.96 -15.96 2.40e+00 1.74e-01 4.42e+01 angle pdb=" C ILE D 199 " pdb=" N PRO D 200 " pdb=" CA PRO D 200 " ideal model delta sigma weight residual 127.00 142.94 -15.94 2.40e+00 1.74e-01 4.41e+01 angle pdb=" C ILE E 199 " pdb=" N PRO E 200 " pdb=" CA PRO E 200 " ideal model delta sigma weight residual 127.00 142.93 -15.93 2.40e+00 1.74e-01 4.41e+01 ... (remaining 131040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 54618 15.16 - 30.32: 2981 30.32 - 45.48: 511 45.48 - 60.64: 40 60.64 - 75.81: 70 Dihedral angle restraints: 58220 sinusoidal: 23310 harmonic: 34910 Sorted by residual: dihedral pdb=" CA PHE A1545 " pdb=" C PHE A1545 " pdb=" N PRO A1546 " pdb=" CA PRO A1546 " ideal model delta harmonic sigma weight residual 180.00 -128.72 -51.28 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA PHE C1545 " pdb=" C PHE C1545 " pdb=" N PRO C1546 " pdb=" CA PRO C1546 " ideal model delta harmonic sigma weight residual 180.00 -128.73 -51.27 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA PHE D1545 " pdb=" C PHE D1545 " pdb=" N PRO D1546 " pdb=" CA PRO D1546 " ideal model delta harmonic sigma weight residual 180.00 -128.74 -51.26 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 58217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 12825 0.086 - 0.172: 1562 0.172 - 0.258: 173 0.258 - 0.344: 8 0.344 - 0.430: 12 Chirality restraints: 14580 Sorted by residual: chirality pdb=" CB ILE C 311 " pdb=" CA ILE C 311 " pdb=" CG1 ILE C 311 " pdb=" CG2 ILE C 311 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CB ILE D 311 " pdb=" CA ILE D 311 " pdb=" CG1 ILE D 311 " pdb=" CG2 ILE D 311 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CB ILE A 311 " pdb=" CA ILE A 311 " pdb=" CG1 ILE A 311 " pdb=" CG2 ILE A 311 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 14577 not shown) Planarity restraints: 17000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 142 " -0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO D 143 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO D 143 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 143 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 142 " -0.058 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO B 143 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 142 " -0.058 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO E 143 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO E 143 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 143 " -0.048 5.00e-02 4.00e+02 ... (remaining 16997 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 18621 2.76 - 3.30: 88871 3.30 - 3.83: 156657 3.83 - 4.37: 178228 4.37 - 4.90: 303291 Nonbonded interactions: 745668 Sorted by model distance: nonbonded pdb=" O PHE B 249 " pdb=" OG1 THR B 253 " model vdw 2.231 2.440 nonbonded pdb=" O PHE C 249 " pdb=" OG1 THR C 253 " model vdw 2.232 2.440 nonbonded pdb=" O PHE A 249 " pdb=" OG1 THR A 253 " model vdw 2.232 2.440 nonbonded pdb=" O PHE E 249 " pdb=" OG1 THR E 253 " model vdw 2.232 2.440 nonbonded pdb=" O PHE D 249 " pdb=" OG1 THR D 253 " model vdw 2.232 2.440 ... (remaining 745663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 16.440 Check model and map are aligned: 1.090 Set scattering table: 0.670 Process input model: 215.180 Find NCS groups from input model: 5.150 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 245.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 96545 Z= 0.491 Angle : 1.058 16.013 131045 Z= 0.593 Chirality : 0.058 0.430 14580 Planarity : 0.007 0.088 17000 Dihedral : 10.140 75.805 35700 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.77 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 4.88 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.07), residues: 11795 helix: -1.43 (0.06), residues: 5085 sheet: -1.81 (0.11), residues: 1650 loop : -2.40 (0.08), residues: 5060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP E 603 HIS 0.020 0.003 HIS A1759 PHE 0.042 0.003 PHE E1545 TYR 0.044 0.003 TYR E1107 ARG 0.016 0.001 ARG A1798 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2649 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2649 time to evaluate : 10.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8832 (mtt180) cc_final: 0.8561 (mtp180) REVERT: A 56 GLN cc_start: 0.8904 (mt0) cc_final: 0.8394 (tm-30) REVERT: A 63 GLU cc_start: 0.7953 (tt0) cc_final: 0.7161 (pt0) REVERT: A 93 ASN cc_start: 0.8748 (m110) cc_final: 0.8295 (t0) REVERT: A 104 VAL cc_start: 0.9172 (t) cc_final: 0.8902 (m) REVERT: A 125 GLU cc_start: 0.7208 (tt0) cc_final: 0.6899 (tt0) REVERT: A 137 HIS cc_start: 0.7866 (t70) cc_final: 0.7253 (t-90) REVERT: A 231 LEU cc_start: 0.8252 (mp) cc_final: 0.8005 (mp) REVERT: A 282 TYR cc_start: 0.8910 (t80) cc_final: 0.8484 (t80) REVERT: A 366 THR cc_start: 0.9005 (m) cc_final: 0.8744 (p) REVERT: A 477 LEU cc_start: 0.9356 (tp) cc_final: 0.9052 (tt) REVERT: A 518 TRP cc_start: 0.7482 (m-10) cc_final: 0.7069 (m-10) REVERT: A 809 PHE cc_start: 0.8325 (t80) cc_final: 0.8120 (t80) REVERT: A 834 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8321 (tttt) REVERT: A 896 TYR cc_start: 0.8048 (m-10) cc_final: 0.7445 (m-10) REVERT: A 925 GLN cc_start: 0.8348 (tt0) cc_final: 0.8033 (tt0) REVERT: A 930 ASP cc_start: 0.7651 (m-30) cc_final: 0.7184 (m-30) REVERT: A 937 SER cc_start: 0.8915 (m) cc_final: 0.8575 (p) REVERT: A 940 GLN cc_start: 0.8311 (mm110) cc_final: 0.7950 (mm-40) REVERT: A 942 ASN cc_start: 0.8499 (t0) cc_final: 0.8227 (t0) REVERT: A 948 ASP cc_start: 0.8100 (m-30) cc_final: 0.7465 (m-30) REVERT: A 1127 TYR cc_start: 0.7691 (m-80) cc_final: 0.7277 (m-80) REVERT: A 1223 TYR cc_start: 0.8277 (m-80) cc_final: 0.7896 (m-10) REVERT: A 1259 TYR cc_start: 0.8467 (m-80) cc_final: 0.8009 (m-80) REVERT: A 1342 ILE cc_start: 0.8574 (mt) cc_final: 0.8323 (mt) REVERT: A 1497 MET cc_start: 0.9163 (tpp) cc_final: 0.8590 (mmm) REVERT: A 1613 PHE cc_start: 0.8528 (m-10) cc_final: 0.8055 (m-80) REVERT: A 1703 LEU cc_start: 0.9447 (mt) cc_final: 0.9230 (mm) REVERT: A 1836 ARG cc_start: 0.8796 (mmt-90) cc_final: 0.8500 (tpp80) REVERT: A 1866 LEU cc_start: 0.8312 (tp) cc_final: 0.7803 (mt) REVERT: A 2031 ILE cc_start: 0.9626 (mt) cc_final: 0.9415 (mm) REVERT: A 2143 CYS cc_start: 0.9246 (m) cc_final: 0.9033 (t) REVERT: A 2192 LEU cc_start: 0.9453 (mt) cc_final: 0.9253 (tp) REVERT: B 50 ARG cc_start: 0.8743 (mtt180) cc_final: 0.8451 (mtp180) REVERT: B 63 GLU cc_start: 0.7891 (tt0) cc_final: 0.7488 (pt0) REVERT: B 93 ASN cc_start: 0.8517 (m110) cc_final: 0.8249 (t0) REVERT: B 104 VAL cc_start: 0.9080 (t) cc_final: 0.8760 (m) REVERT: B 125 GLU cc_start: 0.7038 (tt0) cc_final: 0.6815 (tt0) REVERT: B 137 HIS cc_start: 0.7954 (t70) cc_final: 0.7469 (t-90) REVERT: B 189 MET cc_start: 0.8603 (ptm) cc_final: 0.8339 (ppp) REVERT: B 231 LEU cc_start: 0.8377 (mp) cc_final: 0.8101 (mp) REVERT: B 282 TYR cc_start: 0.8825 (t80) cc_final: 0.8508 (t80) REVERT: B 322 LEU cc_start: 0.9664 (tp) cc_final: 0.9441 (tt) REVERT: B 366 THR cc_start: 0.9073 (m) cc_final: 0.8822 (p) REVERT: B 418 TRP cc_start: 0.7612 (p-90) cc_final: 0.7302 (p-90) REVERT: B 473 THR cc_start: 0.7745 (p) cc_final: 0.6731 (t) REVERT: B 687 ASN cc_start: 0.8780 (m-40) cc_final: 0.8543 (t0) REVERT: B 838 ASP cc_start: 0.8163 (m-30) cc_final: 0.7879 (t0) REVERT: B 888 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8076 (tp-100) REVERT: B 892 ASP cc_start: 0.8219 (m-30) cc_final: 0.7636 (m-30) REVERT: B 896 TYR cc_start: 0.8319 (m-10) cc_final: 0.6988 (m-10) REVERT: B 908 GLN cc_start: 0.8611 (mt0) cc_final: 0.8340 (mp10) REVERT: B 937 SER cc_start: 0.8885 (m) cc_final: 0.8559 (p) REVERT: B 940 GLN cc_start: 0.8263 (mm110) cc_final: 0.7967 (mm-40) REVERT: B 1223 TYR cc_start: 0.8072 (m-80) cc_final: 0.7777 (m-10) REVERT: B 1259 TYR cc_start: 0.8554 (m-80) cc_final: 0.8330 (m-80) REVERT: B 1512 TYR cc_start: 0.8048 (m-80) cc_final: 0.5902 (m-10) REVERT: B 1613 PHE cc_start: 0.8253 (m-10) cc_final: 0.7952 (m-80) REVERT: B 2031 ILE cc_start: 0.9575 (mt) cc_final: 0.9346 (mm) REVERT: B 2171 TYR cc_start: 0.9080 (m-80) cc_final: 0.8816 (m-10) REVERT: B 2178 GLU cc_start: 0.8453 (mp0) cc_final: 0.8013 (mp0) REVERT: B 2192 LEU cc_start: 0.9394 (mt) cc_final: 0.8948 (mm) REVERT: C 50 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8429 (mtp180) REVERT: C 63 GLU cc_start: 0.7741 (tt0) cc_final: 0.7340 (pt0) REVERT: C 93 ASN cc_start: 0.8539 (m110) cc_final: 0.8272 (t0) REVERT: C 104 VAL cc_start: 0.9190 (t) cc_final: 0.8898 (m) REVERT: C 125 GLU cc_start: 0.7250 (tt0) cc_final: 0.6919 (tt0) REVERT: C 282 TYR cc_start: 0.8821 (t80) cc_final: 0.8400 (t80) REVERT: C 322 LEU cc_start: 0.9659 (tp) cc_final: 0.9446 (tt) REVERT: C 833 ILE cc_start: 0.8798 (mt) cc_final: 0.8585 (mt) REVERT: C 860 GLU cc_start: 0.7881 (tp30) cc_final: 0.7571 (tp30) REVERT: C 896 TYR cc_start: 0.8016 (m-10) cc_final: 0.6852 (m-10) REVERT: C 937 SER cc_start: 0.8950 (m) cc_final: 0.8606 (p) REVERT: C 940 GLN cc_start: 0.8324 (mm110) cc_final: 0.8060 (mm-40) REVERT: C 942 ASN cc_start: 0.8611 (t0) cc_final: 0.8380 (t0) REVERT: C 948 ASP cc_start: 0.8176 (m-30) cc_final: 0.7577 (m-30) REVERT: C 1223 TYR cc_start: 0.8327 (m-80) cc_final: 0.7914 (m-10) REVERT: C 1259 TYR cc_start: 0.8552 (m-80) cc_final: 0.8351 (m-80) REVERT: C 1342 ILE cc_start: 0.8580 (mt) cc_final: 0.8266 (mm) REVERT: C 1613 PHE cc_start: 0.8690 (m-10) cc_final: 0.8184 (m-80) REVERT: C 1749 GLU cc_start: 0.8571 (tt0) cc_final: 0.8136 (tp30) REVERT: C 2142 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7446 (mtm-85) REVERT: C 2171 TYR cc_start: 0.9018 (m-80) cc_final: 0.8722 (m-10) REVERT: C 2178 GLU cc_start: 0.8457 (mp0) cc_final: 0.8222 (mp0) REVERT: D 50 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8564 (mtp180) REVERT: D 63 GLU cc_start: 0.7962 (tt0) cc_final: 0.7351 (pt0) REVERT: D 93 ASN cc_start: 0.8610 (m110) cc_final: 0.8262 (t0) REVERT: D 104 VAL cc_start: 0.9190 (t) cc_final: 0.8845 (m) REVERT: D 125 GLU cc_start: 0.7123 (tt0) cc_final: 0.6819 (tt0) REVERT: D 148 MET cc_start: 0.8808 (ttp) cc_final: 0.8278 (ttm) REVERT: D 183 ASP cc_start: 0.8369 (m-30) cc_final: 0.8072 (t0) REVERT: D 282 TYR cc_start: 0.8840 (t80) cc_final: 0.8525 (t80) REVERT: D 283 LEU cc_start: 0.9452 (mt) cc_final: 0.9243 (mt) REVERT: D 366 THR cc_start: 0.9045 (m) cc_final: 0.8839 (p) REVERT: D 424 LYS cc_start: 0.9109 (mtmt) cc_final: 0.8901 (mtpp) REVERT: D 431 ASP cc_start: 0.8522 (m-30) cc_final: 0.8276 (t0) REVERT: D 518 TRP cc_start: 0.7327 (m-10) cc_final: 0.6826 (m-10) REVERT: D 833 ILE cc_start: 0.8906 (mt) cc_final: 0.8639 (mt) REVERT: D 918 ASP cc_start: 0.7937 (t0) cc_final: 0.7240 (p0) REVERT: D 937 SER cc_start: 0.9043 (m) cc_final: 0.8737 (p) REVERT: D 942 ASN cc_start: 0.8515 (t0) cc_final: 0.8305 (t0) REVERT: D 948 ASP cc_start: 0.8070 (m-30) cc_final: 0.7653 (m-30) REVERT: D 1223 TYR cc_start: 0.8198 (m-80) cc_final: 0.7850 (m-10) REVERT: D 1259 TYR cc_start: 0.8583 (m-80) cc_final: 0.7878 (m-80) REVERT: D 1342 ILE cc_start: 0.8636 (mt) cc_final: 0.8109 (mt) REVERT: D 1512 TYR cc_start: 0.7862 (m-80) cc_final: 0.5958 (m-10) REVERT: D 1583 TYR cc_start: 0.6279 (p90) cc_final: 0.5959 (p90) REVERT: D 1613 PHE cc_start: 0.8505 (m-10) cc_final: 0.8197 (m-80) REVERT: D 1813 THR cc_start: 0.7128 (p) cc_final: 0.6860 (p) REVERT: D 1866 LEU cc_start: 0.8167 (tp) cc_final: 0.7430 (mt) REVERT: D 1989 ILE cc_start: 0.9388 (tt) cc_final: 0.9163 (mm) REVERT: D 2142 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7855 (mtm-85) REVERT: E 50 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8551 (mtp180) REVERT: E 63 GLU cc_start: 0.7739 (tt0) cc_final: 0.7331 (pt0) REVERT: E 93 ASN cc_start: 0.8386 (m110) cc_final: 0.8171 (t0) REVERT: E 104 VAL cc_start: 0.9184 (t) cc_final: 0.8888 (m) REVERT: E 125 GLU cc_start: 0.7169 (tt0) cc_final: 0.6906 (tt0) REVERT: E 148 MET cc_start: 0.8688 (ttp) cc_final: 0.8287 (ttm) REVERT: E 231 LEU cc_start: 0.8510 (mp) cc_final: 0.8263 (mp) REVERT: E 282 TYR cc_start: 0.8871 (t80) cc_final: 0.8452 (t80) REVERT: E 424 LYS cc_start: 0.9255 (mtmt) cc_final: 0.8954 (mtmt) REVERT: E 473 THR cc_start: 0.7444 (p) cc_final: 0.6515 (t) REVERT: E 518 TRP cc_start: 0.7326 (m-10) cc_final: 0.6786 (m-10) REVERT: E 555 LYS cc_start: 0.8354 (tttt) cc_final: 0.8153 (tptt) REVERT: E 892 ASP cc_start: 0.8088 (m-30) cc_final: 0.7827 (m-30) REVERT: E 937 SER cc_start: 0.8851 (m) cc_final: 0.8435 (p) REVERT: E 940 GLN cc_start: 0.8298 (mm110) cc_final: 0.7950 (mm-40) REVERT: E 942 ASN cc_start: 0.8731 (t0) cc_final: 0.8452 (t0) REVERT: E 948 ASP cc_start: 0.8180 (m-30) cc_final: 0.7634 (m-30) REVERT: E 1223 TYR cc_start: 0.8079 (m-80) cc_final: 0.7447 (m-10) REVERT: E 1342 ILE cc_start: 0.8631 (mt) cc_final: 0.8417 (mt) REVERT: E 1497 MET cc_start: 0.9060 (tpp) cc_final: 0.8556 (mmm) REVERT: E 1512 TYR cc_start: 0.7867 (m-80) cc_final: 0.5598 (m-80) REVERT: E 1583 TYR cc_start: 0.6758 (p90) cc_final: 0.6371 (p90) REVERT: E 1613 PHE cc_start: 0.8334 (m-10) cc_final: 0.8091 (m-80) REVERT: E 1989 ILE cc_start: 0.9446 (tt) cc_final: 0.9225 (mm) REVERT: E 2031 ILE cc_start: 0.9468 (mt) cc_final: 0.9252 (mm) REVERT: E 2162 ILE cc_start: 0.9070 (mm) cc_final: 0.8751 (mm) REVERT: E 2178 GLU cc_start: 0.8219 (mp0) cc_final: 0.7660 (mp0) REVERT: E 2192 LEU cc_start: 0.9312 (mt) cc_final: 0.9102 (mm) outliers start: 0 outliers final: 0 residues processed: 2649 average time/residue: 0.9153 time to fit residues: 4068.6613 Evaluate side-chains 1358 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1358 time to evaluate : 8.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1180 random chunks: chunk 996 optimal weight: 1.9990 chunk 894 optimal weight: 5.9990 chunk 496 optimal weight: 2.9990 chunk 305 optimal weight: 10.0000 chunk 603 optimal weight: 4.9990 chunk 477 optimal weight: 7.9990 chunk 924 optimal weight: 0.9980 chunk 357 optimal weight: 8.9990 chunk 562 optimal weight: 2.9990 chunk 688 optimal weight: 0.8980 chunk 1071 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 75 GLN A 79 HIS A 215 GLN A 221 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN A 439 HIS A 456 ASN A 684 ASN A 730 ASN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 GLN A 962 ASN A1052 GLN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 ASN A1203 GLN A1212 ASN A1268 ASN A1390 GLN A1403 ASN A1417 ASN A1525 HIS A1576 ASN A1584 GLN ** A1623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1681 GLN A1821 GLN A2002 HIS A2100 GLN A2361 GLN B 75 GLN B 79 HIS B 215 GLN B 221 GLN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 397 ASN B 439 HIS B 456 ASN B 684 ASN B 730 ASN B 758 ASN B 934 GLN B 962 ASN B1052 GLN B1108 GLN B1165 ASN B1203 GLN B1212 ASN B1268 ASN B1390 GLN B1403 ASN B1417 ASN B1525 HIS B1576 ASN ** B1623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1658 GLN ** B1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2002 HIS B2100 GLN B2361 GLN C 75 GLN C 79 HIS C 215 GLN C 221 GLN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN ** C 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN C 439 HIS C 684 ASN C 719 ASN C 730 ASN ** C 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 GLN C 962 ASN C 991 ASN C1027 GLN C1052 GLN ** C1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1165 ASN C1203 GLN C1212 ASN C1268 ASN C1390 GLN C1403 ASN C1417 ASN C1525 HIS C1576 ASN ** C1623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1658 GLN C1681 GLN C1763 ASN C1821 GLN C2002 HIS C2100 GLN D 30 ASN D 75 GLN D 79 HIS D 215 GLN D 221 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 ASN D 397 ASN D 439 HIS D 684 ASN D 730 ASN ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 925 GLN D 962 ASN D 991 ASN D1052 GLN ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1203 GLN D1212 ASN D1268 ASN D1390 GLN D1403 ASN D1417 ASN D1525 HIS D1576 ASN D1584 GLN ** D1623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1658 GLN D1681 GLN D1821 GLN D2002 HIS ** D2067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2100 GLN E 30 ASN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN E 79 HIS E 215 GLN E 221 GLN E 241 ASN ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 GLN E 392 ASN E 397 ASN E 439 HIS E 684 ASN E 730 ASN ** E 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 908 GLN E 925 GLN E 962 ASN E 991 ASN E1052 GLN ** E1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1165 ASN E1203 GLN E1212 ASN E1268 ASN E1390 GLN E1403 ASN E1417 ASN E1525 HIS E1576 ASN E1584 GLN ** E1623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1658 GLN E1681 GLN E2002 HIS Total number of N/Q/H flips: 146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 96545 Z= 0.238 Angle : 0.700 9.411 131045 Z= 0.365 Chirality : 0.042 0.277 14580 Planarity : 0.005 0.065 17000 Dihedral : 6.322 46.810 12850 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 2.71 % Allowed : 9.63 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 3.66 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.07), residues: 11795 helix: 0.36 (0.07), residues: 5310 sheet: -1.42 (0.12), residues: 1675 loop : -2.09 (0.08), residues: 4810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 418 HIS 0.012 0.001 HIS C1759 PHE 0.024 0.002 PHE C 809 TYR 0.029 0.002 TYR C 123 ARG 0.010 0.001 ARG B1620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1888 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1609 time to evaluate : 8.