Starting phenix.real_space_refine on Sun Jul 21 02:05:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgq_31975/07_2024/7vgq_31975_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgq_31975/07_2024/7vgq_31975.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/7vgq_31975/07_2024/7vgq_31975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgq_31975/07_2024/7vgq_31975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgq_31975/07_2024/7vgq_31975_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgq_31975/07_2024/7vgq_31975_neut.cif" } 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= 0.001 sd= 0.017 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 96 5.16 5 C 8398 2.51 5 N 2202 2.21 5 O 2458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A ARG 1169": "NH1" <-> "NH2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "A ARG 1473": "NH1" <-> "NH2" Residue "A ARG 1479": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1591": "NH1" <-> "NH2" Residue "A ARG 1631": "NH1" <-> "NH2" Residue "A TYR 1682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ARG 1741": "NH1" <-> "NH2" Residue "A ARG 1796": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13156 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1612, 12749 Classifications: {'peptide': 1612} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 46, 'TRANS': 1565} Chain breaks: 14 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Chain: "B" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12817 SG CYS B 41 56.193 81.865 17.896 1.00 4.57 S ATOM 12823 SG CYS B 42 59.837 81.536 16.998 1.00 3.86 S ATOM 12957 SG CYS B 58 57.974 82.935 13.980 1.00 12.05 S ATOM 12982 SG CYS B 61 56.989 79.384 15.195 1.00 8.30 S ATOM 13072 SG CYS B 72 47.604 82.865 20.009 1.00 13.30 S ATOM 13096 SG CYS B 75 46.615 86.667 22.432 1.00 11.61 S Time building chain proxies: 10.40, per 1000 atoms: 0.79 Number of scatterers: 13156 At special positions: 0 Unit cell: (115.2, 118.4, 126.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 96 16.00 O 2458 8.00 N 2202 7.00 C 8398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1650 " - pdb=" SG CYS A1664 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.04 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: 5.18 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 41 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " Number of angles added : 6 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3166 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 11 sheets defined 45.5% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 4.189A pdb=" N LYS A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.917A pdb=" N LYS A 26 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 22 through 27' Processing helix chain 'A' and resid 34 through 39 removed outlier: 4.007A pdb=" N LEU A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.574A pdb=" N SER A 48 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 112 through 125 removed outlier: 4.852A pdb=" N ALA A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.673A pdb=" N ARG A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.720A pdb=" N LEU A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.624A pdb=" N LEU A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.071A pdb=" N SER A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 250 removed outlier: 3.554A pdb=" N LYS A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 removed outlier: 4.860A pdb=" N SER A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 4.270A pdb=" N ASN A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.826A pdb=" N ILE A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.782A pdb=" N LYS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 366 removed outlier: 4.531A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.513A pdb=" N ILE A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 451 removed outlier: 4.111A pdb=" N ILE A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.636A pdb=" N MET A 478 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.850A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.978A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 595 removed outlier: 4.344A pdb=" N CYS A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 599 Processing helix chain 'A' and resid 602 through 622 removed outlier: 3.564A pdb=" N ASP A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Proline residue: A 611 - end of helix removed outlier: 3.542A pdb=" N ARG A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 634 removed outlier: 4.406A pdb=" N LEU