Starting phenix.real_space_refine on Fri Feb 23 13:37:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/02_2024/7z88_14546_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/02_2024/7z88_14546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/02_2024/7z88_14546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/02_2024/7z88_14546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/02_2024/7z88_14546_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/02_2024/7z88_14546_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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: 7 Type Number sf(0) Gaussians P 52 5.49 5 S 227 5.16 5 Cl 1 4.86 5 C 24682 2.51 5 N 6575 2.21 5 O 7216 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 607": "OD1" <-> "OD2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A GLU 889": "OE1" <-> "OE2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ASP 1019": "OD1" <-> "OD2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A TYR 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A GLU 1088": "OE1" <-> "OE2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A ARG 1152": "NH1" <-> "NH2" Residue "A ARG 1155": "NH1" <-> "NH2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1420": "NH1" <-> "NH2" Residue "A GLU 1526": "OE1" <-> "OE2" Residue "A ASP 1588": "OD1" <-> "OD2" Residue "A ARG 1608": "NH1" <-> "NH2" Residue "A PHE 1699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1709": "OE1" <-> "OE2" Residue "A ARG 1711": "NH1" <-> "NH2" Residue "A ARG 1712": "NH1" <-> "NH2" Residue "A ARG 1727": "NH1" <-> "NH2" Residue "A PHE 1736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1787": "NH1" <-> "NH2" Residue "A GLU 1799": "OE1" <-> "OE2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1822": "NH1" <-> "NH2" Residue "A ARG 1883": "NH1" <-> "NH2" Residue "A GLU 1910": "OE1" <-> "OE2" Residue "A TYR 1920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A TYR 1962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2143": "NH1" <-> "NH2" Residue "A PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A TYR 2184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2214": "NH1" <-> "NH2" Residue "A ARG 2228": "NH1" <-> "NH2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A PHE 2257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A ARG 2377": "NH1" <-> "NH2" Residue "A PHE 2384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2406": "OE1" <-> "OE2" Residue "A TYR 2412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2427": "NH1" <-> "NH2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A ARG 2452": "NH1" <-> "NH2" Residue "A ASP 2482": "OD1" <-> "OD2" Residue "A ARG 2530": "NH1" <-> "NH2" Residue "A ARG 2800": "NH1" <-> "NH2" Residue "A PHE 2809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2940": "NH1" <-> "NH2" Residue "A GLU 2990": "OE1" <-> "OE2" Residue "A GLU 2995": "OE1" <-> "OE2" Residue "A TYR 3002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3012": "OE1" <-> "OE2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A PHE 3144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3159": "NH1" <-> "NH2" Residue "A ARG 3232": "NH1" <-> "NH2" Residue "A ARG 3247": "NH1" <-> "NH2" Residue "A TYR 3280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3287": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3344": "OE1" <-> "OE2" Residue "A GLU 3361": "OE1" <-> "OE2" Residue "A PHE 3382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3411": "OD1" <-> "OD2" Residue "A ARG 3467": "NH1" <-> "NH2" Residue "A ARG 3474": "NH1" <-> "NH2" Residue "A TYR 3531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3570": "OD1" <-> "OD2" Residue "A ARG 3593": "NH1" <-> "NH2" Residue "A GLU 3611": "OE1" <-> "OE2" Residue "A ARG 3629": "NH1" <-> "NH2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A GLU 3700": "OE1" <-> "OE2" Residue "A TYR 3715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3718": "NH1" <-> "NH2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A ARG 3763": "NH1" <-> "NH2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A ARG 3889": "NH1" <-> "NH2" Residue "A ARG 3923": "NH1" <-> "NH2" Residue "A GLU 3957": "OE1" <-> "OE2" Residue "A PHE 3961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A TYR 3981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4003": "OD1" <-> "OD2" Residue "A ASP 4113": "OD1" <-> "OD2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ASP 266": "OD1" <-> "OD2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "C ARG 489": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C GLU 552": "OE1" <-> "OE2" Residue "C GLU 645": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38754 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 28443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3599, 28443 Classifications: {'peptide': 3599} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PCIS': 1, 'PTRANS': 153, 'TRANS': 3444} Chain breaks: 21 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 33, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 258 Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3937 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 5274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5274 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 27, 'TRANS': 633} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "E" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 540 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'1IX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.36, per 1000 atoms: 0.53 Number of scatterers: 38754 At special positions: 0 Unit cell: (131.704, 179.952, 225.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 227 16.00 P 52 15.00 F 1 9.00 O 7216 8.00 N 6575 7.00 C 24682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.60 Conformation dependent library (CDL) restraints added in 7.5 seconds 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 222 helices and 11 sheets defined 53.6% alpha, 2.9% beta 14 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 25.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.799A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.919A pdb=" N GLU A 94 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 4.346A pdb=" N VAL A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 124 No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 126 through 137 removed outlier: 4.858A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 removed outlier: 4.829A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 183 Processing helix chain 'A' and resid 193 through 208 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 267 through 281 removed outlier: 6.234A pdb=" N SER A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 removed outlier: 3.815A pdb=" N LEU A 287 " --> pdb=" O THR A 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.891A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 359 through 374 removed outlier: 4.160A pdb=" N ARG A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 383 No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 387 through 396 Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 432 through 444 removed outlier: 3.711A pdb=" N MET A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.914A pdb=" N ALA