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8859 (mtt180) cc_final: 0.8526 (mtp180) REVERT: A 56 GLN cc_start: 0.8915 (mt0) cc_final: 0.8487 (tm-30) REVERT: A 63 GLU cc_start: 0.8287 (tt0) cc_final: 0.7564 (pt0) REVERT: A 93 ASN cc_start: 0.8503 (m110) cc_final: 0.7972 (t0) REVERT: A 124 ARG cc_start: 0.7423 (mmt180) cc_final: 0.7213 (mmt180) REVERT: A 125 GLU cc_start: 0.7286 (tt0) cc_final: 0.6848 (tt0) REVERT: A 137 HIS cc_start: 0.8013 (t70) cc_final: 0.7468 (t-90) REVERT: A 232 MET cc_start: 0.8359 (mtp) cc_final: 0.8141 (ttm) REVERT: A 242 ASN cc_start: 0.7474 (t0) cc_final: 0.7143 (t0) REVERT: A 366 THR cc_start: 0.9014 (m) cc_final: 0.8802 (p) REVERT: A 462 MET cc_start: 0.9122 (tmm) cc_final: 0.8907 (tmm) REVERT: A 887 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7045 (mtt180) REVERT: A 914 GLU cc_start: 0.8828 (pm20) cc_final: 0.8418 (pm20) REVERT: A 930 ASP cc_start: 0.7810 (m-30) cc_final: 0.7426 (m-30) REVERT: A 937 SER cc_start: 0.8561 (m) cc_final: 0.8328 (p) REVERT: A 940 GLN cc_start: 0.8267 (mm110) cc_final: 0.7599 (mt0) REVERT: A 985 ASN cc_start: 0.8542 (t0) cc_final: 0.7063 (t0) REVERT: A 1201 LEU cc_start: 0.8567 (tt) cc_final: 0.8360 (mm) REVERT: A 1342 ILE cc_start: 0.8276 (mt) cc_final: 0.8058 (mt) REVERT: A 1396 GLU cc_start: 0.8215 (mp0) cc_final: 0.7976 (tp30) REVERT: A 1613 PHE cc_start: 0.8545 (m-10) cc_final: 0.8130 (m-80) REVERT: A 1703 LEU cc_start: 0.9401 (mt) cc_final: 0.8934 (tt) REVERT: A 1717 MET cc_start: 0.8253 (ppp) cc_final: 0.7760 (ppp) REVERT: A 1832 LYS cc_start: 0.8768 (tttt) cc_final: 0.8354 (ttmm) REVERT: A 1918 ASP cc_start: 0.8067 (m-30) cc_final: 0.7507 (t0) REVERT: B 50 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8446 (mtp180) REVERT: B 56 GLN cc_start: 0.8782 (mt0) cc_final: 0.8308 (tm-30) REVERT: B 63 GLU cc_start: 0.8243 (tt0) cc_final: 0.7837 (pt0) REVERT: B 93 ASN cc_start: 0.8561 (m110) cc_final: 0.8074 (t0) REVERT: B 125 GLU cc_start: 0.7177 (tt0) cc_final: 0.6962 (tt0) REVERT: B 242 ASN cc_start: 0.7283 (t0) cc_final: 0.7064 (m110) REVERT: B 322 LEU cc_start: 0.9596 (tp) cc_final: 0.9314 (tt) REVERT: B 418 TRP cc_start: 0.7778 (p-90) cc_final: 0.7195 (p-90) REVERT: B 462 MET cc_start: 0.9021 (tmm) cc_final: 0.8819 (tmm) REVERT: B 498 GLU cc_start: 0.8801 (mp0) cc_final: 0.8595 (mp0) REVERT: B 838 ASP cc_start: 0.8261 (m-30) cc_final: 0.7871 (t0) REVERT: B 930 ASP cc_start: 0.7400 (m-30) cc_final: 0.6660 (m-30) REVERT: B 937 SER cc_start: 0.8495 (m) cc_final: 0.8246 (p) REVERT: B 940 GLN cc_start: 0.8408 (mm110) cc_final: 0.7717 (mt0) REVERT: B 985 ASN cc_start: 0.8592 (t0) cc_final: 0.8211 (t0) REVERT: B 1132 MET cc_start: 0.7622 (mtm) cc_final: 0.7273 (ppp) REVERT: B 1396 GLU cc_start: 0.8284 (mp0) cc_final: 0.7979 (tp30) REVERT: B 1405 LEU cc_start: 0.8049 (mt) cc_final: 0.7711 (mp) REVERT: B 1613 PHE cc_start: 0.8566 (m-10) cc_final: 0.8121 (m-80) REVERT: B 1752 MET cc_start: 0.8654 (tmm) cc_final: 0.8148 (tmm) REVERT: B 1832 LYS cc_start: 0.8700 (tttt) cc_final: 0.8469 (ttmm) REVERT: B 1849 GLN cc_start: 0.9029 (tp40) cc_final: 0.8777 (mt0) REVERT: B 1918 ASP cc_start: 0.8021 (m-30) cc_final: 0.7524 (t0) REVERT: B 2143 CYS cc_start: 0.9113 (m) cc_final: 0.8893 (t) REVERT: B 2270 MET cc_start: 0.5567 (mmp) cc_final: 0.3179 (ptm) REVERT: C 50 ARG cc_start: 0.8905 (mtt180) cc_final: 0.8476 (mtp180) REVERT: C 56 GLN cc_start: 0.8786 (mt0) cc_final: 0.8277 (tm-30) REVERT: C 63 GLU cc_start: 0.8087 (tt0) cc_final: 0.7560 (pt0) REVERT: C 65 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7448 (ptt180) REVERT: C 93 ASN cc_start: 0.8409 (m110) cc_final: 0.7933 (t0) REVERT: C 124 ARG cc_start: 0.7582 (mmt180) cc_final: 0.7149 (mmt180) REVERT: C 125 GLU cc_start: 0.7295 (tt0) cc_final: 0.6570 (tt0) REVERT: C 386 GLN cc_start: 0.8926 (tt0) cc_final: 0.8596 (tt0) REVERT: C 462 MET cc_start: 0.9090 (tmm) cc_final: 0.8839 (tmm) REVERT: C 513 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9057 (tp) REVERT: C 620 MET cc_start: 0.8672 (mpp) cc_final: 0.8454 (ttt) REVERT: C 653 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8212 (mt-10) REVERT: C 914 GLU cc_start: 0.8742 (pm20) cc_final: 0.8445 (pm20) REVERT: C 918 ASP cc_start: 0.7948 (t0) cc_final: 0.7212 (p0) REVERT: C 925 GLN cc_start: 0.8267 (tt0) cc_final: 0.8047 (tt0) REVERT: C 937 SER cc_start: 0.8702 (m) cc_final: 0.8456 (p) REVERT: C 940 GLN cc_start: 0.8266 (mm110) cc_final: 0.7729 (mt0) REVERT: C 1027 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7586 (mt0) REVERT: C 1085 VAL cc_start: 0.9354 (m) cc_final: 0.9139 (p) REVERT: C 1132 MET cc_start: 0.7260 (mtm) cc_final: 0.7034 (ppp) REVERT: C 1223 TYR cc_start: 0.8280 (m-80) cc_final: 0.8072 (m-10) REVERT: C 1379 TYR cc_start: 0.7599 (m-10) cc_final: 0.7184 (m-10) REVERT: C 1396 GLU cc_start: 0.8512 (mp0) cc_final: 0.8267 (tp30) REVERT: C 1482 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: C 1705 SER cc_start: 0.8788 (p) cc_final: 0.8500 (t) REVERT: C 1749 GLU cc_start: 0.8605 (tt0) cc_final: 0.8383 (tt0) REVERT: C 1866 LEU cc_start: 0.8062 (tp) cc_final: 0.7435 (tp) REVERT: C 2178 GLU cc_start: 0.8549 (mp0) cc_final: 0.8268 (mp0) REVERT: D 50 ARG cc_start: 0.8772 (mtt180) cc_final: 0.8551 (mtp180) REVERT: D 56 GLN cc_start: 0.8689 (mt0) cc_final: 0.8267 (tm-30) REVERT: D 63 GLU cc_start: 0.8177 (tt0) cc_final: 0.7798 (pt0) REVERT: D 93 ASN cc_start: 0.8545 (m110) cc_final: 0.8211 (t0) REVERT: D 125 GLU cc_start: 0.7103 (tt0) cc_final: 0.6766 (tm-30) REVERT: D 148 MET cc_start: 0.8433 (ttp) cc_final: 0.8137 (ttm) REVERT: D 159 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8916 (pp) REVERT: D 232 MET cc_start: 0.8747 (mtt) cc_final: 0.8270 (ttm) REVERT: D 283 LEU cc_start: 0.9137 (mt) cc_final: 0.8895 (mt) REVERT: D 513 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9012 (tp) REVERT: D 559 LYS cc_start: 0.7996 (tttt) cc_final: 0.7775 (tppt) REVERT: D 914 GLU cc_start: 0.8746 (pm20) cc_final: 0.8427 (pm20) REVERT: D 918 ASP cc_start: 0.7984 (t0) cc_final: 0.7422 (p0) REVERT: D 929 MET cc_start: 0.8919 (tpt) cc_final: 0.8608 (tpp) REVERT: D 937 SER cc_start: 0.8648 (m) cc_final: 0.8311 (p) REVERT: D 966 ILE cc_start: 0.9243 (mp) cc_final: 0.9008 (mm) REVERT: D 985 ASN cc_start: 0.8418 (t0) cc_final: 0.8172 (t0) REVERT: D 1259 TYR cc_start: 0.8448 (m-80) cc_final: 0.8115 (m-80) REVERT: D 1272 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6577 (mtm180) REVERT: D 1342 ILE cc_start: 0.8504 (mt) cc_final: 0.8253 (mt) REVERT: D 1396 GLU cc_start: 0.8335 (mp0) cc_final: 0.7933 (tp30) REVERT: D 1648 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8387 (tpp) REVERT: D 1717 MET cc_start: 0.8341 (ppp) cc_final: 0.7861 (ppp) REVERT: D 1752 MET cc_start: 0.8728 (tmm) cc_final: 0.8437 (tmm) REVERT: D 2143 CYS cc_start: 0.9189 (m) cc_final: 0.8869 (t) REVERT: D 2181 MET cc_start: 0.7866 (tpt) cc_final: 0.7338 (tpt) REVERT: D 2192 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9122 (tp) REVERT: D 2270 MET cc_start: 0.5175 (OUTLIER) cc_final: 0.2703 (ptm) REVERT: E 50 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8563 (mtp180) REVERT: E 56 GLN cc_start: 0.8524 (mt0) cc_final: 0.8144 (tm-30) REVERT: E 63 GLU cc_start: 0.8210 (tt0) cc_final: 0.7807 (pt0) REVERT: E 65 ARG cc_start: 0.7655 (ttt180) cc_final: 0.7035 (ttt180) REVERT: E 93 ASN cc_start: 0.8434 (m110) cc_final: 0.7952 (t0) REVERT: E 148 MET cc_start: 0.8398 (ttp) cc_final: 0.8053 (ttm) REVERT: E 232 MET cc_start: 0.8251 (mtp) cc_final: 0.8020 (ttm) REVERT: E 242 ASN cc_start: 0.7369 (t0) cc_final: 0.7138 (t0) REVERT: E 462 MET cc_start: 0.9107 (tmm) cc_final: 0.8834 (tmm) REVERT: E 513 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8922 (tp) REVERT: E 929 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8303 (mmm) REVERT: E 930 ASP cc_start: 0.7399 (m-30) cc_final: 0.7054 (m-30) REVERT: E 937 SER cc_start: 0.8483 (m) cc_final: 0.8223 (p) REVERT: E 940 GLN cc_start: 0.8316 (mm110) cc_final: 0.7938 (mm-40) REVERT: E 966 ILE cc_start: 0.9219 (mp) cc_final: 0.8969 (mm) REVERT: E 985 ASN cc_start: 0.8501 (t0) cc_final: 0.8237 (t0) REVERT: E 1132 MET cc_start: 0.7666 (mtm) cc_final: 0.7034 (ppp) REVERT: E 1223 TYR cc_start: 0.8175 (m-80) cc_final: 0.7842 (m-10) REVERT: E 1342 ILE cc_start: 0.8410 (mt) cc_final: 0.8205 (mt) REVERT: E 1396 GLU cc_start: 0.8332 (mp0) cc_final: 0.8047 (tp30) REVERT: E 1703 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8844 (mm) REVERT: E 1705 SER cc_start: 0.8762 (p) cc_final: 0.8552 (t) REVERT: E 1849 GLN cc_start: 0.9122 (tp40) cc_final: 0.8891 (mt0) REVERT: E 1892 MET cc_start: 0.8023 (mmp) cc_final: 0.7794 (mmp) REVERT: E 2162 ILE cc_start: 0.9174 (mm) cc_final: 0.8736 (mm) REVERT: E 2270 MET cc_start: 0.4617 (mmp) cc_final: 0.2465 (ttt) REVERT: E 2321 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7252 (mm) outliers start: 279 outliers final: 112 residues processed: 1826 average time/residue: 0.8512 time to fit residues: 2694.0629 Evaluate side-chains 1262 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1136 time to evaluate : 8.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1575 ASN Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1912 ASN Chi-restraints excluded: chain A residue 1913 ILE Chi-restraints excluded: chain A residue 1976 ASP Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2050 SER Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 948 ASP Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1108 GLN Chi-restraints excluded: chain B residue 1215 VAL Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1527 THR Chi-restraints excluded: chain B residue 1566 ARG Chi-restraints excluded: chain B residue 1575 ASN Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1690 ARG Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 ASP Chi-restraints excluded: chain B residue 2050 SER Chi-restraints excluded: chain B residue 2138 LEU Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1172 ILE Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1417 ASN Chi-restraints excluded: chain C residue 1455 THR Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1575 ASN Chi-restraints excluded: chain C residue 1938 LEU Chi-restraints excluded: chain C residue 1953 THR Chi-restraints excluded: chain C residue 1976 ASP Chi-restraints excluded: chain C residue 2009 GLU Chi-restraints excluded: chain C residue 2050 SER Chi-restraints excluded: chain C residue 2321 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 1030 ILE Chi-restraints excluded: chain D residue 1272 ARG Chi-restraints excluded: chain D residue 1293 LEU Chi-restraints excluded: chain D residue 1417 ASN Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1473 ILE Chi-restraints excluded: chain D residue 1564 LEU Chi-restraints excluded: chain D residue 1575 ASN Chi-restraints excluded: chain D residue 1648 MET Chi-restraints excluded: chain D residue 1953 THR Chi-restraints excluded: chain D residue 1976 ASP Chi-restraints excluded: chain D residue 2050 SER Chi-restraints excluded: chain D residue 2077 ASP Chi-restraints excluded: chain D residue 2192 LEU Chi-restraints excluded: chain D residue 2270 MET Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 637 ILE Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 843 LEU Chi-restraints excluded: chain E residue 929 MET Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1042 ILE Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1172 ILE Chi-restraints excluded: chain E residue 1188 ILE Chi-restraints excluded: chain E residue 1204 VAL Chi-restraints excluded: chain E residue 1305 VAL Chi-restraints excluded: chain E residue 1455 THR Chi-restraints excluded: chain E residue 1564 LEU Chi-restraints excluded: chain E residue 1575 ASN Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain E residue 1745 ASP Chi-restraints excluded: chain E residue 1913 ILE Chi-restraints excluded: chain E residue 1953 THR Chi-restraints excluded: chain E residue 1955 LEU Chi-restraints excluded: chain E residue 1976 ASP Chi-restraints excluded: chain E residue 1994 ILE Chi-restraints excluded: chain E residue 2050 SER Chi-restraints excluded: chain E residue 2180 LEU Chi-restraints excluded: chain E residue 2321 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1180 random chunks: chunk 595 optimal weight: 6.9990 chunk 332 optimal weight: 0.2980 chunk 891 optimal weight: 0.2980 chunk 729 optimal weight: 0.9990 chunk 295 optimal weight: 20.0000 chunk 1073 optimal weight: 9.9990 chunk 1159 optimal weight: 3.9990 chunk 956 optimal weight: 0.7980 chunk 1064 optimal weight: 4.9990 chunk 365 optimal weight: 10.0000 chunk 861 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 758 ASN A 925 GLN A 940 GLN A1108 GLN A1203 GLN ** A1623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1821 GLN A1902 GLN ** A2103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 128 ASN B 213 GLN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 GLN B1623 GLN ** B1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 758 ASN C1046 GLN C1108 GLN C1203 GLN C1417 ASN ** C1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1821 GLN C1902 GLN ** C2067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2103 GLN D 79 HIS D 128 ASN D 202 HIS ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 758 ASN D 879 HIS ** D 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN D1165 ASN D1203 GLN D1417 ASN ** D1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2067 ASN D2361 GLN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS E 128 ASN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 758 ASN ** E 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 925 GLN E1108 GLN ** E1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2100 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 96545 Z= 0.188 Angle : 0.626 9.021 131045 Z= 0.324 Chirality : 0.041 0.216 14580 Planarity : 0.004 0.065 17000 Dihedral : 5.759 45.684 12850 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 2.61 % Allowed : 12.74 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 2.44 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.08), residues: 11795 helix: 1.04 (0.07), residues: 5380 sheet: -1.11 (0.12), residues: 1670 loop : -1.83 (0.09), residues: 4745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 418 HIS 0.021 0.001 HIS E 79 PHE 0.021 0.001 PHE C 648 TYR 0.026 0.001 TYR D 123 ARG 0.010 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1324 time to evaluate : 8.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8500 (mtp180) REVERT: A 56 GLN cc_start: 0.8928 (mt0) cc_final: 0.8289 (tm-30) REVERT: A 63 GLU cc_start: 0.8359 (tt0) cc_final: 0.7718 (pt0) REVERT: A 93 ASN cc_start: 0.8499 (m110) cc_final: 0.7989 (t0) REVERT: A 124 ARG cc_start: 0.7333 (mmt180) cc_final: 0.7126 (mmt180) REVERT: A 221 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7529 (tt0) REVERT: A 242 ASN cc_start: 0.7240 (t0) cc_final: 0.6910 (t0) REVERT: A 462 MET cc_start: 0.9057 (tmm) cc_final: 0.8700 (tmm) REVERT: A 914 GLU cc_start: 0.8789 (pm20) cc_final: 0.8528 (pm20) REVERT: A 929 MET cc_start: 0.8574 (mmm) cc_final: 0.8045 (mmm) REVERT: A 937 SER cc_start: 0.8555 (m) cc_final: 0.8346 (p) REVERT: A 940 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7629 (mm-40) REVERT: A 985 ASN cc_start: 0.8141 (t0) cc_final: 0.7836 (t0) REVERT: A 1085 VAL cc_start: 0.9408 (m) cc_final: 0.9169 (p) REVERT: A 1201 LEU cc_start: 0.8662 (tt) cc_final: 0.8414 (mm) REVERT: A 1205 TYR cc_start: 0.8080 (t80) cc_final: 0.7809 (t80) REVERT: A 1438 GLU cc_start: 0.8325 (tt0) cc_final: 0.7985 (mt-10) REVERT: A 1482 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: A 1613 PHE cc_start: 0.8568 (m-10) cc_final: 0.8127 (m-80) REVERT: A 1749 GLU cc_start: 0.7839 (tp30) cc_final: 0.7536 (tp30) REVERT: A 1752 MET cc_start: 0.8547 (tmm) cc_final: 0.8214 (tmm) REVERT: A 1755 MET cc_start: 0.8452 (mmm) cc_final: 0.8246 (mmm) REVERT: A 1832 LYS cc_start: 0.8872 (tttt) cc_final: 0.8658 (ttmm) REVERT: A 1918 ASP cc_start: 0.8037 (m-30) cc_final: 0.7457 (t0) REVERT: A 2047 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7398 (mp0) REVERT: A 2188 GLU cc_start: 0.7497 (tm-30) cc_final: 0.6808 (tm-30) REVERT: A 2350 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7236 (t80) REVERT: B 50 ARG cc_start: 0.8813 (mtt180) cc_final: 0.8448 (mtp180) REVERT: B 56 GLN cc_start: 0.8818 (mt0) cc_final: 0.8266 (tm-30) REVERT: B 63 GLU cc_start: 0.8201 (tt0) cc_final: 0.7762 (pt0) REVERT: B 93 ASN cc_start: 0.8428 (m110) cc_final: 0.7984 (t0) REVERT: B 125 GLU cc_start: 0.7196 (tt0) cc_final: 0.5725 (tt0) REVERT: B 137 HIS cc_start: 0.8034 (t70) cc_final: 0.7793 (t-90) REVERT: B 322 LEU cc_start: 0.9568 (tp) cc_final: 0.9309 (tt) REVERT: B 418 TRP cc_start: 0.7843 (p-90) cc_final: 0.7152 (p-90) REVERT: B 462 MET cc_start: 0.9073 (tmm) cc_final: 0.8801 (tmm) REVERT: B 838 ASP cc_start: 0.8325 (m-30) cc_final: 0.7929 (t0) REVERT: B 860 GLU cc_start: 0.7841 (tp30) cc_final: 0.7164 (tp30) REVERT: B 865 ILE cc_start: 0.9143 (mt) cc_final: 0.8892 (mm) REVERT: B 937 SER cc_start: 0.8485 (m) cc_final: 0.8221 (p) REVERT: B 940 GLN cc_start: 0.8390 (mm110) cc_final: 0.7988 (mm-40) REVERT: B 1108 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7557 (mp10) REVERT: B 1405 LEU cc_start: 0.8081 (mt) cc_final: 0.7772 (mp) REVERT: B 1438 GLU cc_start: 0.8236 (tt0) cc_final: 0.7888 (tt0) REVERT: B 1482 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: B 1492 ASP cc_start: 0.8406 (p0) cc_final: 0.8157 (p0) REVERT: B 1512 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: B 1613 PHE cc_start: 0.8632 (m-10) cc_final: 0.8191 (m-80) REVERT: B 1832 LYS cc_start: 0.8808 (tttt) cc_final: 0.8570 (ttmm) REVERT: B 1849 GLN cc_start: 0.9016 (tp40) cc_final: 0.8774 (mt0) REVERT: B 1918 ASP cc_start: 0.8062 (m-30) cc_final: 0.7412 (t0) REVERT: B 2143 CYS cc_start: 0.9047 (m) cc_final: 0.8834 (t) REVERT: B 2270 MET cc_start: 0.5428 (mmp) cc_final: 0.3229 (ttt) REVERT: C 50 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8477 (mtp180) REVERT: C 56 GLN cc_start: 0.8745 (mt0) cc_final: 0.8242 (tm-30) REVERT: C 63 GLU cc_start: 0.8177 (tt0) cc_final: 0.7540 (pt0) REVERT: C 93 ASN cc_start: 0.8431 (m110) cc_final: 0.8196 (t0) REVERT: C 125 GLU cc_start: 0.7249 (tt0) cc_final: 0.6724 (tt0) REVERT: C 137 HIS cc_start: 0.7973 (t70) cc_final: 0.7529 (t-90) REVERT: C 187 MET cc_start: 0.8924 (mmm) cc_final: 0.8706 (mmm) REVERT: C 221 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7408 (tm-30) REVERT: C 357 MET cc_start: 0.8993 (mmm) cc_final: 0.8663 (mmt) REVERT: C 386 GLN cc_start: 0.8948 (tt0) cc_final: 0.8639 (tt0) REVERT: C 462 MET cc_start: 0.9130 (tmm) cc_final: 0.8774 (tmm) REVERT: C 474 ILE cc_start: 0.9097 (mm) cc_final: 0.8893 (mp) REVERT: C 918 ASP cc_start: 0.7904 (t0) cc_final: 0.7063 (p0) REVERT: C 930 ASP cc_start: 0.7763 (m-30) cc_final: 0.7079 (m-30) REVERT: C 937 SER cc_start: 0.8654 (m) cc_final: 0.8419 (p) REVERT: C 940 GLN cc_start: 0.8338 (mm110) cc_final: 0.7890 (mm-40) REVERT: C 1085 VAL cc_start: 0.9301 (m) cc_final: 0.9088 (p) REVERT: C 1116 MET cc_start: 0.8557 (ttp) cc_final: 0.8336 (ttm) REVERT: C 1342 ILE cc_start: 0.8398 (mm) cc_final: 0.8157 (mm) REVERT: C 1438 GLU cc_start: 0.8170 (tt0) cc_final: 0.7804 (tt0) REVERT: C 1482 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: C 1539 PHE cc_start: 0.6506 (t80) cc_final: 0.6174 (t80) REVERT: C 1661 ASP cc_start: 0.7629 (p0) cc_final: 0.7380 (p0) REVERT: C 1705 SER cc_start: 0.8670 (p) cc_final: 0.8416 (t) REVERT: C 2178 GLU cc_start: 0.8478 (mp0) cc_final: 0.8274 (mp0) REVERT: D 50 ARG cc_start: 0.8774 (mtt180) cc_final: 0.8533 (mtp180) REVERT: D 56 GLN cc_start: 0.8685 (mt0) cc_final: 0.8155 (tm-30) REVERT: D 63 GLU cc_start: 0.8263 (tt0) cc_final: 0.7689 (pt0) REVERT: D 76 ASN cc_start: 0.6719 (t0) cc_final: 0.6495 (t0) REVERT: D 93 ASN cc_start: 0.8491 (m110) cc_final: 0.8117 (t0) REVERT: D 125 GLU cc_start: 0.6951 (tt0) cc_final: 0.6146 (tt0) REVERT: D 148 MET cc_start: 0.8411 (ttp) cc_final: 0.8177 (ttm) REVERT: D 159 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8858 (pp) REVERT: D 221 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: D 474 ILE cc_start: 0.9096 (mm) cc_final: 0.8869 (mp) REVERT: D 559 LYS cc_start: 0.7932 (tttt) cc_final: 0.7731 (tppt) REVERT: D 860 GLU cc_start: 0.7867 (tp30) cc_final: 0.7613 (tp30) REVERT: D 865 ILE cc_start: 0.9243 (mt) cc_final: 0.9014 (mm) REVERT: D 914 GLU cc_start: 0.8642 (pm20) cc_final: 0.8334 (pm20) REVERT: D 918 ASP cc_start: 0.7751 (t0) cc_final: 0.7173 (p0) REVERT: D 929 MET cc_start: 0.8925 (tpt) cc_final: 0.8689 (tpp) REVERT: D 937 SER cc_start: 0.8395 (m) cc_final: 0.8076 (p) REVERT: D 966 ILE cc_start: 0.9185 (mp) cc_final: 0.8774 (mt) REVERT: D 1063 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7568 (p90) REVERT: D 1342 ILE cc_start: 0.8417 (mt) cc_final: 0.8208 (mt) REVERT: D 1438 GLU cc_start: 0.8175 (tt0) cc_final: 0.7890 (tt0) REVERT: D 1598 ASN cc_start: 0.7967 (t0) cc_final: 0.7748 (m-40) REVERT: D 1732 MET cc_start: 0.8275 (ttt) cc_final: 0.7934 (ttm) REVERT: D 2143 CYS cc_start: 0.9174 (m) cc_final: 0.8874 (t) REVERT: D 2270 MET cc_start: 0.4801 (OUTLIER) cc_final: 0.2567 (ttt) REVERT: E 50 ARG cc_start: 0.8837 (mtt180) cc_final: 0.8559 (mtp180) REVERT: E 56 GLN cc_start: 0.8467 (mt0) cc_final: 0.8000 (tm-30) REVERT: E 63 GLU cc_start: 0.8167 (tt0) cc_final: 0.7835 (pt0) REVERT: E 93 ASN cc_start: 0.8361 (m110) cc_final: 0.7906 (t0) REVERT: E 148 MET cc_start: 0.8228 (ttp) cc_final: 0.7872 (ttm) REVERT: E 221 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: E 294 LEU cc_start: 0.8053 (tt) cc_final: 0.7315 (tt) REVERT: E 462 MET cc_start: 0.9056 (tmm) cc_final: 0.8808 (tmm) REVERT: E 910 VAL cc_start: 0.9130 (t) cc_final: 0.8844 (t) REVERT: E 937 SER cc_start: 0.8398 (m) cc_final: 0.8110 (p) REVERT: E 940 GLN cc_start: 0.8133 (mm110) cc_final: 0.7677 (mm-40) REVERT: E 966 ILE cc_start: 0.9142 (mp) cc_final: 0.8854 (mm) REVERT: E 985 ASN cc_start: 0.8156 (t0) cc_final: 0.7345 (t0) REVERT: E 1116 MET cc_start: 0.8619 (ttp) cc_final: 0.8246 (ttp) REVERT: E 1132 MET cc_start: 0.7857 (mtm) cc_final: 0.7509 (ppp) REVERT: E 1223 TYR cc_start: 0.8172 (m-80) cc_final: 0.7901 (m-10) REVERT: E 1259 TYR cc_start: 0.8521 (m-80) cc_final: 0.8280 (m-80) REVERT: E 1342 ILE cc_start: 0.8284 (mt) cc_final: 0.8019 (mt) REVERT: E 1377 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7713 (pttm) REVERT: E 1613 PHE cc_start: 0.8618 (m-10) cc_final: 0.8195 (m-80) REVERT: E 1703 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8988 (mm) REVERT: E 1752 MET cc_start: 0.8689 (tmm) cc_final: 0.8462 (tmm) REVERT: E 2270 MET cc_start: 0.4645 (mmp) cc_final: 0.2634 (ttt) REVERT: E 2321 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7321 (mm) outliers start: 269 outliers final: 174 residues processed: 1530 average time/residue: 0.8268 time to fit residues: 2214.0347 Evaluate side-chains 1276 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1087 time to evaluate : 8.