A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.991A pdb=" N ARG A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.733A pdb=" N ARG A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.869A pdb=" N LEU A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 706 " --> pdb=" O CYS A 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 706' Processing helix chain 'A' and resid 716 through 730 removed outlier: 3.689A pdb=" N GLU A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Proline residue: A 727 - end of helix removed outlier: 3.751A pdb=" N LYS A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 760 removed outlier: 3.665A pdb=" N ILE A 751 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 760 " --> pdb=" O LEU A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.691A pdb=" N ASN A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 787 " --> pdb=" O CYS A 783 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 852 removed outlier: 4.348A pdb=" N VAL A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 852 " --> pdb=" O MET A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 874 removed outlier: 4.038A pdb=" N THR A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 894 removed outlier: 3.655A pdb=" N SER A 891 " --> pdb=" O GLN A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 920 removed outlier: 4.092A pdb=" N SER A 904 " --> pdb=" O GLU A 900 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A 907 " --> pdb=" O GLU A 903 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 Processing helix chain 'A' and resid 961 through 970 Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 982 through 990 removed outlier: 3.663A pdb=" N ALA A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1021 removed outlier: 4.062A pdb=" N THR A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A1017 " --> pdb=" O ASN A1013 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A1018 " --> pdb=" O LEU A1014 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A1021 " --> pdb=" O SER A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1035 Processing helix chain 'A' and resid 1079 through 1083 Processing helix chain 'A' and resid 1090 through 1094 removed outlier: 3.999A pdb=" N ASN A1093 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A1094 " --> pdb=" O LEU A1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1090 through 1094' Processing helix chain 'A' and resid 1135 through 1153 removed outlier: 3.670A pdb=" N LEU A1140 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL A1145 " --> pdb=" O MET A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1179 removed outlier: 3.939A pdb=" N PHE A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET A1176 " --> pdb=" O CYS A1172 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A1179 " --> pdb=" O LYS A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1206 removed outlier: 3.690A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1226 Processing helix chain 'A' and resid 1227 through 1233 removed outlier: 3.729A pdb=" N HIS A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1244 removed outlier: 4.029A pdb=" N GLU A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1271 Processing helix chain 'A' and resid 1295 through 1299 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 3.743A pdb=" N THR A1306 " --> pdb=" O TYR A1302 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU A1307 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A1314 " --> pdb=" O LEU A1310 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A1315 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A1316 " --> pdb=" O TYR A1312 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A1317 " --> pdb=" O ALA A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 3.694A pdb=" N ILE A1355 " --> pdb=" O TRP A1351 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A1357 " --> pdb=" O GLU A1353 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A1360 " --> pdb=" O CYS A1356 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A1362 " --> pdb=" O HIS A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1366 No H-bonds generated for 'chain 'A' and resid 1364 through 1366' Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 4.494A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A1400 " --> pdb=" O LEU A1396 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A1401 " --> pdb=" O THR A1397 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS A1405 " --> pdb=" O SER A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1427 removed outlier: 4.048A pdb=" N ILE A1419 " --> pdb=" O LEU A1415 