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 TYR Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1482 GLN Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1575 ASN Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1772 VAL Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1840 LEU Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2050 SER Chi-restraints excluded: chain A residue 2077 ASP Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2350 PHE Chi-restraints excluded: chain A residue 2369 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 948 ASP Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1063 HIS Chi-restraints excluded: chain B residue 1108 GLN Chi-restraints excluded: chain B residue 1215 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1305 VAL Chi-restraints excluded: chain B residue 1444 VAL Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1482 GLN Chi-restraints excluded: chain B residue 1512 TYR Chi-restraints excluded: chain B residue 1566 ARG Chi-restraints excluded: chain B residue 1575 ASN Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1690 ARG Chi-restraints excluded: chain B residue 1706 VAL Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1772 VAL Chi-restraints excluded: chain B residue 1955 LEU Chi-restraints excluded: chain B residue 1976 ASP Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 2011 VAL Chi-restraints excluded: chain B residue 2050 SER Chi-restraints excluded: chain B residue 2077 ASP Chi-restraints excluded: chain B residue 2138 LEU Chi-restraints excluded: chain B residue 2180 LEU Chi-restraints excluded: chain B residue 2369 THR Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 800 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 HIS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1215 VAL Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1417 ASN Chi-restraints excluded: chain C residue 1455 THR Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1488 ASN Chi-restraints excluded: chain C residue 1575 ASN Chi-restraints excluded: chain C residue 1622 ILE Chi-restraints excluded: chain C residue 1772 VAL Chi-restraints excluded: chain C residue 1813 THR Chi-restraints excluded: chain C residue 1938 LEU Chi-restraints excluded: chain C residue 1955 LEU Chi-restraints excluded: chain C residue 2050 SER Chi-restraints excluded: chain C residue 2077 ASP Chi-restraints excluded: chain C residue 2080 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 1030 ILE Chi-restraints excluded: chain D residue 1042 ILE Chi-restraints excluded: chain D residue 1063 HIS Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1417 ASN Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1473 ILE Chi-restraints excluded: chain D residue 1488 ASN Chi-restraints excluded: chain D residue 1564 LEU Chi-restraints excluded: chain D residue 1575 ASN Chi-restraints excluded: chain D residue 1622 ILE Chi-restraints excluded: chain D residue 1772 VAL Chi-restraints excluded: chain D residue 1878 LYS Chi-restraints excluded: chain D residue 1955 LEU Chi-restraints excluded: chain D residue 1994 ILE Chi-restraints excluded: chain D residue 2050 SER Chi-restraints excluded: chain D residue 2077 ASP Chi-restraints excluded: chain D residue 2192 LEU Chi-restraints excluded: chain D residue 2270 MET Chi-restraints excluded: chain D residue 2369 THR Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 637 ILE Chi-restraints excluded: chain E residue 800 THR Chi-restraints excluded: chain E residue 843 LEU Chi-restraints excluded: chain E residue 907 SER Chi-restraints excluded: chain E residue 925 GLN Chi-restraints excluded: chain E residue 960 VAL Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1042 ILE Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1188 ILE Chi-restraints excluded: chain E residue 1204 VAL Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1216 THR Chi-restraints excluded: chain E residue 1272 ARG Chi-restraints excluded: chain E residue 1305 VAL Chi-restraints excluded: chain E residue 1377 LYS Chi-restraints excluded: chain E residue 1455 THR Chi-restraints excluded: chain E residue 1475 LEU Chi-restraints excluded: chain E residue 1488 ASN Chi-restraints excluded: chain E residue 1564 LEU Chi-restraints excluded: chain E residue 1575 ASN Chi-restraints excluded: chain E residue 1622 ILE Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain E residue 1745 ASP Chi-restraints excluded: chain E residue 1758 LEU Chi-restraints excluded: chain E residue 1772 VAL Chi-restraints excluded: chain E residue 1913 ILE Chi-restraints excluded: chain E residue 1953 THR Chi-restraints excluded: chain E residue 1955 LEU Chi-restraints excluded: chain E residue 1976 ASP Chi-restraints excluded: chain E residue 1994 ILE Chi-restraints excluded: chain E residue 2043 LEU Chi-restraints excluded: chain E residue 2050 SER Chi-restraints excluded: chain E residue 2077 ASP Chi-restraints excluded: chain E residue 2080 LEU Chi-restraints excluded: chain E residue 2137 ASP Chi-restraints excluded: chain E residue 2223 ASP Chi-restraints excluded: chain E residue 2321 LEU Chi-restraints excluded: chain E residue 2369 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1180 random chunks: chunk 1060 optimal weight: 4.9990 chunk 807 optimal weight: 6.9990 chunk 557 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 512 optimal weight: 0.7980 chunk 720 optimal weight: 0.9990 chunk 1077 optimal weight: 20.0000 chunk 1140 optimal weight: 1.9990 chunk 562 optimal weight: 5.9990 chunk 1021 optimal weight: 10.0000 chunk 307 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 215 GLN A 241 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 GLN A1046 GLN A1203 GLN A1296 HIS A1821 GLN ** A2103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 79 HIS B 202 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 HIS B 908 GLN ** B 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1027 GLN B1046 GLN B1108 GLN B1190 HIS ** B1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2118 GLN ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 GLN C 940 GLN ** C 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1027 GLN C1190 HIS C1203 GLN C1296 HIS C1417 ASN ** C1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1821 GLN ** C2067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 128 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 GLN D1203 GLN D1296 HIS D1417 ASN ** D1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2067 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS E 202 HIS E 215 GLN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1598 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 96545 Z= 0.199 Angle : 0.607 8.869 131045 Z= 0.315 Chirality : 0.041 0.271 14580 Planarity : 0.004 0.061 17000 Dihedral : 5.464 43.165 12850 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 3.05 % Allowed : 13.72 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 1.71 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.08), residues: 11795 helix: 1.45 (0.07), residues: 5335 sheet: -1.03 (0.12), residues: 1715 loop : -1.67 (0.09), residues: 4745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 418 HIS 0.013 0.001 HIS E 79 PHE 0.026 0.001 PHE B 289 TYR 0.025 0.001 TYR C 123 ARG 0.012 0.000 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1522 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1208 time to evaluate : 8.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8859 (mtt180) cc_final: 0.8505 (mtp180) REVERT: A 56 GLN cc_start: 0.8954 (mt0) cc_final: 0.8251 (tm-30) REVERT: A 63 GLU cc_start: 0.8393 (tt0) cc_final: 0.7720 (pt0) REVERT: A 93 ASN cc_start: 0.8535 (m110) cc_final: 0.8029 (t0) REVERT: A 125 GLU cc_start: 0.7293 (tt0) cc_final: 0.6886 (tt0) REVERT: A 221 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: A 294 LEU cc_start: 0.8074 (tt) cc_final: 0.7513 (tt) REVERT: A 462 MET cc_start: 0.9068 (tmm) cc_final: 0.8739 (tmm) REVERT: A 929 MET cc_start: 0.8717 (mmm) cc_final: 0.8285 (mmm) REVERT: A 940 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7738 (mm-40) REVERT: A 1085 VAL cc_start: 0.9395 (m) cc_final: 0.9177 (p) REVERT: A 1205 TYR cc_start: 0.8009 (t80) cc_final: 0.7773 (t80) REVERT: A 1259 TYR cc_start: 0.8207 (m-80) cc_final: 0.7573 (m-80) REVERT: A 1613 PHE cc_start: 0.8666 (m-10) cc_final: 0.8170 (m-80) REVERT: A 1648 MET cc_start: 0.8711 (tpp) cc_final: 0.8464 (mmm) REVERT: A 1703 LEU cc_start: 0.9297 (mm) cc_final: 0.9096 (mp) REVERT: A 1832 LYS cc_start: 0.8893 (tttt) cc_final: 0.8609 (ttmm) REVERT: A 1837 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9262 (tp) REVERT: A 2044 ILE cc_start: 0.8865 (mm) cc_final: 0.8173 (mm) REVERT: A 2047 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7441 (mp0) REVERT: A 2350 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7304 (t80) REVERT: B 50 ARG cc_start: 0.8829 (mtt180) cc_final: 0.8462 (mtp180) REVERT: B 56 GLN cc_start: 0.8871 (mt0) cc_final: 0.8322 (tm-30) REVERT: B 63 GLU cc_start: 0.8208 (tt0) cc_final: 0.7680 (pt0) REVERT: B 93 ASN cc_start: 0.8390 (m110) cc_final: 0.7881 (t0) REVERT: B 125 GLU cc_start: 0.7229 (tt0) cc_final: 0.6441 (tt0) REVERT: B 221 GLN cc_start: 0.7949 (tp40) cc_final: 0.7422 (tt0) REVERT: B 322 LEU cc_start: 0.9570 (tp) cc_final: 0.9267 (tt) REVERT: B 418 TRP cc_start: 0.7897 (p-90) cc_final: 0.7199 (p-90) REVERT: B 462 MET cc_start: 0.9106 (tmm) cc_final: 0.8715 (tmm) REVERT: B 466 LEU cc_start: 0.9791 (OUTLIER) cc_final: 0.9582 (mm) REVERT: B 838 ASP cc_start: 0.8260 (m-30) cc_final: 0.7854 (t0) REVERT: B 929 MET cc_start: 0.8688 (mmm) cc_final: 0.7925 (mmm) REVERT: B 937 SER cc_start: 0.8467 (m) cc_final: 0.8248 (p) REVERT: B 940 GLN cc_start: 0.8309 (mm110) cc_final: 0.7891 (mm-40) REVERT: B 1108 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: B 1405 LEU cc_start: 0.8145 (mt) cc_final: 0.7855 (mp) REVERT: B 1438 GLU cc_start: 0.8299 (tt0) cc_final: 0.7879 (tt0) REVERT: B 1482 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: B 1492 ASP cc_start: 0.8458 (p0) cc_final: 0.8210 (p0) REVERT: B 1649 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7577 (ttm) REVERT: B 1705 SER cc_start: 0.8616 (p) cc_final: 0.8415 (t) REVERT: B 1717 MET cc_start: 0.8230 (ppp) cc_final: 0.7740 (ppp) REVERT: B 1752 MET cc_start: 0.8607 (tmm) cc_final: 0.8344 (tmm) REVERT: B 1918 ASP cc_start: 0.8221 (m-30) cc_final: 0.7825 (t0) REVERT: B 2270 MET cc_start: 0.5127 (mmp) cc_final: 0.3037 (ttt) REVERT: C 50 ARG cc_start: 0.8922 (mtt180) cc_final: 0.8446 (mtp180) REVERT: C 56 GLN cc_start: 0.8794 (mt0) cc_final: 0.8279 (tm-30) REVERT: C 63 GLU cc_start: 0.8240 (tt0) cc_final: 0.7507 (pt0) REVERT: C 93 ASN cc_start: 0.8453 (m110) cc_final: 0.8238 (t0) REVERT: C 124 ARG cc_start: 0.7723 (mmt180) cc_final: 0.7287 (mmt180) REVERT: C 125 GLU cc_start: 0.7337 (tt0) cc_final: 0.6834 (tt0) REVERT: C 137 HIS cc_start: 0.8030 (t70) cc_final: 0.7698 (t-90) REVERT: C 187 MET cc_start: 0.8953 (mmm) cc_final: 0.8716 (mmm) REVERT: C 221 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: C 289 PHE cc_start: 0.6837 (m-10) cc_final: 0.6555 (m-10) REVERT: C 386 GLN cc_start: 0.8943 (tt0) cc_final: 0.8684 (tt0) REVERT: C 462 MET cc_start: 0.9173 (tmm) cc_final: 0.8804 (tmm) REVERT: C 513 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9054 (tp) REVERT: C 860 GLU cc_start: 0.8638 (pp20) cc_final: 0.8270 (pp20) REVERT: C 918 ASP cc_start: 0.7938 (t0) cc_final: 0.6994 (p0) REVERT: C 927 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8503 (mmmt) REVERT: C 929 MET cc_start: 0.8872 (tpp) cc_final: 0.8585 (tmm) REVERT: C 930 ASP cc_start: 0.7651 (m-30) cc_final: 0.7136 (m-30) REVERT: C 937 SER cc_start: 0.8662 (m) cc_final: 0.8438 (p) REVERT: C 964 GLU cc_start: 0.7219 (pm20) cc_final: 0.6951 (pm20) REVERT: C 1085 VAL cc_start: 0.9319 (m) cc_final: 0.9111 (p) REVERT: C 1201 LEU cc_start: 0.8129 (pt) cc_final: 0.7866 (tt) REVERT: C 1396 GLU cc_start: 0.8629 (tp30) cc_final: 0.8416 (mm-30) REVERT: C 1438 GLU cc_start: 0.8224 (tt0) cc_final: 0.7825 (tt0) REVERT: C 1482 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: C 1507 MET cc_start: 0.8198 (mmm) cc_final: 0.7702 (mtt) REVERT: C 1539 PHE cc_start: 0.6494 (t80) cc_final: 0.5957 (t80) REVERT: C 1649 MET cc_start: 0.8357 (tpp) cc_final: 0.7916 (tpp) REVERT: C 1661 ASP cc_start: 0.7621 (p0) cc_final: 0.7403 (p0) REVERT: C 1705 SER cc_start: 0.8642 (p) cc_final: 0.8413 (t) REVERT: C 2178 GLU cc_start: 0.8522 (mp0) cc_final: 0.8244 (mp0) REVERT: C 2367 MET cc_start: 0.7947 (tmm) cc_final: 0.7649 (tmm) REVERT: D 50 ARG cc_start: 0.8754 (mtt180) cc_final: 0.8524 (mtp180) REVERT: D 56 GLN cc_start: 0.8722 (mt0) cc_final: 0.8190 (tm-30) REVERT: D 63 GLU cc_start: 0.8229 (tt0) cc_final: 0.7666 (pt0) REVERT: D 76 ASN cc_start: 0.6706 (t0) cc_final: 0.6424 (t0) REVERT: D 93 ASN cc_start: 0.8549 (m110) cc_final: 0.8106 (t0) REVERT: D 125 GLU cc_start: 0.7176 (tt0) cc_final: 0.6467 (tt0) REVERT: D 159 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8904 (pp) REVERT: D 221 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: D 473 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8328 (t) REVERT: D 474 ILE cc_start: 0.9069 (mm) cc_final: 0.8856 (mp) REVERT: D 513 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8968 (tp) REVERT: D 865 ILE cc_start: 0.9245 (mt) cc_final: 0.9022 (mm) REVERT: D 914 GLU cc_start: 0.8656 (pm20) cc_final: 0.8407 (pm20) REVERT: D 918 ASP cc_start: 0.7778 (t0) cc_final: 0.7156 (p0) REVERT: D 929 MET cc_start: 0.8929 (tpt) cc_final: 0.8698 (tpp) REVERT: D 937 SER cc_start: 0.8363 (m) cc_final: 0.8039 (p) REVERT: D 964 GLU cc_start: 0.7322 (pm20) cc_final: 0.7071 (pm20) REVERT: D 1063 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7544 (p90) REVERT: D 1190 HIS cc_start: 0.6298 (t70) cc_final: 0.6069 (t-90) REVERT: D 1438 GLU cc_start: 0.8194 (tt0) cc_final: 0.7848 (tt0) REVERT: D 1466 MET cc_start: 0.8858 (ttp) cc_final: 0.8537 (ptm) REVERT: D 1752 MET cc_start: 0.8740 (tmm) cc_final: 0.8477 (tmm) REVERT: D 2143 CYS cc_start: 0.9136 (m) cc_final: 0.8806 (t) REVERT: D 2188 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7546 (tm-30) REVERT: D 2189 ASP cc_start: 0.8709 (m-30) cc_final: 0.8483 (m-30) REVERT: D 2270 MET cc_start: 0.4642 (OUTLIER) cc_final: 0.2441 (ttt) REVERT: E 50 ARG cc_start: 0.8835 (mtt180) cc_final: 0.8540 (mtp180) REVERT: E 56 GLN cc_start: 0.8413 (mt0) cc_final: 0.7993 (tm-30) REVERT: E 63 GLU cc_start: 0.8196 (tt0) cc_final: 0.7897 (pt0) REVERT: E 93 ASN cc_start: 0.8369 (m110) cc_final: 0.7958 (t0) REVERT: E 112 MET cc_start: 0.8482 (mmm) cc_final: 0.8145 (mmm) REVERT: E 148 MET cc_start: 0.8435 (ttp) cc_final: 0.8185 (ttm) REVERT: E 171 LYS cc_start: 0.9091 (tptt) cc_final: 0.8870 (mtmm) REVERT: E 221 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: E 462 MET cc_start: 0.9007 (tmm) cc_final: 0.8759 (tmm) REVERT: E 465 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9492 (mm) REVERT: E 513 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8996 (tp) REVERT: E 910 VAL cc_start: 0.9176 (t) cc_final: 0.8897 (t) REVERT: E 929 MET cc_start: 0.8948 (mmm) cc_final: 0.8599 (mmm) REVERT: E 937 SER cc_start: 0.8355 (m) cc_final: 0.8050 (p) REVERT: E 940 GLN cc_start: 0.8102 (mm110) cc_final: 0.7599 (mm-40) REVERT: E 966 ILE cc_start: 0.9157 (mp) cc_final: 0.8858 (mm) REVERT: E 985 ASN cc_start: 0.7790 (t0) cc_final: 0.7188 (t0) REVERT: E 1132 MET cc_start: 0.7838 (mtm) cc_final: 0.7556 (ppp) REVERT: E 1259 TYR cc_start: 0.8606 (m-80) cc_final: 0.8349 (m-80) REVERT: E 1396 GLU cc_start: 0.8610 (tp30) cc_final: 0.8389 (mm-30) REVERT: E 1438 GLU cc_start: 0.8228 (tt0) cc_final: 0.7900 (mt-10) REVERT: E 1512 TYR cc_start: 0.7266 (m-80) cc_final: 0.6655 (m-80) REVERT: E 1649 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7748 (ttm) REVERT: E 1703 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8985 (mm) REVERT: E 1903 LEU cc_start: 0.8945 (tt) cc_final: 0.8730 (tp) REVERT: E 2188 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7833 (tm-30) REVERT: E 2270 MET cc_start: 0.4497 (mmp) cc_final: 0.2300 (ttt) REVERT: E 2321 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7356 (mm) REVERT: E 2373 LEU cc_start: 0.9165 (mt) cc_final: 0.8905 (tp) outliers start: 314 outliers final: 217 residues processed: 1434 average time/residue: 0.8136 time to fit residues: 2052.2181 Evaluate side-chains 1300 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1061 time to evaluate : 8.