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP A1420 " --> pdb=" O SER A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1449 removed outlier: 3.609A pdb=" N SER A1440 " --> pdb=" O VAL A1436 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS A1441 " --> pdb=" O ALA A1437 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A1442 " --> pdb=" O ARG A1438 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN A1444 " --> pdb=" O SER A1440 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A1447 " --> pdb=" O VAL A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1485 removed outlier: 3.703A pdb=" N ARG A1476 " --> pdb=" O SER A1472 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A1477 " --> pdb=" O ARG A1473 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN A1478 " --> pdb=" O GLY A1474 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A1479 " --> pdb=" O TYR A1475 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A1483 " --> pdb=" O ARG A1479 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A1484 " --> pdb=" O LYS A1480 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A1485 " --> pdb=" O ILE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1506 removed outlier: 4.048A pdb=" N ASN A1503 " --> pdb=" O ARG A1499 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A1504 " --> pdb=" O LYS A1500 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A1506 " --> pdb=" O PHE A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1520 removed outlier: 4.313A pdb=" N GLY A1520 " --> pdb=" O ILE A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1535 removed outlier: 4.303A pdb=" N GLN A1532 " --> pdb=" O THR A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 4.301A pdb=" N VAL A1541 " --> pdb=" O SER A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1590 removed outlier: 3.874A pdb=" N SER A1587 " --> pdb=" O LYS A1583 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS A1588 " --> pdb=" O THR A1584 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1617 Processing helix chain 'A' and resid 1618 through 1622 Processing helix chain 'A' and resid 1640 through 1645 Processing helix chain 'A' and resid 1677 through 1693 removed outlier: 4.082A pdb=" N ASP A1681 " --> pdb=" O PRO A1677 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1750 removed outlier: 3.706A pdb=" N LEU A1747 " --> pdb=" O ASN A1743 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1793 removed outlier: 3.929A pdb=" N LEU A1793 " --> pdb=" O ILE A1789 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 removed outlier: 4.201A pdb=" N GLN B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET B 65 " --> pdb=" O CYS B 61 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 59 through 67' Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.809A pdb=" N LEU A 98 " --> pdb=" O THR A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 459 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534 removed outlier: 3.742A pdb=" N TYR A 545 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 533 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 558 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 559 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 566 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AA6, first strand: chain 'A' and resid 1236 through 1237 removed outlier: 3.597A pdb=" N VAL A1236 " --> pdb=" O ILE A1284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1323 through 1326 removed outlier: 3.976A pdb=" N ILE A1332 " --> pdb=" O TYR A1325 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1548 through 1549 removed outlier: 4.108A pdb=" N ARG A1548 " --> pdb=" O TYR A1663 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1630 through 1631 removed outlier: 3.524A pdb=" N VAL A1630 " --> pdb=" O LEU A1638 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1716 through 1718 Processing sheet with id=AB2, first strand: chain 'B' and resid 49 through 51 360 hydrogen bonds defined for protein. 