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1329 GLU Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1575 ASN Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1624 THR Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1772 VAL Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1821 GLN Chi-restraints excluded: chain A residue 1837 LEU Chi-restraints excluded: chain A residue 1912 ASN Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 ASP Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 2011 VAL Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2050 SER Chi-restraints excluded: chain A residue 2077 ASP Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2350 PHE Chi-restraints excluded: chain A residue 2369 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 521 TYR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 948 ASP Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1042 ILE Chi-restraints excluded: chain B residue 1063 HIS Chi-restraints excluded: chain B residue 1108 GLN Chi-restraints excluded: chain B residue 1215 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1305 VAL Chi-restraints excluded: chain B residue 1444 VAL Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1482 GLN Chi-restraints excluded: chain B residue 1527 THR Chi-restraints excluded: chain B residue 1566 ARG Chi-restraints excluded: chain B residue 1575 ASN Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1649 MET Chi-restraints excluded: chain B residue 1690 ARG Chi-restraints excluded: chain B residue 1706 VAL Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1745 ASP Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1772 VAL Chi-restraints excluded: chain B residue 1813 THR Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 ASP Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 2011 VAL Chi-restraints excluded: chain B residue 2050 SER Chi-restraints excluded: chain B residue 2077 ASP Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2180 LEU Chi-restraints excluded: chain B residue 2369 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 800 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 HIS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1215 VAL Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1329 GLU Chi-restraints excluded: chain C residue 1417 ASN Chi-restraints excluded: chain C residue 1455 THR Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1488 ASN Chi-restraints excluded: chain C residue 1575 ASN Chi-restraints excluded: chain C residue 1772 VAL Chi-restraints excluded: chain C residue 1813 THR Chi-restraints excluded: chain C residue 1821 GLN Chi-restraints excluded: chain C residue 1938 LEU Chi-restraints excluded: chain C residue 1953 THR Chi-restraints excluded: chain C residue 1976 ASP Chi-restraints excluded: chain C residue 1994 ILE Chi-restraints excluded: chain C residue 2009 GLU Chi-restraints excluded: chain C residue 2011 VAL Chi-restraints excluded: chain C residue 2077 ASP Chi-restraints excluded: chain C residue 2080 LEU Chi-restraints excluded: chain C residue 2181 MET Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 736 LYS Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain D residue 1030 ILE Chi-restraints excluded: chain D residue 1063 HIS Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1216 THR Chi-restraints excluded: chain D residue 1293 LEU Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain D residue 1417 ASN Chi-restraints excluded: chain D residue 1420 SER Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1564 LEU Chi-restraints excluded: chain D residue 1575 ASN Chi-restraints excluded: chain D residue 1622 ILE Chi-restraints excluded: chain D residue 1624 THR Chi-restraints excluded: chain D residue 1772 VAL Chi-restraints excluded: chain D residue 1878 LYS Chi-restraints excluded: chain D residue 1953 THR Chi-restraints excluded: chain D residue 1994 ILE Chi-restraints excluded: chain D residue 2050 SER Chi-restraints excluded: chain D residue 2077 ASP Chi-restraints excluded: chain D residue 2192 LEU Chi-restraints excluded: chain D residue 2270 MET Chi-restraints excluded: chain D residue 2321 LEU Chi-restraints excluded: chain D residue 2369 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 521 TYR Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 637 ILE Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 800 THR Chi-restraints excluded: chain E residue 837 ASP Chi-restraints excluded: chain E residue 960 VAL Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1042 ILE Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1188 ILE Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1216 THR Chi-restraints excluded: chain E residue 1305 VAL Chi-restraints excluded: chain E residue 1329 GLU Chi-restraints excluded: chain E residue 1420 SER Chi-restraints excluded: chain E residue 1455 THR Chi-restraints excluded: chain E residue 1475 LEU Chi-restraints excluded: chain E residue 1488 ASN Chi-restraints excluded: chain E residue 1564 LEU Chi-restraints excluded: chain E residue 1575 ASN Chi-restraints excluded: chain E residue 1622 ILE Chi-restraints excluded: chain E residue 1649 MET Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain E residue 1745 ASP Chi-restraints excluded: chain E residue 1758 LEU Chi-restraints excluded: chain E residue 1772 VAL Chi-restraints excluded: chain E residue 1813 THR Chi-restraints excluded: chain E residue 1953 THR Chi-restraints excluded: chain E residue 1955 LEU Chi-restraints excluded: chain E residue 1976 ASP Chi-restraints excluded: chain E residue 1994 ILE Chi-restraints excluded: chain E residue 1996 SER Chi-restraints excluded: chain E residue 2011 VAL Chi-restraints excluded: chain E residue 2043 LEU Chi-restraints excluded: chain E residue 2050 SER Chi-restraints excluded: chain E residue 2077 ASP Chi-restraints excluded: chain E residue 2080 LEU Chi-restraints excluded: chain E residue 2092 LEU Chi-restraints excluded: chain E residue 2137 ASP Chi-restraints excluded: chain E residue 2223 ASP Chi-restraints excluded: chain E residue 2321 LEU Chi-restraints excluded: chain E residue 2350 PHE Chi-restraints excluded: chain E residue 2369 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1180 random chunks: chunk 949 optimal weight: 0.9980 chunk 647 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 849 optimal weight: 8.9990 chunk 470 optimal weight: 2.9990 chunk 973 optimal weight: 3.9990 chunk 788 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 582 optimal weight: 3.9990 chunk 1023 optimal weight: 6.9990 chunk 287 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 GLN ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1525 HIS A1714 HIS ** A2103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 GLN B 940 GLN B1027 GLN B1190 HIS ** B1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1169 ASN C1190 HIS C1417 ASN ** C1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2103 GLN ** C2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 79 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1169 ASN D1417 ASN D1525 HIS ** D1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2183 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS E 215 GLN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 908 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 96545 Z= 0.221 Angle : 0.615 9.841 131045 Z= 0.318 Chirality : 0.041 0.243 14580 Planarity : 0.004 0.064 17000 Dihedral : 5.354 40.839 12850 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.30 % Favored : 94.69 % Rotamer: Outliers : 3.51 % Allowed : 14.35 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 1.71 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.08), residues: 11795 helix: 1.63 (0.07), residues: 5315 sheet: -1.07 (0.12), residues: 1785 loop : -1.57 (0.09), residues: 4695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 418 HIS 0.014 0.001 HIS E 79 PHE 0.030 0.001 PHE D 289 TYR 0.024 0.001 TYR C 123 ARG 0.007 0.000 ARG E1841 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1486 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1124 time to evaluate : 8.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8558 (mtp180) REVERT: A 56 GLN cc_start: 0.8944 (mt0) cc_final: 0.8565 (tm-30) REVERT: A 63 GLU cc_start: 0.8427 (tt0) cc_final: 0.7522 (pt0) REVERT: A 93 ASN cc_start: 0.8522 (m110) cc_final: 0.8012 (t0) REVERT: A 221 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: A 462 MET cc_start: 0.9110 (tmm) cc_final: 0.8763 (tmm) REVERT: A 513 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8823 (tp) REVERT: A 940 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7581 (mm-40) REVERT: A 1132 MET cc_start: 0.6346 (ppp) cc_final: 0.6095 (ppp) REVERT: A 1259 TYR cc_start: 0.8257 (m-80) cc_final: 0.7563 (m-80) REVERT: A 1482 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: A 1648 MET cc_start: 0.8683 (tpp) cc_final: 0.8452 (mmm) REVERT: A 1703 LEU cc_start: 0.9338 (mm) cc_final: 0.9049 (tt) REVERT: A 1717 MET cc_start: 0.8271 (ppp) cc_final: 0.7799 (ppp) REVERT: A 1749 GLU cc_start: 0.7784 (tp30) cc_final: 0.7554 (tp30) REVERT: A 1752 MET cc_start: 0.8563 (tmm) cc_final: 0.8319 (tmm) REVERT: A 1832 LYS cc_start: 0.8923 (tttt) cc_final: 0.8596 (ttmm) REVERT: A 1986 ASP cc_start: 0.8323 (t70) cc_final: 0.8006 (t70) REVERT: A 2044 ILE cc_start: 0.8954 (mm) cc_final: 0.8338 (mm) REVERT: A 2047 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7483 (mp0) REVERT: A 2188 GLU cc_start: 0.8233 (tp30) cc_final: 0.7852 (tm-30) REVERT: A 2350 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7227 (t80) REVERT: B 50 ARG cc_start: 0.8859 (mtt180) cc_final: 0.8504 (mtp180) REVERT: B 56 GLN cc_start: 0.8923 (mt0) cc_final: 0.8375 (tm-30) REVERT: B 63 GLU cc_start: 0.8167 (tt0) cc_final: 0.7692 (pt0) REVERT: B 93 ASN cc_start: 0.8423 (m110) cc_final: 0.7978 (t0) REVERT: B 125 GLU cc_start: 0.7166 (tt0) cc_final: 0.6903 (tt0) REVERT: B 155 MET cc_start: 0.9001 (tpp) cc_final: 0.8427 (tpp) REVERT: B 322 LEU cc_start: 0.9598 (tp) cc_final: 0.9312 (tt) REVERT: B 357 MET cc_start: 0.8578 (mmt) cc_final: 0.8369 (mmt) REVERT: B 418 TRP cc_start: 0.7939 (p-90) cc_final: 0.7217 (p-90) REVERT: B 462 MET cc_start: 0.9109 (tmm) cc_final: 0.8795 (tmm) REVERT: B 838 ASP cc_start: 0.8257 (m-30) cc_final: 0.7840 (t0) REVERT: B 929 MET cc_start: 0.8743 (mmm) cc_final: 0.8152 (mmm) REVERT: B 937 SER cc_start: 0.8494 (m) cc_final: 0.8273 (p) REVERT: B 940 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7861 (mm-40) REVERT: B 1405 LEU cc_start: 0.8172 (mt) cc_final: 0.7888 (mp) REVERT: B 1438 GLU cc_start: 0.8311 (tt0) cc_final: 0.8080 (tt0) REVERT: B 1482 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: B 1492 ASP cc_start: 0.8609 (p0) cc_final: 0.8345 (p0) REVERT: B 1507 MET cc_start: 0.8254 (mmm) cc_final: 0.8043 (mmm) REVERT: B 1649 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7552 (ttm) REVERT: B 1705 SER cc_start: 0.8649 (p) cc_final: 0.8429 (t) REVERT: B 1918 ASP cc_start: 0.8208 (m-30) cc_final: 0.7831 (t0) REVERT: B 2270 MET cc_start: 0.5012 (mmp) cc_final: 0.2928 (ttt) REVERT: B 2373 LEU cc_start: 0.9147 (mt) cc_final: 0.8812 (tp) REVERT: C 50 ARG cc_start: 0.8884 (mtt180) cc_final: 0.8479 (mtp180) REVERT: C 56 GLN cc_start: 0.8859 (mt0) cc_final: 0.8325 (tm-30) REVERT: C 63 GLU cc_start: 0.8400 (tt0) cc_final: 0.7062 (pt0) REVERT: C 92 TYR cc_start: 0.6312 (m-80) cc_final: 0.5541 (m-10) REVERT: C 93 ASN cc_start: 0.8494 (m110) cc_final: 0.8216 (t0) REVERT: C 187 MET cc_start: 0.8962 (mmm) cc_final: 0.8760 (mmm) REVERT: C 221 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: C 242 ASN cc_start: 0.7950 (p0) cc_final: 0.7667 (m-40) REVERT: C 386 GLN cc_start: 0.8958 (tt0) cc_final: 0.8711 (tt0) REVERT: C 462 MET cc_start: 0.9201 (tmm) cc_final: 0.8810 (tmm) REVERT: C 513 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9079 (tp) REVERT: C 638 TYR cc_start: 0.8825 (t80) cc_final: 0.8622 (t80) REVERT: C 860 GLU cc_start: 0.8690 (pp20) cc_final: 0.8255 (pp20) REVERT: C 918 ASP cc_start: 0.7934 (t0) cc_final: 0.6961 (p0) REVERT: C 937 SER cc_start: 0.8716 (m) cc_final: 0.8487 (p) REVERT: C 964 GLU cc_start: 0.7278 (pm20) cc_final: 0.7012 (pm20) REVERT: C 1201 LEU cc_start: 0.8165 (pt) cc_final: 0.7929 (tt) REVERT: C 1274 MET cc_start: 0.7849 (ptp) cc_final: 0.7468 (ptp) REVERT: C 1438 GLU cc_start: 0.8168 (tt0) cc_final: 0.7746 (tt0) REVERT: C 1482 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: C 1506 MET cc_start: 0.8376 (tpp) cc_final: 0.7994 (ttm) REVERT: C 1507 MET cc_start: 0.8277 (mmm) cc_final: 0.7672 (mtt) REVERT: C 1661 ASP cc_start: 0.7634 (p0) cc_final: 0.7387 (p0) REVERT: C 1705 SER cc_start: 0.8612 (p) cc_final: 0.8397 (t) REVERT: C 2178 GLU cc_start: 0.8535 (mp0) cc_final: 0.8285 (mp0) REVERT: C 2373 LEU cc_start: 0.9211 (mt) cc_final: 0.8967 (tp) REVERT: D 50 ARG cc_start: 0.8773 (mtt180) cc_final: 0.8545 (mtp180) REVERT: D 56 GLN cc_start: 0.8738 (mt0) cc_final: 0.8191 (tm-30) REVERT: D 63 GLU cc_start: 0.8322 (tt0) cc_final: 0.7602 (pt0) REVERT: D 76 ASN cc_start: 0.6556 (t0) cc_final: 0.6306 (t0) REVERT: D 93 ASN cc_start: 0.8533 (m110) cc_final: 0.8102 (t0) REVERT: D 125 GLU cc_start: 0.7215 (tt0) cc_final: 0.6506 (tt0) REVERT: D 159 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8922 (pp) REVERT: D 221 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: D 473 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8280 (t) REVERT: D 474 ILE cc_start: 0.9050 (mm) cc_final: 0.8850 (mp) REVERT: D 513 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8992 (tp) REVERT: D 518 TRP cc_start: 0.7165 (m-10) cc_final: 0.6839 (m-10) REVERT: D 914 GLU cc_start: 0.8665 (pm20) cc_final: 0.8390 (pm20) REVERT: D 918 ASP cc_start: 0.7782 (t0) cc_final: 0.7081 (p0) REVERT: D 937 SER cc_start: 0.8497 (m) cc_final: 0.8188 (p) REVERT: D 1063 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7496 (p90) REVERT: D 1438 GLU cc_start: 0.8209 (tt0) cc_final: 0.7851 (tt0) REVERT: D 1648 MET cc_start: 0.8672 (tpp) cc_final: 0.8346 (tpp) REVERT: D 1717 MET cc_start: 0.8400 (ppp) cc_final: 0.8002 (ppp) REVERT: D 2143 CYS cc_start: 0.9205 (m) cc_final: 0.8941 (t) REVERT: D 2188 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7652 (tm-30) REVERT: D 2270 MET cc_start: 0.4776 (OUTLIER) cc_final: 0.2895 (ttt) REVERT: E 50 ARG cc_start: 0.8856 (mtt180) cc_final: 0.8550 (mtp180) REVERT: E 56 GLN cc_start: 0.8452 (mt0) cc_final: 0.8019 (tm-30) REVERT: E 63 GLU cc_start: 0.8205 (tt0) cc_final: 0.7872 (pt0) REVERT: E 93 ASN cc_start: 0.8335 (m110) cc_final: 0.7956 (t0) REVERT: E 112 MET cc_start: 0.8401 (mmm) cc_final: 0.7592 (mtp) REVERT: E 148 MET cc_start: 0.8417 (ttp) cc_final: 0.8132 (ttm) REVERT: E 221 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: E 462 MET cc_start: 0.9013 (tmm) cc_final: 0.8781 (tmm) REVERT: E 513 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9056 (tp) REVERT: E 910 VAL cc_start: 0.9197 (t) cc_final: 0.8948 (t) REVERT: E 929 MET cc_start: 0.8936 (mmm) cc_final: 0.8580 (mmm) REVERT: E 937 SER cc_start: 0.8438 (m) cc_final: 0.8143 (p) REVERT: E 940 GLN cc_start: 0.8099 (mm110) cc_final: 0.7582 (mm-40) REVERT: E 1146 MET cc_start: 0.7056 (mtt) cc_final: 0.6493 (ptt) REVERT: E 1259 TYR cc_start: 0.8551 (m-80) cc_final: 0.8326 (m-80) REVERT: E 1438 GLU cc_start: 0.8194 (tt0) cc_final: 0.7844 (mt-10) REVERT: E 1512 TYR cc_start: 0.7461 (m-80) cc_final: 0.7049 (m-80) REVERT: E 1703 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8946 (mm) REVERT: E 2188 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7588 (tm-30) REVERT: E 2270 MET cc_start: 0.4362 (mmp) cc_final: 0.2247 (ttt) REVERT: E 2321 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7326 (mm) REVERT: E 2373 LEU cc_start: 0.9184 (mt) cc_final: 0.8906 (tp) outliers start: 362 outliers final: 261 residues processed: 1393 average time/residue: 0.8066 time to fit residues: 1985.3535 Evaluate side-chains 1324 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1044 time to evaluate : 8.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1329 GLU Chi-restraints excluded: chain A residue 1396 GLU Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1482 GLN Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1525 HIS Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1575 ASN Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1624 THR Chi-restraints excluded: chain A residue 1649 MET Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1772 VAL Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1912 ASN Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 ASP Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2050 SER Chi-restraints excluded: chain A residue 2077 ASP Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2350 PHE Chi-restraints excluded: chain A residue 2369 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 521 TYR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 715 ASN Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 948 ASP Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1063 HIS Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1215 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1305 VAL Chi-restraints excluded: chain B residue 1329 GLU Chi-restraints excluded: chain B residue 1444 VAL Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1482 GLN Chi-restraints excluded: chain B residue 1525 HIS Chi-restraints excluded: chain B residue 1527 THR Chi-restraints excluded: chain B residue 1566 ARG Chi-restraints excluded: chain B residue 1575 ASN Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1649 MET Chi-restraints excluded: chain B residue 1682 ILE Chi-restraints excluded: chain B residue 1690 ARG Chi-restraints excluded: chain B residue 1693 LEU Chi-restraints excluded: chain B residue 1706 VAL Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1772 VAL Chi-restraints excluded: chain B residue 1813 THR Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1976 ASP Chi-restraints excluded: chain B residue 2011 VAL Chi-restraints excluded: chain B residue 2050 SER Chi-restraints excluded: chain B residue 2077 ASP Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2144 LEU Chi-restraints excluded: chain B residue 2180 LEU Chi-restraints excluded: chain B residue 2262 LEU Chi-restraints excluded: chain B residue 2369 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 521 TYR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 800 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 HIS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1189 ASN Chi-restraints excluded: chain C residue 1215 VAL Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1305 VAL Chi-restraints excluded: chain C residue 1329 GLU Chi-restraints excluded: chain C residue 1417 ASN Chi-restraints excluded: chain C residue 1420 SER Chi-restraints excluded: chain C residue 1455 THR Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1488 ASN Chi-restraints excluded: chain C residue 1575 ASN Chi-restraints excluded: chain C residue 1624 THR Chi-restraints excluded: chain C residue 1682 ILE Chi-restraints excluded: chain C residue 1758 LEU Chi-restraints excluded: chain C residue 1772 VAL Chi-restraints excluded: chain C residue 1813 THR Chi-restraints excluded: chain C residue 1938 LEU Chi-restraints excluded: chain C residue 1953 THR Chi-restraints excluded: chain C residue 1976 ASP Chi-restraints excluded: chain C residue 1994 ILE Chi-restraints excluded: chain C residue 2009 GLU Chi-restraints excluded: chain C residue 2011 VAL Chi-restraints excluded: chain C residue 2050 SER Chi-restraints excluded: chain C residue 2077 ASP Chi-restraints excluded: chain C residue 2080 LEU Chi-restraints excluded: chain C residue 2092 LEU Chi-restraints excluded: chain C residue 2181 MET Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 736 LYS Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain D residue 1030 ILE Chi-restraints excluded: chain D residue 1063 HIS Chi-restraints excluded: chain D residue 1079 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1216 THR Chi-restraints excluded: chain D residue 1293 LEU Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain D residue 1329 GLU Chi-restraints excluded: chain D residue 1417 ASN Chi-restraints excluded: chain D residue 1420 SER Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1488 ASN Chi-restraints excluded: chain D residue 1525 HIS Chi-restraints excluded: chain D residue 1564 LEU Chi-restraints excluded: chain D residue 1575 ASN Chi-restraints excluded: chain D residue 1622 ILE Chi-restraints excluded: chain D residue 1624 THR Chi-restraints excluded: chain D residue 1745 ASP Chi-restraints excluded: chain D residue 1772 VAL Chi-restraints excluded: chain D residue 1813 THR Chi-restraints excluded: chain D residue 1878 