1011 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: 4.95 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3632 1.33 - 1.46: 2728 1.46 - 1.58: 6887 1.58 - 1.70: 0 1.70 - 1.82: 137 Bond restraints: 13384 Sorted by residual: bond pdb=" CA ASP A1470 " pdb=" CB ASP A1470 " ideal model delta sigma weight residual 1.531 1.432 0.099 3.28e-02 9.30e+02 9.13e+00 bond pdb=" CG LEU A 613 " pdb=" CD1 LEU A 613 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.68e+00 bond pdb=" CB ASN A 698 " pdb=" CG ASN A 698 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.44e+00 bond pdb=" N ILE A 396 " pdb=" CA ILE A 396 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.14e+00 bond pdb=" CG LEU A 696 " pdb=" CD2 LEU A 696 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.89e+00 ... (remaining 13379 not shown) Histogram of bond angle deviations from ideal: 95.88 - 103.54: 138 103.54 - 111.19: 4906 111.19 - 118.85: 5814 118.85 - 126.51: 7045 126.51 - 134.16: 150 Bond angle restraints: 18053 Sorted by residual: angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 109.34 133.23 -23.89 2.08e+00 2.31e-01 1.32e+02 angle pdb=" N ILE A 958 " pdb=" CA ILE A 958 " pdb=" C ILE A 958 " ideal model delta sigma weight residual 110.62 100.04 10.58 1.02e+00 9.61e-01 1.08e+02 angle pdb=" C ASP A 971 " pdb=" N PRO A 972 " pdb=" CA PRO A 972 " ideal model delta sigma weight residual 119.28 128.18 -8.90 1.10e+00 8.26e-01 6.54e+01 angle pdb=" C LYS A 401 " pdb=" N LEU A 402 " pdb=" CA LEU A 402 " ideal model delta sigma weight residual 120.44 130.18 -9.74 1.30e+00 5.92e-01 5.61e+01 angle pdb=" N VAL A 962 " pdb=" CA VAL A 962 " pdb=" C VAL A 962 " ideal model delta sigma weight residual 110.62 116.55 -5.93 1.02e+00 9.61e-01 3.38e+01 ... (remaining 18048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 7462 16.43 - 32.87: 578 32.87 - 49.30: 96 49.30 - 65.73: 6 65.73 - 82.17: 7 Dihedral angle restraints: 8149 sinusoidal: 3285 harmonic: 4864 Sorted by residual: dihedral pdb=" CA LEU A1693 " pdb=" C LEU A1693 " pdb=" N GLY A1694 " pdb=" CA GLY A1694 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA SER A1440 " pdb=" C SER A1440 " pdb=" N LYS A1441 " pdb=" CA LYS A1441 " ideal model delta harmonic sigma weight residual 180.00 151.78 28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA HIS A1271 " pdb=" C HIS A1271 " pdb=" N GLN A1272 " pdb=" CA GLN A1272 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 8146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1950 0.131 - 0.263: 114 0.263 - 0.394: 9 0.394 - 0.526: 1 0.526 - 0.657: 1 Chirality restraints: 2075 Sorted by residual: chirality pdb=" CA ILE A 396 " pdb=" N ILE A 396 " pdb=" C ILE A 396 " pdb=" CB ILE A 396 " both_signs ideal model delta sigma weight residual False 2.43 1.78 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CB ILE A1332 " pdb=" CA ILE A1332 " pdb=" CG1 ILE A1332 " pdb=" CG2 ILE A1332 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CA VAL A 389 " pdb=" N VAL A 389 " pdb=" C VAL A 389 " pdb=" CB VAL A 389 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 2072 not shown) Planarity restraints: 2279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 395 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C ASP A 395 " 0.065 2.00e-02 2.50e+03 pdb=" O ASP A 395 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 396 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 610 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.87e+00 pdb=" N PRO A 611 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1193 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C GLY A1193 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY A1193 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO A1194 " -0.017 2.00e-02 2.50e+03 ... (remaining 2276 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1902 2.75 - 3.29: 12364 3.29 - 3.82: 19643 3.82 - 4.36: 22158 4.36 - 4.90: 37373 Nonbonded interactions: 93440 Sorted by model distance: nonbonded pdb=" N SER A 479 " pdb=" OE2 GLU A 482 " model vdw 2.211 2.520 nonbonded pdb=" O ILE A 958 " pdb=" N ALA A 960 " model vdw 2.219 2.520 nonbonded pdb=" O LEU A 497 " pdb=" OG SER A 500 " model vdw 2.272 2.440 nonbonded pdb=" O LEU A1668 " pdb=" OG SER A1672 " model vdw 2.281 2.440 nonbonded pdb=" ND2 ASN A 788 " pdb=" OE1 GLU A1209 " model vdw 2.293 2.520 ... (remaining 93435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.680 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 43.060 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.009 0.099 13384 Z= 0.615 Angle : 1.269 23.888 18053 Z= 0.684 Chirality : 0.072 0.657 2075 Planarity : 0.008 0.074 2279 Dihedral : 12.164 82.167 4974 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.87 % Favored : 85.94 % Rotamer: Outliers : 0.74 % Allowed : 7.53 % Favored : 91.73 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -5.44 (0.15), residues: 1629 helix: -3.80 (0.12), residues: 708 sheet: -4.49 (0.38), residues: 77 loop : -3.38 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP B 43 HIS 0.014 0.003 HIS A1231 PHE 0.032 0.004 PHE A 852 TYR 0.031 0.004 TYR A 695 ARG 0.010 0.001 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 302 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.7045 (p0) cc_final: 0.6457 (p0) REVERT: A 361 MET cc_start: 0.7348 (ttp) cc_final: 0.7130 (ttm) REVERT: A 387 MET cc_start: 0.6529 (ttt) cc_final: 0.5872 (ttt) REVERT: A 394 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8078 (tm) REVERT: A 543 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7431 (tt) REVERT: A 900 GLU cc_start: 0.5549 (mt-10) cc_final: 0.4643 (tp30) REVERT: A 989 LYS cc_start: 0.4295 (tmtt) cc_final: 0.3959 (tmtt) REVERT: A 1156 MET cc_start: 0.8253 (mmt) cc_final: 0.7907 (mmt) REVERT: A 1226 SER cc_start: 0.8504 (m) cc_final: 0.7619 (t) REVERT: A 1318 TYR cc_start: 0.7636 (m-80) cc_final: 0.7233 (m-10) REVERT: A 1489 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7225 (ttmm) REVERT: A 1548 ARG cc_start: 0.6797 (mmt90) cc_final: 0.6581 (mmt-90) REVERT: A 1647 ILE cc_start: 0.8353 (tt) cc_final: 0.8113 (mm) outliers start: 11 outliers final: 2 residues processed: 309 average time/residue: 0.2783 time to fit residues: 121.3117 Evaluate side-chains 202 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 971 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 63 ASN A 369 GLN A 384 GLN A 390 ASN A 412 ASN A 499 ASN A 522 ASN A 629 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN A1013 ASN A1111 ASN A1114 ASN A1206 GLN A1296 HIS A1358 HIS A1405 HIS A1665 ASN A1689 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN A1714 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13384 Z= 0.153 Angle : 0.649 10.306 18053 Z= 0.338 Chirality : 0.042 0.193 2075 Planarity : 0.005 0.054 2279 Dihedral : 6.504 51.747 1777 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.09 % Favored : 90.79 % Rotamer: Outliers : 3.49 % Allowed : 11.42 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.35 (0.17), residues: 1629 helix: -2.65 (0.16), residues: 703 sheet: -3.40 (0.51), residues: 66 loop : -3.11 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 116 HIS 0.004 0.001 HIS A1812 PHE 0.028 0.001 PHE A 223 TYR 0.020 0.001 TYR A 782 ARG 0.003 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 234 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 PHE cc_start: 0.7240 (m-80) cc_final: 0.6788 (m-80) REVERT: A 261 THR cc_start: 0.6264 (p) cc_final: 0.5832 (p) REVERT: A 280 ASP cc_start: 0.7024 (p0) cc_final: 0.6533 (p0) REVERT: A 527 GLU cc_start: 0.8062 (pp20) cc_final: 0.7822 (pp20) REVERT: A 591 MET cc_start: 0.8931 (ttp) cc_final: 0.8664 (ptm) REVERT: A 726 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 840 LEU cc_start: 0.8252 (pp) cc_final: 0.7998 (tt) REVERT: A 914 VAL cc_start: 0.8910 (t) cc_final: 0.8555 (p) REVERT: A 989 LYS cc_start: 0.4950 (tmtt) cc_final: 0.4251 (tmtt) REVERT: A 1156 MET cc_start: 0.8175 (mmt) cc_final: 0.7925 (mmt) REVERT: A 1174 MET cc_start: 0.8030 (ttp) cc_final: 0.7755 (mtt) REVERT: A 1490 GLU cc_start: 0.7830 (tp30) cc_final: 0.7576 (tp30) REVERT: A 1688 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8151 (m) outliers start: 52 outliers final: 20 residues processed: 274 average time/residue: 0.2409 time to fit residues: 97.5254 Evaluate side-chains 216 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1808 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 120 optimal weight: 0.0670 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN A1358 HIS ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN A1714 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13384 Z= 0.180 Angle : 0.622 10.837 18053 Z= 0.320 Chirality : 0.043 0.187 2075 Planarity : 0.004 0.050 2279 Dihedral : 5.828 52.066 1772 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.01 % Favored : 89.93 % Rotamer: Outliers : 4.44 % Allowed : 12.90 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.81 (0.18), residues: 1629 helix: -2.03 (0.17), residues: 707 sheet: -3.34 (0.48), residues: 84 loop : -2.93 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.004 0.001 HIS A1358 PHE 0.028 0.002 PHE A 731 TYR 0.014 0.001 TYR A 867 ARG 0.004 0.000 ARG A1741 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 208 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.7836 (p0) cc_final: 0.7560 (p0) REVERT: A 148 ASN cc_start: 0.8028 (m-40) cc_final: 0.7685 (t0) REVERT: A 191 LEU cc_start: 0.8221 (mm) cc_final: 0.7858 (mt) REVERT: A 280 ASP cc_start: 0.7088 (p0) cc_final: 0.6410 (p0) REVERT: A 543 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8001 (mt) REVERT: A 731 PHE cc_start: 0.7220 (t80) cc_final: 0.7000 (t80) REVERT: A 914 VAL cc_start: 0.8922 (t) cc_final: 0.8642 (p) REVERT: A 989 LYS cc_start: 0.4923 (tmtt) cc_final: 0.4480 (tmtt) REVERT: A 1156 MET cc_start: 0.8020 (mmt) cc_final: 0.7767 (mmt) REVERT: A 1274 MET cc_start: 0.6758 (mmp) cc_final: 0.6473 (mmt) REVERT: A 1490 GLU cc_start: 0.7983 (tp30) cc_final: 0.7631 (tp30) REVERT: A 1586 GLN cc_start: 0.7052 (pp30) cc_final: 0.6838 (pp30) REVERT: A 1625 MET cc_start: 0.7832 (ttt) cc_final: 0.7589 (ttt) REVERT: A 1688 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8164 (m) REVERT: A 1714 ASN cc_start: 0.6609 (t0) cc_final: 0.6392 (t0) outliers start: 66 outliers final: 38 residues processed: 257 average time/residue: 0.2451 time to fit residues: 93.0191 Evaluate side-chains 226 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 186 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1530 PHE Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1561 VAL Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain B residue 74 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 159 optimal weight: 0.1980 chunk 78 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN A1358 HIS ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13384 Z= 0.258 Angle : 0.655 8.700 18053 Z= 0.335 Chirality : 0.044 0.164 2075 Planarity : 0.004 0.043 2279 Dihedral : 5.645 29.291 1770 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.37 % Favored : 89.56 % Rotamer: Outliers : 5.65 % Allowed : 13.71 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.41 (0.19), residues: 1629 helix: -1.62 (0.18), residues: 704 sheet: -3.20 (0.49), residues: 84 loop : -2.79 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1192 HIS 0.005 0.001 HIS A1231 PHE 0.030 0.002 PHE A 43 TYR 0.016 0.001 TYR A 214 ARG 0.003 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 201 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7059 (tt) REVERT: A 96 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7585 (mmtp) REVERT: A 108 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7611 (p0) REVERT: A 227 LYS cc_start: 0.7914 (mmtm) cc_final: 0.7655 (mmtp) REVERT: A 280 ASP cc_start: 0.7198 (p0) cc_final: 0.6473 (p0) REVERT: A 527 GLU cc_start: 0.7972 (pp20) cc_final: 0.7768 (pp20) REVERT: A 543 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7246 (tt) REVERT: A 651 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6772 (pt) REVERT: A 914 VAL cc_start: 0.8947 (t) cc_final: 0.8570 (p) REVERT: A 989 LYS cc_start: 0.4884 (tmtt) cc_final: 0.4340 (tmtt) REVERT: A 1156 MET cc_start: 0.8071 (mmt) cc_final: 0.7788 (mmt) REVERT: A 1274 MET cc_start: 0.6533 (mmp) cc_final: 0.6255 (mmt) REVERT: A 1490 GLU cc_start: 0.8093 (tp30) cc_final: 0.7782 (tp30) outliers start: 84 outliers final: 54 residues processed: 261 average time/residue: 0.2254 time to fit residues: 88.7788 Evaluate side-chains 244 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 186 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1561 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1804 LYS Chi-restraints excluded: chain A residue 1808 CYS Chi-restraints excluded: chain B residue 47 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 81 optimal weight: 7.9990 chunk 143 optimal weight: 0.4980 chunk 40 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN A1358 HIS ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13384 Z= 0.199 Angle : 0.617 8.546 18053 Z= 0.315 Chirality : 0.043 0.168 2075 Planarity : 0.004 0.042 2279 Dihedral : 5.369 27.765 1770 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.94 % Favored : 89.99 % Rotamer: Outliers : 5.44 % Allowed : 15.12 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.13 (0.20), residues: 1629 helix: -1.36 (0.19), residues: 710 sheet: -3.16 (0.49), residues: 85 loop : -2.64 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1192 HIS 0.004 0.001 HIS A1358 PHE 0.030 0.002 PHE A 731 TYR 0.013 0.001 TYR A 214 ARG 0.006 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 198 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7937 (mmtm) cc_final: 0.7563 (mmtp) REVERT: A 280 ASP cc_start: 0.7168 (p0) cc_final: 0.6440 (p0) REVERT: A 353 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7147 (pp) REVERT: A 543 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7863 (mt) REVERT: A 651 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6716 (pt) REVERT: A 778 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 914 VAL cc_start: 0.8952 (t) cc_final: 0.8567 (p) REVERT: A 989 LYS cc_start: 0.4820 (tmtt) cc_final: 0.4211 (tmtt) REVERT: A 1490 GLU cc_start: 0.8142 (tp30) cc_final: 0.7857 (tp30) REVERT: A 1530 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6852 (t80) REVERT: A 1774 ASP cc_start: 0.7250 (m-30) cc_final: 0.6938 (p0) outliers start: 81 outliers final: 56 residues processed: 