LYS Chi-restraints excluded: chain D residue 1953 THR Chi-restraints excluded: chain D residue 1994 ILE Chi-restraints excluded: chain D residue 2011 VAL Chi-restraints excluded: chain D residue 2043 LEU Chi-restraints excluded: chain D residue 2050 SER Chi-restraints excluded: chain D residue 2077 ASP Chi-restraints excluded: chain D residue 2187 MET Chi-restraints excluded: chain D residue 2192 LEU Chi-restraints excluded: chain D residue 2270 MET Chi-restraints excluded: chain D residue 2321 LEU Chi-restraints excluded: chain D residue 2369 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 521 TYR Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 637 ILE Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 837 ASP Chi-restraints excluded: chain E residue 843 LEU Chi-restraints excluded: chain E residue 849 VAL Chi-restraints excluded: chain E residue 945 THR Chi-restraints excluded: chain E residue 960 VAL Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1188 ILE Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1216 THR Chi-restraints excluded: chain E residue 1300 SER Chi-restraints excluded: chain E residue 1305 VAL Chi-restraints excluded: chain E residue 1329 GLU Chi-restraints excluded: chain E residue 1420 SER Chi-restraints excluded: chain E residue 1455 THR Chi-restraints excluded: chain E residue 1475 LEU Chi-restraints excluded: chain E residue 1488 ASN Chi-restraints excluded: chain E residue 1564 LEU Chi-restraints excluded: chain E residue 1622 ILE Chi-restraints excluded: chain E residue 1682 ILE Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain E residue 1745 ASP Chi-restraints excluded: chain E residue 1758 LEU Chi-restraints excluded: chain E residue 1772 VAL Chi-restraints excluded: chain E residue 1813 THR Chi-restraints excluded: chain E residue 1833 LEU Chi-restraints excluded: chain E residue 1953 THR Chi-restraints excluded: chain E residue 1955 LEU Chi-restraints excluded: chain E residue 1994 ILE Chi-restraints excluded: chain E residue 1996 SER Chi-restraints excluded: chain E residue 2011 VAL Chi-restraints excluded: chain E residue 2050 SER Chi-restraints excluded: chain E residue 2077 ASP Chi-restraints excluded: chain E residue 2092 LEU Chi-restraints excluded: chain E residue 2180 LEU Chi-restraints excluded: chain E residue 2223 ASP Chi-restraints excluded: chain E residue 2321 LEU Chi-restraints excluded: chain E residue 2350 PHE Chi-restraints excluded: chain E residue 2369 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1180 random chunks: chunk 383 optimal weight: 3.9990 chunk 1027 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 669 optimal weight: 7.9990 chunk 281 optimal weight: 1.9990 chunk 1141 optimal weight: 2.9990 chunk 947 optimal weight: 10.0000 chunk 528 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 377 optimal weight: 8.9990 chunk 599 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN A 633 GLN A 897 ASN A 925 GLN ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN A1169 ASN A1528 ASN A1635 ASN A1658 GLN ** A1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN B 79 HIS B 241 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN B 897 ASN B 962 ASN B1046 GLN ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN ** B1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1528 ASN ** B1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 213 GLN C 215 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 GLN C 897 ASN ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 ASN C1148 ASN C1190 HIS ** C1417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1528 ASN ** C1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2361 GLN D 26 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN D 296 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN D 444 ASN D 551 GLN ** D1417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1467 GLN D1528 ASN ** D1714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 ASN E 551 GLN E 897 ASN E 962 ASN ** E1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1169 ASN ** E1296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1528 ASN E1635 ASN ** E1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2361 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 96545 Z= 0.440 Angle : 0.782 10.758 131045 Z= 0.408 Chirality : 0.045 0.260 14580 Planarity : 0.005 0.062 17000 Dihedral : 5.982 42.040 12850 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.40 % Rotamer: Outliers : 4.23 % Allowed : 14.69 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 1.95 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.08), residues: 11795 helix: 1.16 (0.07), residues: 5310 sheet: -1.18 (0.13), residues: 1660 loop : -1.72 (0.09), residues: 4825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 418 HIS 0.028 0.002 HIS D 79 PHE 0.028 0.003 PHE B1724 TYR 0.026 0.002 TYR A1583 ARG 0.011 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1461 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 1025 time to evaluate : 8.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8568 (mtp180) REVERT: A 56 GLN cc_start: 0.9042 (mt0) cc_final: 0.8415 (tm-30) REVERT: A 93 ASN cc_start: 0.8436 (m110) cc_final: 0.8067 (t0) REVERT: A 112 MET cc_start: 0.8778 (mmm) cc_final: 0.8116 (mmm) REVERT: A 462 MET cc_start: 0.9192 (tmm) cc_final: 0.8947 (tmm) REVERT: A 513 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8987 (tp) REVERT: A 860 GLU cc_start: 0.8863 (pp20) cc_final: 0.8499 (pp20) REVERT: A 940 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7903 (mm-40) REVERT: A 1482 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: A 1648 MET cc_start: 0.8787 (tpp) cc_final: 0.8504 (mmm) REVERT: A 1686 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.7445 (t70) REVERT: A 1747 LEU cc_start: 0.9272 (mt) cc_final: 0.9070 (mt) REVERT: A 1832 LYS cc_start: 0.8940 (tttt) cc_final: 0.8604 (ttmm) REVERT: A 1986 ASP cc_start: 0.8365 (t70) cc_final: 0.8039 (t70) REVERT: A 2047 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7620 (mp0) REVERT: A 2144 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9264 (mm) REVERT: A 2350 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.6915 (t80) REVERT: B 50 ARG cc_start: 0.8887 (mtt180) cc_final: 0.8517 (mtp180) REVERT: B 56 GLN cc_start: 0.9076 (mt0) cc_final: 0.8561 (tm-30) REVERT: B 63 GLU cc_start: 0.8271 (tt0) cc_final: 0.7232 (pt0) REVERT: B 93 ASN cc_start: 0.8496 (m110) cc_final: 0.7898 (t0) REVERT: B 638 TYR cc_start: 0.8560 (t80) cc_final: 0.8337 (t80) REVERT: B 918 ASP cc_start: 0.7827 (t0) cc_final: 0.7190 (p0) REVERT: B 937 SER cc_start: 0.8691 (m) cc_final: 0.8489 (p) REVERT: B 940 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7936 (mm-40) REVERT: B 1042 ILE cc_start: 0.9687 (OUTLIER) cc_final: 0.9319 (pt) REVERT: B 1405 LEU cc_start: 0.8164 (mt) cc_final: 0.7891 (mp) REVERT: B 1438 GLU cc_start: 0.8461 (tt0) cc_final: 0.8252 (tt0) REVERT: B 1482 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: B 1492 ASP cc_start: 0.8785 (p0) cc_final: 0.8552 (p0) REVERT: B 1649 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7912 (ttm) REVERT: B 1717 MET cc_start: 0.8513 (ppp) cc_final: 0.8038 (ppp) REVERT: B 2270 MET cc_start: 0.5439 (mmp) cc_final: 0.3439 (ttt) REVERT: C 50 ARG cc_start: 0.8875 (mtt180) cc_final: 0.8509 (mtp180) REVERT: C 56 GLN cc_start: 0.8998 (mt0) cc_final: 0.8355 (tm-30) REVERT: C 92 TYR cc_start: 0.6742 (m-80) cc_final: 0.6135 (m-80) REVERT: C 93 ASN cc_start: 0.8283 (m110) cc_final: 0.7896 (t0) REVERT: C 462 MET cc_start: 0.9241 (tmm) cc_final: 0.8916 (tmm) REVERT: C 513 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9229 (tp) REVERT: C 918 ASP cc_start: 0.7966 (t0) cc_final: 0.7171 (p0) REVERT: C 937 SER cc_start: 0.8824 (m) cc_final: 0.8562 (p) REVERT: C 940 GLN cc_start: 0.8317 (mm110) cc_final: 0.7897 (mm-40) REVERT: C 1116 MET cc_start: 0.8535 (ttt) cc_final: 0.8029 (ttt) REVERT: C 1201 LEU cc_start: 0.8185 (pt) cc_final: 0.7945 (tt) REVERT: C 1438 GLU cc_start: 0.8213 (tt0) cc_final: 0.7898 (tt0) REVERT: C 1507 MET cc_start: 0.8361 (mmm) cc_final: 0.7773 (mtt) REVERT: C 1525 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7612 (t-90) REVERT: C 1686 HIS cc_start: 0.8954 (OUTLIER) cc_final: 0.7800 (t70) REVERT: C 1705 SER cc_start: 0.8737 (p) cc_final: 0.8488 (t) REVERT: C 2367 MET cc_start: 0.8040 (tmm) cc_final: 0.7835 (tmm) REVERT: D 50 ARG cc_start: 0.8790 (mtt180) cc_final: 0.8566 (mtp180) REVERT: D 56 GLN cc_start: 0.8880 (mt0) cc_final: 0.8277 (tm-30) REVERT: D 63 GLU cc_start: 0.8470 (tt0) cc_final: 0.7444 (pt0) REVERT: D 93 ASN cc_start: 0.8590 (m110) cc_final: 0.8101 (t0) REVERT: D 159 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8951 (pp) REVERT: D 221 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: D 473 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.7631 (t) REVERT: D 513 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9113 (tp) REVERT: D 531 TYR cc_start: 0.3571 (m-10) cc_final: 0.2938 (m-80) REVERT: D 760 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8400 (t0) REVERT: D 918 ASP cc_start: 0.7740 (t0) cc_final: 0.7010 (p0) REVERT: D 928 MET cc_start: 0.8374 (mtm) cc_final: 0.7959 (mtm) REVERT: D 937 SER cc_start: 0.8817 (m) cc_final: 0.8488 (p) REVERT: D 1063 HIS cc_start: 0.8616 (OUTLIER) cc_final: 0.7785 (p90) REVERT: D 1438 GLU cc_start: 0.8263 (tt0) cc_final: 0.7960 (tt0) REVERT: D 1648 MET cc_start: 0.8754 (tpp) cc_final: 0.8448 (tpp) REVERT: D 1986 ASP cc_start: 0.8495 (t0) cc_final: 0.8198 (t70) REVERT: D 2270 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.3585 (ttt) REVERT: E 50 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8551 (mtp180) REVERT: E 63 GLU cc_start: 0.8283 (tt0) cc_final: 0.7847 (pt0) REVERT: E 69 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7367 (ttt-90) REVERT: E 93 ASN cc_start: 0.8465 (m110) cc_final: 0.7991 (t0) REVERT: E 112 MET cc_start: 0.8573 (mmm) cc_final: 0.8132 (mtm) REVERT: E 148 MET cc_start: 0.8570 (ttp) cc_final: 0.8247 (ttm) REVERT: E 462 MET cc_start: 0.9084 (tmm) cc_final: 0.8817 (tmm) REVERT: E 513 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9290 (tp) REVERT: E 940 GLN cc_start: 0.7973 (mm110) cc_final: 0.7677 (mm-40) REVERT: E 1146 MET cc_start: 0.7145 (mtt) cc_final: 0.6682 (ttp) REVERT: E 1703 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8873 (mm) REVERT: E 1717 MET cc_start: 0.8509 (ppp) cc_final: 0.7793 (ppp) REVERT: E 2321 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7667 (mm) REVERT: E 2367 MET cc_start: 0.8127 (tmm) cc_final: 0.7915 (tmm) REVERT: E 2376 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8372 (mtp180) outliers start: 436 outliers final: 310 residues processed: 1365 average time/residue: 0.8033 time to fit residues: 1941.3254 Evaluate side-chains 1257 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 924 time to evaluate : 8.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1329 GLU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1396 GLU Chi-restraints excluded: chain A residue 1417 ASN Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1482 GLN Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1624 THR Chi-restraints excluded: chain A residue 1682 ILE Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1772 VAL Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1912 ASN Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1976 ASP Chi-restraints excluded: chain A residue 2011 VAL Chi-restraints excluded: chain A residue 2037 ILE Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2050 SER Chi-restraints excluded: chain A residue 2077 ASP Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2350 PHE Chi-restraints excluded: chain A residue 2369 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 521 TYR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 715 ASN Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain B residue 944 ASP Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 948 ASP Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain B residue 1042 ILE Chi-restraints excluded: chain B residue 1063 HIS Chi-restraints excluded: chain B residue 1146 MET Chi-restraints excluded: chain B residue 1215 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1329 GLU Chi-restraints excluded: chain B residue 1444 VAL Chi-restraints excluded: chain B residue 1455 THR Chi-restraints excluded: chain B residue 1482 GLN Chi-restraints excluded: chain B residue 1488 ASN Chi-restraints excluded: chain B residue 1525 HIS Chi-restraints excluded: chain B residue 1527 THR Chi-restraints excluded: chain B residue 1566 ARG Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1649 MET Chi-restraints excluded: chain B residue 1667 LEU Chi-restraints excluded: chain B residue 1682 ILE Chi-restraints excluded: chain B residue 1690 ARG Chi-restraints excluded: chain B residue 1693 LEU Chi-restraints excluded: chain B residue 1706 VAL Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1772 VAL Chi-restraints excluded: chain B residue 1840 LEU Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 1953 THR Chi-restraints excluded: chain B residue 1955 LEU Chi-restraints excluded: chain B residue 1976 ASP Chi-restraints excluded: chain B residue 1994 ILE Chi-restraints excluded: chain B residue 2011 VAL Chi-restraints excluded: chain B residue 2037 ILE Chi-restraints excluded: chain B residue 2050 SER Chi-restraints excluded: chain B residue 2077 ASP Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2180 LEU Chi-restraints excluded: chain B residue 2187 MET Chi-restraints excluded: chain B residue 2262 LEU Chi-restraints excluded: chain B residue 2369 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 521 TYR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 715 ASN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 838 ASP Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 944 ASP Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 HIS Chi-restraints excluded: chain C residue 1071 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1189 ASN Chi-restraints excluded: chain C residue 1215 VAL Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1329 GLU Chi-restraints excluded: chain C residue 1417 ASN Chi-restraints excluded: chain C residue 1420 SER Chi-restraints excluded: chain C residue 1488 ASN Chi-restraints excluded: chain C residue 1525 HIS Chi-restraints excluded: chain C residue 1622 ILE Chi-restraints excluded: chain C residue 1624 THR Chi-restraints excluded: chain C residue 1682 ILE Chi-restraints excluded: chain C residue 1686 HIS Chi-restraints excluded: chain C residue 1758 LEU Chi-restraints excluded: chain C residue 1772 VAL Chi-restraints excluded: chain C residue 1833 LEU Chi-restraints excluded: chain C residue 1938 LEU Chi-restraints excluded: chain C residue 1953 THR Chi-restraints excluded: chain C residue 1955 LEU Chi-restraints excluded: chain C residue 1976 ASP Chi-restraints excluded: chain C residue 1994 ILE Chi-restraints excluded: chain C residue 1995 THR Chi-restraints excluded: chain C residue 2009 GLU Chi-restraints excluded: chain C residue 2011 VAL Chi-restraints excluded: chain C residue 2037 ILE Chi-restraints excluded: chain C residue 2050 SER Chi-restraints excluded: chain C residue 2077 ASP Chi-restraints excluded: chain C residue 2080 LEU Chi-restraints excluded: chain C residue 2092 LEU Chi-restraints excluded: chain C residue 2181 MET Chi-restraints excluded: chain C residue 2262 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 715 ASN Chi-restraints excluded: chain D residue 760 ASN Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain D residue 1030 ILE Chi-restraints excluded: chain D residue 1063 HIS Chi-restraints excluded: chain D residue 1079 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1216 THR Chi-restraints excluded: chain D residue 1293 LEU Chi-restraints excluded: chain D residue 1329 GLU Chi-restraints excluded: chain D residue 1417 ASN Chi-restraints excluded: chain D residue 1420 SER Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1488 ASN Chi-restraints excluded: chain D residue 1564 LEU Chi-restraints excluded: chain D residue 1622 ILE Chi-restraints excluded: chain D residue 1624 THR Chi-restraints excluded: chain D residue 1682 ILE Chi-restraints excluded: chain D residue 1686 HIS Chi-restraints excluded: chain D residue 1772 VAL Chi-restraints excluded: chain D residue 1878 LYS Chi-restraints excluded: chain D residue 1938 LEU Chi-restraints excluded: chain D residue 1953 THR Chi-restraints excluded: chain D residue 1954 VAL Chi-restraints excluded: chain D residue 1955 LEU Chi-restraints excluded: chain D residue 1976 ASP Chi-restraints excluded: chain D residue 1994 ILE Chi-restraints excluded: chain D residue 2011 VAL Chi-restraints excluded: chain D residue 2037 ILE Chi-restraints excluded: chain D residue 2050 SER Chi-restraints excluded: chain D residue 2077 ASP Chi-restraints excluded: chain D residue 2187 MET Chi-restraints excluded: chain D residue 2192 LEU Chi-restraints excluded: chain D residue 2270 MET Chi-restraints excluded: chain D residue 2321 LEU Chi-restraints excluded: chain D residue 2369 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 487 ASP Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 521 TYR Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 637 ILE Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 715 ASN Chi-restraints excluded: chain E residue 810 LEU Chi-restraints excluded: chain E residue 837 ASP Chi-restraints excluded: chain E residue 838 ASP Chi-restraints excluded: chain E residue 843 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 849 VAL Chi-restraints excluded: chain E residue 907 SER Chi-restraints excluded: chain E residue 945 THR Chi-restraints excluded: chain E residue 960 VAL Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1188 ILE Chi-restraints excluded: chain E residue 1208 ASN Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1216 THR Chi-restraints excluded: chain E residue 1300 SER Chi-restraints excluded: chain E residue 1329 GLU Chi-restraints excluded: chain E residue 1420 SER Chi-restraints excluded: chain E residue 1455 THR Chi-restraints excluded: chain E residue 1475 LEU Chi-restraints excluded: chain E residue 1488 ASN Chi-restraints excluded: chain E residue 1560 VAL Chi-restraints excluded: chain E residue 1564 LEU Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1622 ILE Chi-restraints excluded: chain E residue 1646 THR Chi-restraints excluded: chain E residue 1682 ILE Chi-restraints excluded: chain E residue 1686 HIS Chi-restraints excluded: chain E residue 1703 LEU Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain E residue 1745 ASP Chi-restraints excluded: chain E residue 1758 LEU Chi-restraints excluded: chain E residue 1772 VAL Chi-restraints excluded: chain E residue 1813 THR Chi-restraints excluded: chain E residue 1833 LEU Chi-restraints excluded: chain E residue 1953 THR Chi-restraints excluded: chain E residue 1955 LEU Chi-restraints excluded: chain E residue 1989 ILE Chi-restraints excluded: chain E residue 1994 ILE Chi-restraints excluded: chain E residue 1995 THR Chi-restraints excluded: chain E residue 1996 SER Chi-restraints excluded: chain E residue 2011 VAL Chi-restraints excluded: chain E residue 2037 ILE Chi-restraints excluded: chain E residue 2043 LEU Chi-restraints excluded: chain E residue 2050 SER Chi-restraints excluded: chain E residue 2077 ASP Chi-restraints excluded: chain E residue 2092 LEU Chi-restraints excluded: chain E residue 2144 LEU Chi-restraints excluded: chain E residue 2180 LEU Chi-restraints excluded: chain E residue 2189 ASP Chi-restraints excluded: chain E residue 2223 ASP Chi-restraints excluded: chain E residue 2321 LEU Chi-restraints excluded: chain E residue 2350 PHE Chi-restraints excluded: chain E residue 2369 THR Chi-restraints excluded: chain E residue 2376 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1180 random chunks: chunk 1100 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 650 optimal weight: 0.2980 chunk 833 optimal weight: 5.9990 chunk 645 optimal weight: 0.9980 chunk 961 optimal weight: 5.9990 chunk 637 optimal weight: 0.7980 chunk 1137 optimal weight: 1.9990 chunk 711 optimal weight: 2.9990 chunk 693 optimal weight: 8.9990 chunk 525 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN A 925 GLN ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN A1203 GLN ** A1652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1763 ASN ** A2155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 215 GLN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 ASN ** B 925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 ASN ** B 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 GLN B1052 GLN ** B1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1157 ASN B1203 GLN ** B1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1296 HIS ** B1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1714 HIS ** B1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2155 ASN ** B2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 ASN ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1027 GLN C1052 GLN C1190 HIS C1203 GLN C1714 HIS C1763 ASN ** C1843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2155 ASN ** C2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 ASN D 925 GLN D1046 GLN D1203 GLN D1714 HIS ** D1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 581 HIS E 730 ASN E 925 GLN E 962 ASN E1046 GLN E1052 GLN E1203 GLN E1714 HIS E2155 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 96545 Z= 0.173 Angle : 0.629 14.018 131045 Z= 0.321 Chirality : 0.042 0.265 14580 Planarity : 0.004 0.058 17000 Dihedral : 5.371 38.145 12850 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.90 % Allowed : 16.50 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 1.22 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.08), residues: 11795 helix: 1.68 (0.07), residues: 5315 sheet: -1.07 (0.12), residues: 1745 loop : -1.55 (0.09), residues: 4735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 418 HIS 0.013 0.001 HIS D 79 PHE 0.035 0.001 PHE C 113 TYR 0.027 0.001 TYR D 118 ARG 0.007 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1136 time to evaluate : 8.