255 average time/residue: 0.2205 time to fit residues: 85.1703 Evaluate side-chains 251 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 191 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1530 PHE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1561 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1624 SER Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1804 LYS Chi-restraints excluded: chain A residue 1808 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A1013 ASN A1358 HIS ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13384 Z= 0.241 Angle : 0.639 8.428 18053 Z= 0.326 Chirality : 0.044 0.179 2075 Planarity : 0.004 0.040 2279 Dihedral : 5.377 28.288 1770 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.62 % Favored : 89.32 % Rotamer: Outliers : 5.11 % Allowed : 16.47 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.95 (0.20), residues: 1629 helix: -1.18 (0.19), residues: 718 sheet: -3.04 (0.49), residues: 85 loop : -2.60 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1192 HIS 0.004 0.001 HIS A1231 PHE 0.032 0.002 PHE A 731 TYR 0.014 0.001 TYR A 695 ARG 0.003 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 190 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.5812 (pt0) cc_final: 0.5521 (pt0) REVERT: A 227 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7535 (mmtp) REVERT: A 280 ASP cc_start: 0.7221 (p0) cc_final: 0.6821 (p0) REVERT: A 387 MET cc_start: 0.5980 (ttt) cc_final: 0.5756 (ttt) REVERT: A 543 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7283 (tt) REVERT: A 651 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6804 (pt) REVERT: A 914 VAL cc_start: 0.8909 (t) cc_final: 0.8577 (p) REVERT: A 989 LYS cc_start: 0.5020 (tmtt) cc_final: 0.4230 (tmtt) REVERT: A 1156 MET cc_start: 0.8183 (mmt) cc_final: 0.7881 (mmt) REVERT: A 1274 MET cc_start: 0.6450 (mmp) cc_final: 0.6139 (mmt) REVERT: A 1490 GLU cc_start: 0.8178 (tp30) cc_final: 0.7897 (tp30) REVERT: A 1530 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 1774 ASP cc_start: 0.7105 (m-30) cc_final: 0.6904 (p0) outliers start: 76 outliers final: 62 residues processed: 242 average time/residue: 0.2262 time to fit residues: 83.1637 Evaluate side-chains 250 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 185 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1530 PHE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1561 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1804 LYS Chi-restraints excluded: chain A residue 1808 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN A1128 ASN A1358 HIS ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13384 Z= 0.270 Angle : 0.657 8.157 18053 Z= 0.336 Chirality : 0.044 0.171 2075 Planarity : 0.004 0.040 2279 Dihedral : 5.434 28.539 1770 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.99 % Favored : 88.95 % Rotamer: Outliers : 5.44 % Allowed : 16.94 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.85 (0.20), residues: 1629 helix: -1.04 (0.19), residues: 713 sheet: -2.84 (0.51), residues: 78 loop : -2.62 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1192 HIS 0.005 0.001 HIS A1189 PHE 0.032 0.002 PHE A 731 TYR 0.017 0.002 TYR A 214 ARG 0.003 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 190 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7969 (mmtm) cc_final: 0.7410 (mmtp) REVERT: A 280 ASP cc_start: 0.7237 (p0) cc_final: 0.6840 (p0) REVERT: A 353 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7161 (pp) REVERT: A 543 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7308 (tt) REVERT: A 628 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8238 (p0) REVERT: A 651 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6969 (pt) REVERT: A 798 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6752 (tt) REVERT: A 839 LYS cc_start: 0.7853 (tptt) cc_final: 0.6604 (tmmt) REVERT: A 914 VAL cc_start: 0.8947 (t) cc_final: 0.8593 (p) REVERT: A 989 LYS cc_start: 0.5130 (tmtt) cc_final: 0.4256 (tmtt) REVERT: A 1100 ASP cc_start: 0.6167 (t0) cc_final: 0.5720 (t0) REVERT: A 1156 MET cc_start: 0.8057 (mmt) cc_final: 0.7713 (mmt) REVERT: A 1274 MET cc_start: 0.6472 (mmp) cc_final: 0.6165 (mmt) REVERT: A 1490 GLU cc_start: 0.8183 (tp30) cc_final: 0.7919 (tp30) REVERT: A 1774 ASP cc_start: 0.7279 (m-30) cc_final: 0.6987 (p0) outliers start: 81 outliers final: 66 residues processed: 247 average time/residue: 0.2373 time to fit residues: 88.5155 Evaluate side-chains 259 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 188 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1561 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1804 LYS