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8929 (mtt180) cc_final: 0.8544 (mtp180) REVERT: A 56 GLN cc_start: 0.8977 (mt0) cc_final: 0.8500 (tm-30) REVERT: A 69 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6609 (ttp80) REVERT: A 93 ASN cc_start: 0.8354 (m110) cc_final: 0.7968 (t0) REVERT: A 221 GLN cc_start: 0.7604 (tp-100) cc_final: 0.7202 (tm-30) REVERT: A 294 LEU cc_start: 0.8180 (tt) cc_final: 0.7723 (mt) REVERT: A 462 MET cc_start: 0.9089 (tmm) cc_final: 0.8732 (tmm) REVERT: A 638 TYR cc_start: 0.8635 (t80) cc_final: 0.8431 (t80) REVERT: A 860 GLU cc_start: 0.8662 (pp20) cc_final: 0.8380 (pp20) REVERT: A 1146 MET cc_start: 0.6147 (mtp) cc_final: 0.5592 (mtp) REVERT: A 1482 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: A 1622 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7060 (mt) REVERT: A 1703 LEU cc_start: 0.9389 (mm) cc_final: 0.9089 (tt) REVERT: A 1717 MET cc_start: 0.8255 (ppp) cc_final: 0.7699 (ppp) REVERT: A 1832 LYS cc_start: 0.8913 (tttt) cc_final: 0.8600 (ttmm) REVERT: A 1918 ASP cc_start: 0.8158 (m-30) cc_final: 0.7484 (t0) REVERT: A 1986 ASP cc_start: 0.8316 (t70) cc_final: 0.7979 (t70) REVERT: A 2073 MET cc_start: 0.8581 (ttt) cc_final: 0.8320 (ttm) REVERT: A 2083 LEU cc_start: 0.9397 (tp) cc_final: 0.8979 (tt) REVERT: A 2144 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9159 (mm) REVERT: A 2350 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 2367 MET cc_start: 0.7948 (tmm) cc_final: 0.7694 (tmm) REVERT: B 50 ARG cc_start: 0.8858 (mtt180) cc_final: 0.8487 (mtp180) REVERT: B 56 GLN cc_start: 0.9022 (mt0) cc_final: 0.8527 (tm-30) REVERT: B 63 GLU cc_start: 0.8226 (tt0) cc_final: 0.7626 (pt0) REVERT: B 93 ASN cc_start: 0.8519 (m110) cc_final: 0.7914 (t0) REVERT: B 386 GLN cc_start: 0.8540 (tt0) cc_final: 0.8314 (tt0) REVERT: B 838 ASP cc_start: 0.8063 (m-30) cc_final: 0.7708 (t0) REVERT: B 918 ASP cc_start: 0.7756 (t0) cc_final: 0.6996 (p0) REVERT: B 940 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7915 (mm-40) REVERT: B 1482 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8279 (tm-30) REVERT: B 1492 ASP cc_start: 0.8625 (p0) cc_final: 0.8353 (p0) REVERT: B 1826 MET cc_start: 0.8468 (tpp) cc_final: 0.8235 (tpp) REVERT: B 1830 TRP cc_start: 0.8208 (OUTLIER) cc_final: 0.7492 (m-90) REVERT: B 1918 ASP cc_start: 0.8060 (m-30) cc_final: 0.7481 (t0) REVERT: B 2250 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6886 (t) REVERT: B 2270 MET cc_start: 0.4894 (mmp) cc_final: 0.3256 (ttt) REVERT: B 2367 MET cc_start: 0.7846 (tmm) cc_final: 0.7591 (tmm) REVERT: C 50 ARG cc_start: 0.8834 (mtt180) cc_final: 0.8471 (mtp180) REVERT: C 56 GLN cc_start: 0.8711 (mt0) cc_final: 0.8192 (tm-30) REVERT: C 63 GLU cc_start: 0.8387 (tt0) cc_final: 0.7286 (pt0) REVERT: C 93 ASN cc_start: 0.8310 (m110) cc_final: 0.7909 (t0) REVERT: C 112 MET cc_start: 0.8896 (mmp) cc_final: 0.8664 (mmp) REVERT: C 221 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: C 242 ASN cc_start: 0.7920 (p0) cc_final: 0.7625 (m-40) REVERT: C 382 ASN cc_start: 0.7565 (t0) cc_final: 0.7192 (p0) REVERT: C 462 MET cc_start: 0.9199 (tmm) cc_final: 0.8845 (tmm) REVERT: C 860 GLU cc_start: 0.8646 (pp20) cc_final: 0.8148 (pp20) REVERT: C 918 ASP cc_start: 0.7637 (t0) cc_final: 0.6963 (p0) REVERT: C 937 SER cc_start: 0.8680 (m) cc_final: 0.8436 (p) REVERT: C 1201 LEU cc_start: 0.8110 (pt) cc_final: 0.7816 (tt) REVERT: C 1438 GLU cc_start: 0.8270 (tt0) cc_final: 0.7877 (tt0) REVERT: C 1482 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: C 1507 MET cc_start: 0.8404 (mmm) cc_final: 0.7850 (mtp) REVERT: C 1648 MET cc_start: 0.8559 (mmm) cc_final: 0.8188 (mmm) REVERT: C 2137 ASP cc_start: 0.8129 (m-30) cc_final: 0.7863 (m-30) REVERT: C 2367 MET cc_start: 0.7967 (tmm) cc_final: 0.7762 (tmm) REVERT: C 2373 LEU cc_start: 0.9223 (mt) cc_final: 0.8931 (tp) REVERT: D 50 ARG cc_start: 0.8852 (mtt180) cc_final: 0.8569 (mtp180) REVERT: D 56 GLN cc_start: 0.8839 (mt0) cc_final: 0.8177 (tm-30) REVERT: D 63 GLU cc_start: 0.8332 (tt0) cc_final: 0.7160 (pt0) REVERT: D 93 ASN cc_start: 0.8517 (m110) cc_final: 0.8133 (t0) REVERT: D 112 MET cc_start: 0.8030 (mtp) cc_final: 0.7497 (ttm) REVERT: D 159 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8991 (pp) REVERT: D 221 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: D 531 TYR cc_start: 0.3204 (m-10) cc_final: 0.2635 (m-80) REVERT: D 918 ASP cc_start: 0.7838 (t0) cc_final: 0.7233 (p0) REVERT: D 928 MET cc_start: 0.8241 (mtm) cc_final: 0.7861 (mtm) REVERT: D 937 SER cc_start: 0.8594 (m) cc_final: 0.8347 (p) REVERT: D 1063 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7448 (p90) REVERT: D 1438 GLU cc_start: 0.8256 (tt0) cc_final: 0.7921 (tt0) REVERT: D 1717 MET cc_start: 0.8363 (ppp) cc_final: 0.7706 (ppp) REVERT: D 2145 MET cc_start: 0.9143 (ptp) cc_final: 0.8722 (ptp) REVERT: D 2270 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.3359 (ttt) REVERT: E 50 ARG cc_start: 0.8882 (mtt180) cc_final: 0.8534 (mtp180) REVERT: E 63 GLU cc_start: 0.8231 (tt0) cc_final: 0.7858 (pt0) REVERT: E 93 ASN cc_start: 0.8513 (m110) cc_final: 0.8075 (t0) REVERT: E 112 MET cc_start: 0.8398 (mmm) cc_final: 0.6844 (mtp) REVERT: E 118 TYR cc_start: 0.7677 (t80) cc_final: 0.7465 (t80) REVERT: E 124 ARG cc_start: 0.7893 (mmp-170) cc_final: 0.7666 (tpm170) REVERT: E 148 MET cc_start: 0.8305 (ttp) cc_final: 0.7940 (ttm) REVERT: E 221 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: E 294 LEU cc_start: 0.8453 (tt) cc_final: 0.8023 (mt) REVERT: E 462 MET cc_start: 0.9025 (tmm) cc_final: 0.8747 (tmm) REVERT: E 523 LEU cc_start: 0.9154 (tp) cc_final: 0.8953 (tt) REVERT: E 908 GLN cc_start: 0.8534 (mm110) cc_final: 0.7876 (mm110) REVERT: E 940 GLN cc_start: 0.8230 (mm110) cc_final: 0.7816 (mm-40) REVERT: E 1146 MET cc_start: 0.7176 (mtt) cc_final: 0.6299 (ptt) REVERT: E 1717 MET cc_start: 0.8206 (ppp) cc_final: 0.7544 (ppp) REVERT: E 1830 TRP cc_start: 0.8266 (OUTLIER) cc_final: 0.7605 (m-90) REVERT: E 2270 MET cc_start: 0.4584 (mmp) cc_final: 0.2309 (ttt) REVERT: E 2367 MET cc_start: 0.7929 (tmm) cc_final: 0.7728 (tmm) REVERT: E 2376 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8233 (mtp180) outliers start: 299 outliers final: 195 residues processed: 1347 average time/residue: 0.8080 time to fit residues: 1925.2179 Evaluate side-chains 1217 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1005 time to evaluate : 8.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1396 GLU Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1457 PHE Chi-restraints excluded: chain A residue 1482 GLN Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1772 VAL Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1912 ASN Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 2011 VAL Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2050 SER Chi-restraints excluded: chain A residue 2077 ASP Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2350 PHE Chi-restraints excluded: chain A residue 2369 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 715 ASN Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 948 ASP Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1063 HIS Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1215 VAL Chi-restraints excluded: chain B residue 1417 ASN Chi-restraints excluded: chain B residue 1444 VAL Chi-restraints excluded: chain B residue 1482 GLN Chi-restraints excluded: chain B residue 1525 HIS Chi-restraints excluded: chain B residue 1527 THR Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1624 THR Chi-restraints excluded: chain B residue 1686 HIS Chi-restraints excluded: chain B residue 1693 LEU Chi-restraints excluded: chain B residue 1706 VAL Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1745 ASP Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1772 VAL Chi-restraints excluded: chain B residue 1830 TRP Chi-restraints excluded: chain B residue 1840 LEU Chi-restraints excluded: chain B residue 2011 VAL Chi-restraints excluded: chain B residue 2050 SER Chi-restraints excluded: chain B residue 2077 ASP Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2180 LEU Chi-restraints excluded: chain B residue 2250 THR Chi-restraints excluded: chain B residue 2262 LEU Chi-restraints excluded: chain B residue 2369 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 521 TYR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 876 ILE Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 HIS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1215 VAL Chi-restraints excluded: chain C residue 1420 SER Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1488 ASN Chi-restraints excluded: chain C residue 1833 LEU Chi-restraints excluded: chain C residue 1935 LEU Chi-restraints excluded: chain C residue 1994 ILE Chi-restraints excluded: chain C residue 2011 VAL Chi-restraints excluded: chain C residue 2077 ASP Chi-restraints excluded: chain C residue 2092 LEU Chi-restraints excluded: chain C residue 2181 MET Chi-restraints excluded: chain C residue 2262 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 958 GLU Chi-restraints excluded: chain D residue 1030 ILE Chi-restraints excluded: chain D residue 1063 HIS Chi-restraints excluded: chain D residue 1079 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1216 THR Chi-restraints excluded: chain D residue 1420 SER Chi-restraints excluded: chain D residue 1450 THR Chi-restraints excluded: chain D residue 1488 ASN Chi-restraints excluded: chain D residue 1564 LEU Chi-restraints excluded: chain D residue 1622 ILE Chi-restraints excluded: chain D residue 2011 VAL Chi-restraints excluded: chain D residue 2050 SER Chi-restraints excluded: chain D residue 2077 ASP Chi-restraints excluded: chain D residue 2187 MET Chi-restraints excluded: chain D residue 2192 LEU Chi-restraints excluded: chain D residue 2270 MET Chi-restraints excluded: chain D residue 2369 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 487 ASP Chi-restraints excluded: chain E residue 521 TYR Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 810 LEU Chi-restraints excluded: chain E residue 843 LEU Chi-restraints excluded: chain E residue 876 ILE Chi-restraints excluded: chain E residue 909 LEU Chi-restraints excluded: chain E residue 945 THR Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1116 MET Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1300 SER Chi-restraints excluded: chain E residue 1329 GLU Chi-restraints excluded: chain E residue 1417 ASN Chi-restraints excluded: chain E residue 1420 SER Chi-restraints excluded: chain E residue 1475 LEU Chi-restraints excluded: chain E residue 1560 VAL Chi-restraints excluded: chain E residue 1564 LEU Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1622 ILE Chi-restraints excluded: chain E residue 1646 THR Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain E residue 1745 ASP Chi-restraints excluded: chain E residue 1758 LEU Chi-restraints excluded: chain E residue 1772 VAL Chi-restraints excluded: chain E residue 1813 THR Chi-restraints excluded: chain E residue 1830 TRP Chi-restraints excluded: chain E residue 1955 LEU Chi-restraints excluded: chain E residue 1994 ILE Chi-restraints excluded: chain E residue 2011 VAL Chi-restraints excluded: chain E residue 2043 LEU Chi-restraints excluded: chain E residue 2077 ASP Chi-restraints excluded: chain E residue 2092 LEU Chi-restraints excluded: chain E residue 2144 LEU Chi-restraints excluded: chain E residue 2180 LEU Chi-restraints excluded: chain E residue 2223 ASP Chi-restraints excluded: chain E residue 2350 PHE Chi-restraints excluded: chain E residue 2369 THR Chi-restraints excluded: chain E residue 2376 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1180 random chunks: chunk 703 optimal weight: 3.9990 chunk 454 optimal weight: 0.8980 chunk 679 optimal weight: 4.9990 chunk 342 optimal weight: 0.0070 chunk 223 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 723 optimal weight: 9.9990 chunk 774 optimal weight: 5.9990 chunk 562 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 893 optimal weight: 7.9990 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 GLN A1203 GLN ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 GLN ** B1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1027 GLN C1203 GLN C1525 HIS ** C2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1203 GLN D1525 HIS ** D1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 925 GLN E 940 GLN ** E 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1296 HIS ** E1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 96545 Z= 0.279 Angle : 0.670 11.735 131045 Z= 0.344 Chirality : 0.043 0.287 14580 Planarity : 0.004 0.068 17000 Dihedral : 5.459 37.460 12850 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.20 % Allowed : 16.78 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 1.46 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.08), residues: 11795 helix: 1.65 (0.07), residues: 5290 sheet: -1.08 (0.12), residues: 1775 loop : -1.60 (0.09), residues: 4730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C1308 HIS 0.018 0.001 HIS D 79 PHE 0.033 0.002 PHE B1724 TYR 0.031 0.002 TYR C1583 ARG 0.009 0.001 ARG D1744 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 995 time to evaluate : 8.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8932 (mtt180) cc_final: 0.8559 (mtp180) REVERT: A 56 GLN cc_start: 0.9024 (mt0) cc_final: 0.8377 (tm-30) REVERT: A 63 GLU cc_start: 0.8520 (tt0) cc_final: 0.7646 (tt0) REVERT: A 69 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6788 (ttp80) REVERT: A 92 TYR cc_start: 0.6060 (m-10) cc_final: 0.5609 (m-80) REVERT: A 93 ASN cc_start: 0.8433 (m110) cc_final: 0.8039 (t0) REVERT: A 221 GLN cc_start: 0.7598 (tp-100) cc_final: 0.7171 (tm-30) REVERT: A 462 MET cc_start: 0.9100 (tmm) cc_final: 0.8765 (tmm) REVERT: A 513 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9053 (tp) REVERT: A 636 MET cc_start: 0.9257 (tpt) cc_final: 0.9032 (mmm) REVERT: A 687 ASN cc_start: 0.8689 (m110) cc_final: 0.8437 (t0) REVERT: A 860 GLU cc_start: 0.8735 (pp20) cc_final: 0.8272 (pp20) REVERT: A 887 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.7060 (mtt-85) REVERT: A 911 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8461 (t80) REVERT: A 1482 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: A 1525 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7442 (t-90) REVERT: A 1622 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7187 (mt) REVERT: A 1717 MET cc_start: 0.8331 (ppp) cc_final: 0.7869 (ppp) REVERT: A 1752 MET cc_start: 0.8657 (tmm) cc_final: 0.8447 (tmm) REVERT: A 1832 LYS cc_start: 0.8949 (tttt) cc_final: 0.8626 (ttmm) REVERT: A 1986 ASP cc_start: 0.8308 (t70) cc_final: 0.7983 (t70) REVERT: A 2047 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7480 (mp0) REVERT: A 2144 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9114 (mm) REVERT: A 2188 GLU cc_start: 0.7679 (tm-30) cc_final: 0.6918 (tm-30) REVERT: A 2189 ASP cc_start: 0.8162 (m-30) cc_final: 0.7815 (m-30) REVERT: A 2250 THR cc_start: 0.7206 (OUTLIER) cc_final: 0.6987 (t) REVERT: A 2350 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.6588 (t80) REVERT: B 50 ARG cc_start: 0.8869 (mtt180) cc_final: 0.8491 (mtp180) REVERT: B 56 GLN cc_start: 0.9062 (mt0) cc_final: 0.8447 (tm-30) REVERT: B 63 GLU cc_start: 0.8312 (tt0) cc_final: 0.7157 (pt0) REVERT: B 93 ASN cc_start: 0.8495 (m110) cc_final: 0.7883 (t0) REVERT: B 386 GLN cc_start: 0.8527 (tt0) cc_final: 0.8269 (tt0) REVERT: B 638 TYR cc_start: 0.8069 (t80) cc_final: 0.7708 (t80) REVERT: B 918 ASP cc_start: 0.7859 (t0) cc_final: 0.7164 (p0) REVERT: B 940 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7844 (mm-40) REVERT: B 1042 ILE cc_start: 0.9646 (OUTLIER) cc_final: 0.9308 (pt) REVERT: B 1344 MET cc_start: 0.8745 (mtp) cc_final: 0.8535 (tpp) REVERT: B 1405 LEU cc_start: 0.8075 (mp) cc_final: 0.7870 (mp) REVERT: B 1492 ASP cc_start: 0.8765 (p0) cc_final: 0.8515 (p0) REVERT: B 1717 MET cc_start: 0.8390 (ppp) cc_final: 0.7874 (ppp) REVERT: B 1830 TRP cc_start: 0.8354 (OUTLIER) cc_final: 0.7588 (m-90) REVERT: B 1918 ASP cc_start: 0.8228 (m-30) cc_final: 0.7596 (t0) REVERT: B 2250 THR cc_start: 0.7218 (OUTLIER) cc_final: 0.6980 (t) REVERT: B 2270 MET cc_start: 0.5203 (mmp) cc_final: 0.3391 (ttt) REVERT: C 50 ARG cc_start: 0.8871 (mtt180) cc_final: 0.8501 (mtp180) REVERT: C 56 GLN cc_start: 0.8761 (mt0) cc_final: 0.7946 (tm-30) REVERT: C 92 TYR cc_start: 0.6610 (m-80) cc_final: 0.5831 (m-10) REVERT: C 93 ASN cc_start: 0.8291 (m110) cc_final: 0.7874 (t0) REVERT: C 112 MET cc_start: 0.8857 (mmp) cc_final: 0.8568 (mmp) REVERT: C 124 ARG cc_start: 0.8000 (mmt180) cc_final: 0.7541 (tpt-90) REVERT: C 382 ASN cc_start: 0.7610 (t0) cc_final: 0.7265 (p0) REVERT: C 462 MET cc_start: 0.9230 (tmm) cc_final: 0.8828 (tmm) REVERT: C 860 GLU cc_start: 0.8598 (pp20) cc_final: 0.8092 (pp20) REVERT: C 918 ASP cc_start: 0.7615 (t0) cc_final: 0.6871 (p0) REVERT: C 1201 LEU cc_start: 0.8190 (pt) cc_final: 0.7909 (tt) REVERT: C 1274 MET cc_start: 0.7895 (ptp) cc_final: 0.7491 (ptp) REVERT: C 1438 GLU cc_start: 0.8172 (tt0) cc_final: 0.7836 (tt0) REVERT: C 1482 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: C 1507 MET cc_start: 0.8432 (mmm) cc_final: 0.7919 (mtp) REVERT: C 2367 MET cc_start: 0.8014 (tmm) cc_final: 0.7748 (tmm) REVERT: D 50 ARG cc_start: 0.8809 (mtt180) cc_final: 0.8553 (mtp180) REVERT: D 56 GLN cc_start: 0.8890 (mt0) cc_final: 0.8277 (tm-30) REVERT: D 63 GLU cc_start: 0.8424 (tt0) cc_final: 0.7242 (pt0) REVERT: D 93 ASN cc_start: 0.8520 (m110) cc_final: 0.8070 (t0) REVERT: D 159 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9004 (pp) REVERT: D 221 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: D 513 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9148 (tp) REVERT: D 531 TYR cc_start: 0.3432 (m-10) cc_final: 0.2941 (m-80) REVERT: D 918 ASP cc_start: 0.7679 (t0) cc_final: 0.7067 (p0) REVERT: D 929 MET cc_start: 0.8819 (tpp) cc_final: 0.8573 (tmm) REVERT: D 937 SER cc_start: 0.8775 (m) cc_final: 0.8531 (p) REVERT: D 1063 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.7658 (p90) REVERT: D 1438 GLU cc_start: 0.8247 (tt0) cc_final: 0.7890 (tt0) REVERT: D 1649 MET cc_start: 0.8291 (tpp) cc_final: 0.8043 (tpp) REVERT: D 1986 ASP cc_start: 0.8405 (t70) cc_final: 0.8124 (t70) REVERT: D 2270 MET cc_start: 0.5292 (OUTLIER) cc_final: 0.3531 (ttt) REVERT: E 50 ARG cc_start: 0.8893 (mtt180) cc_final: 0.8543 (mtp180) REVERT: E 63 GLU cc_start: 0.8307 (tt0) cc_final: 0.7341 (pt0) REVERT: E 93 ASN cc_start: 0.8462 (m110) cc_final: 0.8001 (t0) REVERT: E 112 MET cc_start: 0.8510 (mmm) cc_final: 0.7272 (mtm) REVERT: E 124 ARG cc_start: 0.7981 (mmp-170) cc_final: 0.7688 (tpm170) REVERT: E 148 MET cc_start: 0.8382 (ttp) cc_final: 0.8091 (ttm) REVERT: E 462 MET cc_start: 0.9038 (tmm) cc_final: 0.8782 (tmm) REVERT: E 908 GLN cc_start: 0.8776 (mm110) cc_final: 0.8247 (mm110) REVERT: E 911 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8260 (t80) REVERT: E 918 ASP cc_start: 0.7776 (t0) cc_final: 0.7110 (p0) REVERT: E 940 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7732 (mm-40) REVERT: E 1146 MET cc_start: 0.7391 (mtt) cc_final: 0.6391 (ptp) REVERT: E 1717 MET cc_start: 0.8360 (ppp) cc_final: 0.7625 (ppp) REVERT: E 1826 MET cc_start: 0.8536 (tpp) cc_final: 0.8132 (tpp) REVERT: E 1830 TRP cc_start: 0.8392 (OUTLIER) cc_final: 0.7493 (m-90) REVERT: E 2187 MET cc_start: 0.8916 (tpp) cc_final: 0.8632 (tpp) REVERT: E 2376 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8184 (mtp180) outliers start: 330 outliers final: 251 residues processed: 1242 average time/residue: 0.8222 time to fit residues: 1807.4582 Evaluate side-chains 1235 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 962 time to evaluate : 8.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 ARG Chi-restraints excluded: chain A residue 911 TYR Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1329 GLU Chi-restraints excluded: chain A residue 1396 GLU Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1482 GLN Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1525 HIS Chi-restraints excluded: chain A residue 1560 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1772 VAL Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1912 ASN Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 2011 VAL Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2050 SER Chi-restraints excluded: chain A residue 2064 ILE Chi-restraints excluded: chain A residue 2077 ASP Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2250 THR Chi-restraints excluded: chain A residue 2350 PHE Chi-restraints excluded: chain A residue 2369 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 715 ASN Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 948 ASP Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1042 ILE Chi-restraints excluded: chain B residue 1063 HIS Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1215 VAL Chi-restraints excluded: chain B residue 1329 GLU Chi-restraints excluded: chain B residue 1417 ASN Chi-restraints excluded: chain B residue 1444 VAL Chi-restraints excluded: chain B residue 1525 HIS Chi-restraints excluded: chain B residue 1527 THR Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1566 ARG Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1682 ILE Chi-restraints excluded: chain B residue 1686 HIS Chi-restraints excluded: chain B residue 1690 ARG Chi-restraints excluded: chain B residue 1693 LEU Chi-restraints excluded: chain B residue 1706 VAL Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1745 ASP Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1772 VAL Chi-restraints excluded: chain B residue 1830 TRP Chi-restraints excluded: chain B residue 1840 LEU Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 1995 THR Chi-restraints excluded: chain B residue 2011 VAL Chi-restraints excluded: chain B residue 2050 SER Chi-restraints excluded: chain B residue 2077 ASP Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2180 LEU Chi-restraints excluded: chain B residue 2187 MET Chi-restraints excluded: chain B residue 2250 THR Chi-restraints excluded: chain B residue 2262 LEU Chi-restraints excluded: chain B residue 2369 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 876 ILE Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 HIS Chi-restraints excluded: chain C residue 1079 VAL Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1189 ASN Chi-restraints excluded: chain C residue 1215 VAL Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1329 GLU Chi-restraints excluded: chain C residue 1417 ASN Chi-restraints excluded: chain C residue 1420 SER Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1488 ASN Chi-restraints excluded: chain C residue 1525 HIS Chi-restraints excluded: chain C residue 1935 LEU Chi-restraints excluded: chain C residue 1994 ILE Chi-restraints excluded: chain C residue 1995 THR Chi-restraints excluded: chain C residue 2011 VAL Chi-restraints excluded: chain C residue 2050 SER Chi-restraints excluded: chain C residue 2077 ASP Chi-restraints excluded: chain C residue 2092 LEU Chi-restraints excluded: chain C residue 2181 MET Chi-restraints excluded: chain C residue 2262 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain D residue 958 GLU Chi-restraints excluded: chain D residue 1030 ILE Chi-restraints excluded: chain D residue 1063 HIS Chi-restraints excluded: chain D residue 1079 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1216 THR Chi-restraints excluded: chain D residue 1293 LEU Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain D residue 1329 GLU Chi-restraints excluded: chain D residue 1342 ILE Chi-restraints excluded: chain D residue 1417 ASN Chi-restraints excluded: chain D residue 1420 SER Chi-restraints excluded: chain D residue 1450 THR Chi-restraints excluded: chain D residue 1488 ASN Chi-restraints excluded: chain D residue 1525 HIS Chi-restraints excluded: chain D residue 1560 VAL Chi-restraints excluded: chain D residue 1564 LEU Chi-restraints excluded: chain D residue 1622 ILE Chi-restraints excluded: chain D residue 1682 ILE Chi-restraints excluded: chain D residue 1813 THR Chi-restraints excluded: chain D residue 1953 THR Chi-restraints excluded: chain D residue 1994 ILE Chi-restraints excluded: chain D residue 1995 THR Chi-restraints excluded: chain D residue 2011 VAL Chi-restraints excluded: chain D residue 2043 LEU Chi-restraints excluded: chain D residue 2050 SER Chi-restraints excluded: chain D residue 2077 ASP Chi-restraints excluded: chain D residue 2180 LEU Chi-restraints excluded: chain D residue 2187 MET Chi-restraints excluded: chain D residue 2192 LEU Chi-restraints excluded: chain D residue 2270 MET Chi-restraints excluded: chain D residue 2369 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 487 ASP Chi-restraints excluded: chain E residue 521 TYR Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 810 LEU Chi-restraints excluded: chain E residue 843 LEU Chi-restraints excluded: chain E residue 876 ILE Chi-restraints excluded: chain E residue 911 TYR Chi-restraints excluded: chain E residue 925 GLN Chi-restraints excluded: chain E residue 945 THR Chi-restraints excluded: chain E residue 960 VAL Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1116 MET Chi-restraints excluded: chain E residue 1188 ILE Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1300 SER Chi-restraints excluded: chain E residue 1329 GLU Chi-restraints excluded: chain E residue 1417 ASN Chi-restraints excluded: chain E residue 1420 SER Chi-restraints excluded: chain E residue 1475 LEU Chi-restraints excluded: chain E residue 1488 ASN Chi-restraints excluded: chain E residue 1560 VAL Chi-restraints excluded: chain E residue 1564 LEU Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1622 ILE Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain E residue 1745 ASP Chi-restraints excluded: chain E residue 1758 LEU Chi-restraints excluded: chain E residue 1772 VAL Chi-restraints excluded: chain E residue 1813 THR Chi-restraints excluded: chain E residue 1830 TRP Chi-restraints excluded: chain E residue 1833 LEU Chi-restraints excluded: chain E residue 1955 LEU Chi-restraints excluded: chain E residue 1989 ILE Chi-restraints excluded: chain E residue 1994 ILE Chi-restraints excluded: chain E residue 2011 VAL Chi-restraints excluded: chain E residue 2043 LEU Chi-restraints excluded: chain E residue 2050 SER Chi-restraints excluded: chain E residue 2077 ASP Chi-restraints excluded: chain E residue 2092 LEU Chi-restraints excluded: chain E residue 2144 LEU Chi-restraints excluded: chain E residue 2180 LEU Chi-restraints excluded: chain E residue 2223 ASP Chi-restraints excluded: chain E residue 2350 PHE Chi-restraints excluded: chain E residue 2369 THR Chi-restraints excluded: chain E residue 2376 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1180 random chunks: chunk 1034 optimal weight: 7.9990 chunk 1089 optimal weight: 0.9990 chunk 994 optimal weight: 6.9990 chunk 1059 optimal weight: 1.9990 chunk 637 optimal weight: 3.9990 chunk 461 optimal weight: 9.9990 chunk 832 optimal weight: 9.9990 chunk 325 optimal weight: 0.0970 chunk 957 optimal weight: 0.9990 chunk 1002 optimal weight: 1.9990 chunk 1056 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 HIS A 633 GLN ** A 925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 GLN ** A2103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 GLN ** B1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 GLN ** C 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1190 HIS C1203 GLN ** C1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1052 GLN D1203 GLN ** D1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2155 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 HIS E 730 ASN E 879 HIS ** E1968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 96545 Z= 0.170 Angle : 0.628 12.424 131045 Z= 0.318 Chirality : 0.041 0.257 14580 Planarity : 0.004 0.074 17000 Dihedral : 5.165 37.902 12850 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.36 % Allowed : 17.74 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 1.22 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.08), residues: 11795 helix: 1.81 (0.07), residues: 5325 sheet: -0.98 (0.13), residues: 1740 loop : -1.51 (0.09), residues: 4730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C1308 HIS 0.025 0.001 HIS B 79 PHE 0.036 0.001 PHE B1724 TYR 0.027 0.001 TYR D1583 ARG 0.008 0.000 ARG D1679 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1072 time to evaluate : 8.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8935 (mtt180) cc_final: 0.8529 (mtp180) REVERT: A 56 GLN cc_start: 0.9029 (mt0) cc_final: 0.8328 (tm-30) REVERT: A 63 GLU cc_start: 0.8485 (tt0) cc_final: 0.7707 (tt0) REVERT: A 69 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6587 (ttp80) REVERT: A 93 ASN cc_start: 0.8354 (m110) cc_final: 0.7878 (t0) REVERT: A 221 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7248 (tt0) REVERT: A 462 MET cc_start: 0.9091 (tmm) cc_final: 0.8743 (tmm) REVERT: A 638 TYR cc_start: 0.8004 (t80) cc_final: 0.7538 (t80) REVERT: A 860 GLU cc_start: 0.8717 (pp20) cc_final: 0.8252 (pp20) REVERT: A 914 GLU cc_start: 0.8759 (pm20) cc_final: 0.8541 (pm20) REVERT: A 1146 MET cc_start: 0.5784 (mtp) cc_final: 0.4233 (mtp) REVERT: A 1525 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7030 (t-90) REVERT: A 1622 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7155 (mt) REVERT: A 1717 MET cc_start: 0.8206 (ppp) cc_final: 0.7712 (ppp) REVERT: A 1832 LYS cc_start: 0.8913 (tttt) cc_final: 0.8605 (ttmm) REVERT: A 1918 ASP cc_start: 0.8180 (m-30) cc_final: 0.7522 (t0) REVERT: A 1986 ASP cc_start: 0.8297 (t70) cc_final: 0.7943 (t70) REVERT: A 2010 MET cc_start: 0.8733 (mmm) cc_final: 0.8526 (mmm) REVERT: A 2047 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7521 (mp0) REVERT: A 2083 LEU cc_start: 0.9334 (tp) cc_final: 0.8953 (tt) REVERT: A 2144 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9097 (mm) REVERT: A 2188 GLU cc_start: 0.7597 (tm-30) cc_final: 0.6772 (tm-30) REVERT: A 2189 ASP cc_start: 0.8108 (m-30) cc_final: 0.7749 (m-30) REVERT: A 2350 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.6486 (t80) REVERT: A 2367 MET cc_start: 0.7891 (tmm) cc_final: 0.7637 (tmm) REVERT: B 50 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8489 (mtp180) REVERT: B 56 GLN cc_start: 0.9030 (mt0) cc_final: 0.8384 (tm-30) REVERT: B 93 ASN cc_start: 0.8494 (m110) cc_final: 0.7900 (t0) REVERT: B 221 GLN cc_start: 0.7888 (tp40) cc_final: 0.7406 (tt0) REVERT: B 638 TYR cc_start: 0.8061 (t80) cc_final: 0.7729 (t80) REVERT: B 838 ASP cc_start: 0.8049 (m-30) cc_final: 0.7688 (t0) REVERT: B 918 ASP cc_start: 0.7817 (t0) cc_final: 0.7091 (p0) REVERT: B 940 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7776 (mm-40) REVERT: B 1405 LEU cc_start: 0.8086 (mp) cc_final: 0.7869 (mp) REVERT: B 1492 ASP cc_start: 0.8672 (p0) cc_final: 0.8437 (p0) REVERT: B 1622 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7196 (mt) REVERT: B 1830 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.7631 (m-90) REVERT: B 1918 ASP cc_start: 0.8073 (m-30) cc_final: 0.7508 (t0) REVERT: B 2270 MET cc_start: 0.4997 (mmp) cc_final: 0.3391 (ttt) REVERT: C 50 ARG cc_start: 0.8840 (mtt180) cc_final: 0.8474 (mtp180) REVERT: C 56 GLN cc_start: 0.8735 (mt0) cc_final: 0.8075 (tm-30) REVERT: C 93 ASN cc_start: 0.8308 (m110) cc_final: 0.7900 (t0) REVERT: C 124 ARG cc_start: 0.7963 (mmt180) cc_final: 0.7619 (tpt-90) REVERT: C 221 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: C 382 ASN cc_start: 0.7521 (t0) cc_final: 0.7199 (p0) REVERT: C 462 MET cc_start: 0.9210 (tmm) cc_final: 0.8847 (tmm) REVERT: C 860 GLU cc_start: 0.8692 (pp20) cc_final: 0.8132 (pp20) REVERT: C 918 ASP cc_start: 0.7540 (t0) cc_final: 0.6934 (p0) REVERT: C 1201 LEU cc_start: 0.8123 (pt) cc_final: 0.7855 (tt) REVERT: C 1274 MET cc_start: 0.7922 (ptp) cc_final: 0.7529 (pmm) REVERT: C 1398 MET cc_start: 0.8789 (mmm) cc_final: 0.8415 (mmm) REVERT: C 1438 GLU cc_start: 0.8192 (tt0) cc_final: 0.7779 (tt0) REVERT: C 1482 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: C 1507 MET cc_start: 0.8386 (mmm) cc_final: 0.7841 (mtp) REVERT: C 2083 LEU cc_start: 0.9411 (tp) cc_final: 0.9055 (tt) REVERT: C 2367 MET cc_start: 0.7990 (tmm) cc_final: 0.7746 (tmm) REVERT: D 50 ARG cc_start: 0.8852 (mtt180) cc_final: 0.8565 (mtp180) REVERT: D 56 GLN cc_start: 0.8931 (mt0) cc_final: 0.8200 (tm-30) REVERT: D 93 ASN cc_start: 0.8528 (m110) cc_final: 0.8134 (t0) REVERT: D 124 ARG cc_start: 0.7614 (tpm170) cc_final: 0.7180 (tpm170) REVERT: D 159 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9015 (pp) REVERT: D 221 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: D 531 TYR cc_start: 0.3417 (m-10) cc_final: 0.2983 (m-80) REVERT: D 638 TYR cc_start: 0.8043 (t80) cc_final: 0.7811 (t80) REVERT: D 806 LEU cc_start: 0.9133 (tp) cc_final: 0.8866 (tt) REVERT: D 918 ASP cc_start: 0.7727 (t0) cc_final: 0.7164 (p0) REVERT: D 937 SER cc_start: 0.8654 (m) cc_final: 0.8449 (p) REVERT: D 1063 HIS cc_start: 0.8365 (OUTLIER) cc_final: 0.7480 (p90) REVERT: D 1274 MET cc_start: 0.8171 (pmm) cc_final: 0.7624 (pmm) REVERT: D 1438 GLU cc_start: 0.8248 (tt0) cc_final: 0.7929 (tt0) REVERT: D 1507 MET cc_start: 0.7883 (mmm) cc_final: 0.7375 (mtt) REVERT: D 1622 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7131 (mt) REVERT: D 1717 MET cc_start: 0.8428 (ppp) cc_final: 0.7898 (ppp) REVERT: D 1986 ASP cc_start: 0.8414 (t70) cc_final: 0.8061 (t70) REVERT: D 2083 LEU cc_start: 0.9384 (tp) cc_final: 0.8984 (tt) REVERT: D 2270 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.3551 (ttt) REVERT: E 50 ARG cc_start: 0.8906 (mtt180) cc_final: 0.8548 (mtp180) REVERT: E 63 GLU cc_start: 0.8195 (tt0) cc_final: 0.7634 (pt0) REVERT: E 93 ASN cc_start: 0.8533 (m110) cc_final: 0.8096 (t0) REVERT: E 112 MET cc_start: 0.8445 (mmm) cc_final: 0.7625 (mtm) REVERT: E 124 ARG cc_start: 0.7915 (mmp-170) cc_final: 0.7644 (tpm170) REVERT: E 294 LEU cc_start: 0.8117 (tt) cc_final: 0.7714 (mt) REVERT: E 462 MET cc_start: 0.9027 (tmm) cc_final: 0.8752 (tmm) REVERT: E 839 LEU cc_start: 0.9420 (tp) cc_final: 0.9114 (tp) REVERT: E 908 GLN cc_start: 0.8523 (mm110) cc_final: 0.8311 (mm110) REVERT: E 911 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8285 (t80) REVERT: E 918 ASP cc_start: 0.7721 (t0) cc_final: 0.7063 (p0) REVERT: E 930 ASP cc_start: 0.7610 (m-30) cc_final: 0.7394 (m-30) REVERT: E 940 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7676 (mm-40) REVERT: E 1146 MET cc_start: 0.7116 (mtt) cc_final: 0.6268 (ptt) REVERT: E 1622 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7119 (mt) REVERT: E 1648 MET cc_start: 0.8536 (tpp) cc_final: 0.8142 (tpt) REVERT: E 1717 MET cc_start: 0.8170 (ppp) cc_final: 0.7548 (ppp) REVERT: E 1826 MET cc_start: 0.8521 (tpp) cc_final: 0.8095 (tpp) REVERT: E 1830 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.7383 (m-90) REVERT: E 2083 LEU cc_start: 0.9363 (tp) cc_final: 0.9053 (tt) REVERT: E 2187 MET cc_start: 0.8858 (tpp) cc_final: 0.8556 (tpp) REVERT: E 2376 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8254 (mtp180) outliers start: 243 outliers final: 186 residues processed: 1246 average time/residue: 0.8702 time to fit residues: 1930.8819 Evaluate side-chains 1196 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 992 time to evaluate : 8.