Chi-restraints excluded: chain A residue 1808 CYS Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.0070 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1358 HIS ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13384 Z= 0.147 Angle : 0.596 10.488 18053 Z= 0.298 Chirality : 0.041 0.176 2075 Planarity : 0.003 0.041 2279 Dihedral : 4.965 26.600 1770 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.35 % Favored : 91.59 % Rotamer: Outliers : 3.97 % Allowed : 18.35 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.58 (0.21), residues: 1629 helix: -0.76 (0.20), residues: 717 sheet: -2.76 (0.54), residues: 77 loop : -2.53 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.005 0.001 HIS A1358 PHE 0.034 0.001 PHE A 731 TYR 0.018 0.001 TYR A 214 ARG 0.003 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 201 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8363 (tt) cc_final: 0.8087 (mt) REVERT: A 227 LYS cc_start: 0.7614 (mmtm) cc_final: 0.7084 (mmtp) REVERT: A 280 ASP cc_start: 0.6828 (p0) cc_final: 0.6471 (p0) REVERT: A 353 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7142 (pp) REVERT: A 628 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7886 (p0) REVERT: A 651 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6575 (pt) REVERT: A 798 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6660 (tt) REVERT: A 914 VAL cc_start: 0.8904 (t) cc_final: 0.8539 (p) REVERT: A 989 LYS cc_start: 0.4794 (tmtt) cc_final: 0.4251 (tmtt) REVERT: A 1100 ASP cc_start: 0.6062 (t0) cc_final: 0.5625 (t0) REVERT: A 1156 MET cc_start: 0.7995 (mmt) cc_final: 0.7707 (mmt) REVERT: A 1192 TRP cc_start: 0.8853 (t-100) cc_final: 0.8482 (t-100) REVERT: A 1274 MET cc_start: 0.6583 (mmp) cc_final: 0.6303 (mmt) REVERT: A 1490 GLU cc_start: 0.8194 (tp30) cc_final: 0.7939 (tp30) REVERT: A 1530 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6965 (t80) outliers start: 59 outliers final: 45 residues processed: 243 average time/residue: 0.2261 time to fit residues: 83.3518 Evaluate side-chains 236 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 186 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1530 PHE Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1808 CYS Chi-restraints excluded: chain B residue 47 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6993 > 50: distance: 111 - 120: 33.718 distance: 120 - 121: 16.338 distance: 121 - 122: 45.363 distance: 121 - 124: 56.729 distance: 122 - 123: 50.013 distance: 122 - 128: 27.904 distance: 124 - 125: 40.032 distance: 125 - 126: 48.170 distance: 125 - 127: 40.458 distance: 128 - 129: 35.914 distance: 129 - 130: 42.173 distance: 129 - 132: 35.961 distance: 130 - 131: 40.575 distance: 130 - 136: 6.576 distance: 132 - 133: 43.410 distance: 133 - 134: 66.873 distance: 133 - 135: 4.198 distance: 136 - 137: 51.990 distance: 137 - 138: 54.216 distance: 137 - 140: 55.084 distance: 138 - 139: 69.666 distance: 138 - 142: 20.432 distance: 140 - 141: 55.029 distance: 142 - 143: 33.063 distance: 143 - 144: 18.107 distance: 143 - 146: 20.516 distance: 144 - 145: 55.504 distance: 144 - 153: 32.118 distance: 146 - 147: 40.766 distance: 147 - 148: 65.099 distance: 147 - 149: 43.075 distance: 148 - 150: 32.964 distance: 149 - 151: 54.756 distance: 150 - 152: 37.410 distance: 151 - 152: 52.598 distance: 153 - 154: 33.193 distance: 154 - 155: 39.956 distance: 154 - 157: 47.518 distance: 155 - 156: 68.016 distance: 155 - 165: 56.898 distance: 157 - 158: 29.860 distance: 158 - 159: 31.323 distance: 158 - 160: 27.878 distance: 159 - 161: 41.911 distance: 160 - 162: 17.131 distance: 161 - 163: 31.261 distance: 162 - 163: 36.449 distance: 163 - 164: 38.470 distance: 165 - 166: 57.830 distance: 166 - 169: 41.405 distance: 167 - 168: 69.046 distance: 167 - 171: 40.485 distance: 169 - 170: 56.437 distance: 171 - 172: 39.129 distance: 172 - 173: 30.887 distance: 172 - 175: 66.941 distance: 173 - 174: 49.276 distance: 173 - 180: 50.648 distance: 175 - 176: 59.163 distance: 176 - 177: 14.738 distance: 177 - 178: 55.815 distance: 177 - 179: 41.462 distance: 180 - 181: 6.051 distance: 181 - 182: 39.239 distance: 181 - 184: 49.251 distance: 182 - 183: 39.898 distance: 182 - 188: 30.373 distance: 184 - 185: 41.403 distance: 185 - 186: 40.321 distance: 185 - 187: 18.666 distance: 188 - 189: 9.050 distance: 189 - 190: 36.523 distance: 189 - 192: 53.531 distance: 190 - 191: 46.579 distance: 190 - 194: 52.177 distance: 194 - 195: 5.297 distance: 194 - 200: 7.461 distance: 195 - 196: 70.577 distance: 195 - 198: 40.487 distance: 196 - 197: 11.708 distance: 196 - 201: 33.636 distance: 198 - 199: 13.709 distance: 199 - 200: 41.991