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1525 HIS Chi-restraints excluded: chain A residue 1560 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1912 ASN Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1994 ILE Chi-restraints excluded: chain A residue 2011 VAL Chi-restraints excluded: chain A residue 2043 LEU Chi-restraints excluded: chain A residue 2050 SER Chi-restraints excluded: chain A residue 2077 ASP Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2350 PHE Chi-restraints excluded: chain A residue 2369 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 715 ASN Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1063 HIS Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1215 VAL Chi-restraints excluded: chain B residue 1444 VAL Chi-restraints excluded: chain B residue 1525 HIS Chi-restraints excluded: chain B residue 1527 THR Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1686 HIS Chi-restraints excluded: chain B residue 1690 ARG Chi-restraints excluded: chain B residue 1693 LEU Chi-restraints excluded: chain B residue 1706 VAL Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1830 TRP Chi-restraints excluded: chain B residue 1840 LEU Chi-restraints excluded: chain B residue 1995 THR Chi-restraints excluded: chain B residue 2011 VAL Chi-restraints excluded: chain B residue 2050 SER Chi-restraints excluded: chain B residue 2077 ASP Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2111 LEU Chi-restraints excluded: chain B residue 2180 LEU Chi-restraints excluded: chain B residue 2187 MET Chi-restraints excluded: chain B residue 2262 LEU Chi-restraints excluded: chain B residue 2369 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 HIS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1215 VAL Chi-restraints excluded: chain C residue 1329 GLU Chi-restraints excluded: chain C residue 1420 SER Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1488 ASN Chi-restraints excluded: chain C residue 1935 LEU Chi-restraints excluded: chain C residue 1994 ILE Chi-restraints excluded: chain C residue 1995 THR Chi-restraints excluded: chain C residue 2011 VAL Chi-restraints excluded: chain C residue 2050 SER Chi-restraints excluded: chain C residue 2077 ASP Chi-restraints excluded: chain C residue 2092 LEU Chi-restraints excluded: chain C residue 2181 MET Chi-restraints excluded: chain C residue 2262 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 636 MET Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 958 GLU Chi-restraints excluded: chain D residue 1030 ILE Chi-restraints excluded: chain D residue 1063 HIS Chi-restraints excluded: chain D residue 1079 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1216 THR Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain D residue 1329 GLU Chi-restraints excluded: chain D residue 1342 ILE Chi-restraints excluded: chain D residue 1420 SER Chi-restraints excluded: chain D residue 1488 ASN Chi-restraints excluded: chain D residue 1560 VAL Chi-restraints excluded: chain D residue 1564 LEU Chi-restraints excluded: chain D residue 1579 VAL Chi-restraints excluded: chain D residue 1622 ILE Chi-restraints excluded: chain D residue 1995 THR Chi-restraints excluded: chain D residue 2011 VAL Chi-restraints excluded: chain D residue 2050 SER Chi-restraints excluded: chain D residue 2077 ASP Chi-restraints excluded: chain D residue 2180 LEU Chi-restraints excluded: chain D residue 2187 MET Chi-restraints excluded: chain D residue 2192 LEU Chi-restraints excluded: chain D residue 2270 MET Chi-restraints excluded: chain D residue 2369 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 487 ASP Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 843 LEU Chi-restraints excluded: chain E residue 876 ILE Chi-restraints excluded: chain E residue 911 TYR Chi-restraints excluded: chain E residue 925 GLN Chi-restraints excluded: chain E residue 945 THR Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1116 MET Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1300 SER Chi-restraints excluded: chain E residue 1344 MET Chi-restraints excluded: chain E residue 1417 ASN Chi-restraints excluded: chain E residue 1420 SER Chi-restraints excluded: chain E residue 1560 VAL Chi-restraints excluded: chain E residue 1564 LEU Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1622 ILE Chi-restraints excluded: chain E residue 1649 MET Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain E residue 1745 ASP Chi-restraints excluded: chain E residue 1813 THR Chi-restraints excluded: chain E residue 1830 TRP Chi-restraints excluded: chain E residue 1948 ILE Chi-restraints excluded: chain E residue 1955 LEU Chi-restraints excluded: chain E residue 1989 ILE Chi-restraints excluded: chain E residue 2011 VAL Chi-restraints excluded: chain E residue 2050 SER Chi-restraints excluded: chain E residue 2077 ASP Chi-restraints excluded: chain E residue 2092 LEU Chi-restraints excluded: chain E residue 2144 LEU Chi-restraints excluded: chain E residue 2180 LEU Chi-restraints excluded: chain E residue 2223 ASP Chi-restraints excluded: chain E residue 2350 PHE Chi-restraints excluded: chain E residue 2369 THR Chi-restraints excluded: chain E residue 2376 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1180 random chunks: chunk 695 optimal weight: 0.9980 chunk 1120 optimal weight: 5.9990 chunk 684 optimal weight: 8.9990 chunk 531 optimal weight: 0.4980 chunk 779 optimal weight: 0.0970 chunk 1175 optimal weight: 1.9990 chunk 1081 optimal weight: 1.9990 chunk 936 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 723 optimal weight: 3.9990 chunk 574 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN A1203 GLN A2155 ASN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 991 ASN ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 GLN C 962 ASN ** C1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 925 GLN D1203 GLN D1763 ASN ** D1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN E 241 ASN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 GLN E 925 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 96545 Z= 0.166 Angle : 0.632 13.035 131045 Z= 0.317 Chirality : 0.041 0.382 14580 Planarity : 0.004 0.080 17000 Dihedral : 4.975 37.229 12850 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.97 % Allowed : 18.32 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 1.46 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.08), residues: 11795 helix: 1.85 (0.07), residues: 5345 sheet: -0.84 (0.13), residues: 1730 loop : -1.48 (0.09), residues: 4720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 418 HIS 0.010 0.001 HIS B1759 PHE 0.046 0.001 PHE D 289 TYR 0.028 0.001 TYR B1136 ARG 0.009 0.000 ARG A 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23590 Ramachandran restraints generated. 11795 Oldfield, 0 Emsley, 11795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1105 time to evaluate : 9.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8957 (mtt180) cc_final: 0.8540 (mtp180) REVERT: A 56 GLN cc_start: 0.8984 (mt0) cc_final: 0.8240 (tm-30) REVERT: A 69 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6811 (ttt90) REVERT: A 93 ASN cc_start: 0.8343 (m110) cc_final: 0.7791 (t0) REVERT: A 124 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7814 (tpm170) REVERT: A 155 MET cc_start: 0.9008 (tpp) cc_final: 0.8107 (tpp) REVERT: A 221 GLN cc_start: 0.7479 (tp-100) cc_final: 0.7202 (tt0) REVERT: A 462 MET cc_start: 0.9092 (tmm) cc_final: 0.8753 (tmm) REVERT: A 638 TYR cc_start: 0.8012 (t80) cc_final: 0.7702 (t80) REVERT: A 860 GLU cc_start: 0.8695 (pp20) cc_final: 0.8253 (pp20) REVERT: A 1525 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.7154 (t-90) REVERT: A 1622 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7186 (mt) REVERT: A 1629 MET cc_start: 0.8231 (tpp) cc_final: 0.8003 (tpp) REVERT: A 1703 LEU cc_start: 0.9378 (mm) cc_final: 0.9082 (mm) REVERT: A 1717 MET cc_start: 0.8191 (ppp) cc_final: 0.7733 (ppp) REVERT: A 1826 MET cc_start: 0.8603 (tpp) cc_final: 0.8369 (tpp) REVERT: A 1832 LYS cc_start: 0.8885 (tttt) cc_final: 0.8590 (ttmm) REVERT: A 1918 ASP cc_start: 0.8149 (m-30) cc_final: 0.7532 (t0) REVERT: A 2047 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7396 (mp0) REVERT: A 2083 LEU cc_start: 0.9290 (tp) cc_final: 0.8907 (tt) REVERT: A 2188 GLU cc_start: 0.7566 (tm-30) cc_final: 0.6770 (tm-30) REVERT: A 2189 ASP cc_start: 0.8108 (m-30) cc_final: 0.7744 (m-30) REVERT: A 2350 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.6459 (t80) REVERT: B 50 ARG cc_start: 0.8883 (mtt180) cc_final: 0.8510 (mtp180) REVERT: B 56 GLN cc_start: 0.9019 (mt0) cc_final: 0.8370 (tm-30) REVERT: B 93 ASN cc_start: 0.8384 (m110) cc_final: 0.7815 (t0) REVERT: B 221 GLN cc_start: 0.7908 (tp40) cc_final: 0.7468 (tt0) REVERT: B 638 TYR cc_start: 0.8060 (t80) cc_final: 0.7764 (t80) REVERT: B 838 ASP cc_start: 0.8029 (m-30) cc_final: 0.7661 (t0) REVERT: B 899 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.8128 (mtm-85) REVERT: B 911 TYR cc_start: 0.8305 (t80) cc_final: 0.8002 (t80) REVERT: B 918 ASP cc_start: 0.7778 (t0) cc_final: 0.7149 (p0) REVERT: B 947 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7983 (tm-30) REVERT: B 1146 MET cc_start: 0.6135 (ptm) cc_final: 0.5866 (ppp) REVERT: B 1201 LEU cc_start: 0.8708 (tt) cc_final: 0.8464 (mm) REVERT: B 1405 LEU cc_start: 0.8084 (mp) cc_final: 0.7858 (mp) REVERT: B 1438 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8213 (mp0) REVERT: B 1492 ASP cc_start: 0.8643 (p0) cc_final: 0.8385 (p0) REVERT: B 1622 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7192 (mt) REVERT: B 1830 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7509 (m-90) REVERT: B 1918 ASP cc_start: 0.8143 (m-30) cc_final: 0.7547 (t0) REVERT: B 2083 LEU cc_start: 0.9346 (tp) cc_final: 0.8944 (tt) REVERT: B 2270 MET cc_start: 0.4840 (mmp) cc_final: 0.3384 (ttt) REVERT: C 50 ARG cc_start: 0.8815 (mtt180) cc_final: 0.8478 (mtp180) REVERT: C 56 GLN cc_start: 0.8598 (mt0) cc_final: 0.7996 (tm-30) REVERT: C 93 ASN cc_start: 0.8235 (m110) cc_final: 0.7772 (t0) REVERT: C 124 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7618 (tpt-90) REVERT: C 221 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: C 382 ASN cc_start: 0.7574 (t0) cc_final: 0.7270 (p0) REVERT: C 462 MET cc_start: 0.9224 (tmm) cc_final: 0.8826 (tmm) REVERT: C 860 GLU cc_start: 0.8711 (pp20) cc_final: 0.8041 (pp20) REVERT: C 918 ASP cc_start: 0.7509 (t0) cc_final: 0.6965 (p0) REVERT: C 1146 MET cc_start: 0.6883 (ttp) cc_final: 0.6327 (tmm) REVERT: C 1201 LEU cc_start: 0.8222 (pt) cc_final: 0.7951 (tt) REVERT: C 1274 MET cc_start: 0.7911 (ptp) cc_final: 0.7528 (pmm) REVERT: C 1438 GLU cc_start: 0.8157 (tt0) cc_final: 0.7746 (tt0) REVERT: C 1482 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: C 1507 MET cc_start: 0.8320 (mmm) cc_final: 0.7793 (mtp) REVERT: C 2072 GLU cc_start: 0.8035 (tt0) cc_final: 0.7815 (tt0) REVERT: C 2083 LEU cc_start: 0.9399 (tp) cc_final: 0.9052 (tt) REVERT: C 2145 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8713 (ptm) REVERT: D 50 ARG cc_start: 0.8852 (mtt180) cc_final: 0.8550 (mtp180) REVERT: D 56 GLN cc_start: 0.8847 (mt0) cc_final: 0.8128 (tm-30) REVERT: D 93 ASN cc_start: 0.8498 (m110) cc_final: 0.8093 (t0) REVERT: D 124 ARG cc_start: 0.7684 (tpm170) cc_final: 0.7284 (tpm170) REVERT: D 159 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9020 (pp) REVERT: D 187 MET cc_start: 0.8774 (mmm) cc_final: 0.8056 (mmm) REVERT: D 531 TYR cc_start: 0.3202 (m-10) cc_final: 0.2808 (m-80) REVERT: D 638 TYR cc_start: 0.8130 (t80) cc_final: 0.7881 (t80) REVERT: D 918 ASP cc_start: 0.7672 (t0) cc_final: 0.7048 (p0) REVERT: D 937 SER cc_start: 0.8682 (m) cc_final: 0.8466 (p) REVERT: D 1063 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.7492 (p90) REVERT: D 1438 GLU cc_start: 0.8261 (tt0) cc_final: 0.7886 (tt0) REVERT: D 1507 MET cc_start: 0.7833 (mmm) cc_final: 0.7362 (mtt) REVERT: D 1622 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7089 (mt) REVERT: D 1717 MET cc_start: 0.8368 (ppp) cc_final: 0.7896 (ppp) REVERT: D 2083 LEU cc_start: 0.9360 (tp) cc_final: 0.9015 (tt) REVERT: D 2270 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.3575 (ttt) REVERT: D 2373 LEU cc_start: 0.9189 (mt) cc_final: 0.8921 (tp) REVERT: E 50 ARG cc_start: 0.8887 (mtt180) cc_final: 0.8518 (mtp180) REVERT: E 63 GLU cc_start: 0.8187 (tt0) cc_final: 0.7229 (pt0) REVERT: E 93 ASN cc_start: 0.8533 (m110) cc_final: 0.8107 (t0) REVERT: E 112 MET cc_start: 0.8405 (mmm) cc_final: 0.8096 (mmm) REVERT: E 118 TYR cc_start: 0.7868 (t80) cc_final: 0.7635 (t80) REVERT: E 124 ARG cc_start: 0.7957 (mmp-170) cc_final: 0.7698 (tpm170) REVERT: E 155 MET cc_start: 0.8855 (tpp) cc_final: 0.8233 (tpp) REVERT: E 294 LEU cc_start: 0.8209 (tt) cc_final: 0.7823 (mt) REVERT: E 410 LEU cc_start: 0.9164 (mt) cc_final: 0.8719 (tt) REVERT: E 462 MET cc_start: 0.9034 (tmm) cc_final: 0.8764 (tmm) REVERT: E 839 LEU cc_start: 0.9400 (tp) cc_final: 0.9093 (tp) REVERT: E 918 ASP cc_start: 0.7677 (t0) cc_final: 0.6942 (p0) REVERT: E 1146 MET cc_start: 0.7032 (mtt) cc_final: 0.6329 (ptt) REVERT: E 1398 MET cc_start: 0.8828 (mmm) cc_final: 0.8542 (mmm) REVERT: E 1622 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7115 (mt) REVERT: E 1717 MET cc_start: 0.8123 (ppp) cc_final: 0.7550 (ppp) REVERT: E 1826 MET cc_start: 0.8526 (tpp) cc_final: 0.8110 (tpp) REVERT: E 1830 TRP cc_start: 0.8152 (OUTLIER) cc_final: 0.7425 (m-90) REVERT: E 2083 LEU cc_start: 0.9419 (tp) cc_final: 0.9074 (tt) REVERT: E 2145 MET cc_start: 0.8925 (ptp) cc_final: 0.8532 (ptm) REVERT: E 2270 MET cc_start: 0.4656 (mmp) cc_final: 0.2573 (ttt) outliers start: 203 outliers final: 152 residues processed: 1245 average time/residue: 0.8726 time to fit residues: 1930.6799 Evaluate side-chains 1164 residues out of total 10300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 997 time to evaluate : 8.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1488 ASN Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1525 HIS Chi-restraints excluded: chain A residue 1560 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1912 ASN Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 2011 VAL Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2350 PHE Chi-restraints excluded: chain A residue 2369 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1063 HIS Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1215 VAL Chi-restraints excluded: chain B residue 1444 VAL Chi-restraints excluded: chain B residue 1527 THR Chi-restraints excluded: chain B residue 1560 VAL Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1686 HIS Chi-restraints excluded: chain B residue 1690 ARG Chi-restraints excluded: chain B residue 1706 VAL Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1758 LEU Chi-restraints excluded: chain B residue 1830 TRP Chi-restraints excluded: chain B residue 1840 LEU Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 1995 THR Chi-restraints excluded: chain B residue 2011 VAL Chi-restraints excluded: chain B residue 2077 ASP Chi-restraints excluded: chain B residue 2092 LEU Chi-restraints excluded: chain B residue 2187 MET Chi-restraints excluded: chain B residue 2262 LEU Chi-restraints excluded: chain B residue 2369 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 876 ILE Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 HIS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1188 ILE Chi-restraints excluded: chain C residue 1215 VAL Chi-restraints excluded: chain C residue 1420 SER Chi-restraints excluded: chain C residue 1482 GLN Chi-restraints excluded: chain C residue 1488 ASN Chi-restraints excluded: chain C residue 1935 LEU Chi-restraints excluded: chain C residue 1995 THR Chi-restraints excluded: chain C residue 2011 VAL Chi-restraints excluded: chain C residue 2092 LEU Chi-restraints excluded: chain C residue 2145 MET Chi-restraints excluded: chain C residue 2181 MET Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 958 GLU Chi-restraints excluded: chain D residue 1030 ILE Chi-restraints excluded: chain D residue 1063 HIS Chi-restraints excluded: chain D residue 1079 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1216 THR Chi-restraints excluded: chain D residue 1305 VAL Chi-restraints excluded: chain D residue 1329 GLU Chi-restraints excluded: chain D residue 1342 ILE Chi-restraints excluded: chain D residue 1420 SER Chi-restraints excluded: chain D residue 1450 THR Chi-restraints excluded: chain D residue 1488 ASN Chi-restraints excluded: chain D residue 1560 VAL Chi-restraints excluded: chain D residue 1564 LEU Chi-restraints excluded: chain D residue 1579 VAL Chi-restraints excluded: chain D residue 1622 ILE Chi-restraints excluded: chain D residue 1995 THR Chi-restraints excluded: chain D residue 2011 VAL Chi-restraints excluded: chain D residue 2077 ASP Chi-restraints excluded: chain D residue 2187 MET Chi-restraints excluded: chain D residue 2192 LEU Chi-restraints excluded: chain D residue 2250 THR Chi-restraints excluded: chain D residue 2270 MET Chi-restraints excluded: chain D residue 2369 THR Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 487 ASP Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 843 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1116 MET Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1344 MET Chi-restraints excluded: chain E residue 1420 SER Chi-restraints excluded: chain E residue 1560 VAL Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1622 ILE Chi-restraints excluded: chain E residue 1728 LEU Chi-restraints excluded: chain E residue 1730 LEU Chi-restraints excluded: chain E residue 1745 ASP Chi-restraints excluded: chain E residue 1813 THR Chi-restraints excluded: chain E residue 1830 TRP Chi-restraints excluded: chain E residue 1948 ILE Chi-restraints excluded: chain E residue 1955 LEU Chi-restraints excluded: chain E residue 1989 ILE Chi-restraints excluded: chain E residue 2011 VAL Chi-restraints excluded: chain E residue 2092 LEU Chi-restraints excluded: chain E residue 2144 LEU Chi-restraints excluded: chain E residue 2223 ASP Chi-restraints excluded: chain E residue 2350 PHE Chi-restraints excluded: chain E residue 2369 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1180 random chunks: chunk 743 optimal weight: 8.9990 chunk 997 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 863 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 937 optimal weight: 8.9990 chunk 392 optimal weight: 7.9990 chunk 962 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 GLN ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 ASN ** B 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 GLN B1052 GLN ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN C 288 ASN ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 GLN C1203 GLN ** C1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 GLN ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.076440 restraints weight = 284095.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.077948 restraints weight = 189764.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.078879 restraints weight = 148759.682| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 96545 Z= 0.341 Angle : 0.731 15.739 131045 Z= 0.374 Chirality : 0.044 0.378 14580 Planarity : 0.004 0.074 17000 Dihedral : 5.415 37.252 12850 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.39 % Allowed : 18.57 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.04 % Twisted Proline : 1.22 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.08), residues: 11795 helix: 1.60 (0.07), residues: 5285 sheet: -0.95 (0.13), residues: 1765 loop : -1.55 (0.09), residues: 4745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1308 HIS 0.008 0.002 HIS E1891 PHE 0.036 0.002 PHE D 289 TYR 0.028 0.002 TYR B1136 ARG 0.017 0.001 ARG B1679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29746.69 seconds wall clock time: 520 minutes 1.15 seconds (31201.15 seconds total)