A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 490 removed outlier: 4.479A pdb=" N CYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 535 removed outlier: 3.583A pdb=" N LEU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 Processing helix chain 'A' and resid 617 through 633 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 646 through 659 Processing helix chain 'A' and resid 666 through 679 Processing helix chain 'A' and resid 701 through 720 removed outlier: 4.352A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLN A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 removed outlier: 3.545A pdb=" N SER A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.593A pdb=" N ALA A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 778 Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 829 through 836 Processing helix chain 'A' and resid 848 through 861 Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 908 through 919 Proline residue: A 912 - end of helix removed outlier: 3.667A pdb=" N LEU A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 944 Processing helix chain 'A' and resid 959 through 973 removed outlier: 3.714A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 4.039A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 995 removed outlier: 4.495A pdb=" N TYR A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 998 through 1000 No H-bonds generated for 'chain 'A' and resid 998 through 1000' Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1023 through 1043 removed outlier: 3.734A pdb=" N PHE A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1075 through 1085 Processing helix chain 'A' and resid 1102 through 1115 removed outlier: 3.994A pdb=" N VAL A1105 " --> pdb=" O GLU A1102 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A1106 " --> pdb=" O ALA A1103 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A1114 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1121 No H-bonds generated for 'chain 'A' and resid 1119 through 1121' Processing helix chain 'A' and resid 1123 through 1144 removed outlier: 3.925A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER A1144 " --> pdb=" O LYS A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1174 Processing helix chain 'A' and resid 1181 through 1197 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1204 through 1214 removed outlier: 4.033A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.680A pdb=" N LEU A1220 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A1221 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A1223 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1271 Processing helix chain 'A' and resid 1278 through 1281 No H-bonds generated for 'chain 'A' and resid 1278 through 1281' Processing helix chain 'A' and resid 1284 through 1286 No H-bonds generated for 'chain 'A' and resid 1284 through 1286' Processing helix chain 'A' and resid 1290 through 1299 Processing helix chain 'A' and resid 1326 through 1349 removed outlier: 3.993A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1358 No H-bonds generated for 'chain 'A' and resid 1356 through 1358' Processing helix chain 'A' and resid 1368 through 1376 Processing helix chain 'A' and resid 1379 through 1382 removed outlier: 3.508A pdb=" N ILE A1382 " --> pdb=" O PRO A1379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1379 through 1382' Processing helix chain 'A' and resid 1390 through 1408 Proline residue: A1396 - end of helix removed outlier: 3.740A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1422 removed outlier: 4.186A pdb=" N GLU A1421 " --> pdb=" O THR A1417 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1441 through 1460 Processing helix chain 'A' and resid 1478 through 1490 Processing helix chain 'A' and resid 1506 through 1521 Processing helix chain 'A' and resid 1525 through 1533 Processing helix chain 'A' and resid 1557 through 1563 removed outlier: 3.747A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1573 removed outlier: 3.529A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1585 removed outlier: 4.270A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1606 Processing helix chain 'A' and resid 1614 through 1624 Processing helix chain 'A' and resid 1641 through 1655 Processing helix chain 'A' and resid 1668 through 1678 removed outlier: 3.877A pdb=" N THR A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1692 Processing helix chain 'A' and resid 1696 through 1698 No H-bonds generated for 'chain 'A' and resid 1696 through 1698' Processing helix chain 'A' and resid 1704 through 1721 Processing helix chain 'A' and resid 1736 through 1752 Processing helix chain 'A' and resid 1756 through 1766 Processing helix chain 'A' and resid 1775 through 1786 Processing helix chain 'A' and resid 1791 through 1806 Processing helix chain 'A' and resid 1813 through 1821 removed outlier: 3.742A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1830 Processing helix chain 'A' and resid 1838 through 1851 removed outlier: 5.121A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1883 Processing helix chain 'A' and resid 1887 through 1890 No H-bonds generated for 'chain 'A' and resid 1887 through 1890' Processing helix chain 'A' and resid 1910 through 1920 Processing helix chain 'A' and resid 1934 through 1952 Processing helix chain 'A' and resid 1961 through 1964 No H-bonds generated for 'chain 'A' and resid 1961 through 1964' Processing helix chain 'A' and resid 1977 through 1981 Processing helix chain 'A' and resid 2038 through 2045 removed outlier: 3.677A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2105 Processing helix chain 'A' and resid 2126 through 2134 Processing helix chain 'A' and resid 2140 through 2152 Processing helix chain 'A' and resid 2154 through 2158 removed outlier: 3.673A pdb=" N ARG A2158 " --> pdb=" O GLU A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2173 Processing helix chain 'A' and resid 2183 through 2195 Processing helix chain 'A' and resid 2206 through 2221 Processing helix chain 'A' and resid 2228 through 2244 Processing helix chain 'A' and resid 2256 through 2260 Processing helix chain 'A' and resid 2271 through 2282 Processing helix chain 'A' and resid 2296 through 2308 removed outlier: 3.913A pdb=" N GLN A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2332 Processing helix chain 'A' and resid 2338 through 2353 removed outlier: 3.794A pdb=" N LEU A2344 " --> pdb=" O SER A2340 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2370 removed outlier: 4.524A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2379 through 2388 Proline residue: A2387 - end of helix Processing helix chain 'A' and resid 2392 through 2404 removed outlier: 3.890A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2418 Processing helix chain 'A' and resid 2420 through 2423 No H-bonds generated for 'chain 'A' and resid 2420 through 2423' Processing helix chain 'A' and resid 2429 through 2441 Processing helix chain 'A' and resid 2443 through 2445 No H-bonds generated for 'chain 'A' and resid 2443 through 2445' Processing helix chain 'A' and resid 2448 through 2461 removed outlier: 3.646A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix removed outlier: 4.515A pdb=" N PHE A2461 " --> pdb=" O PRO A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2467 through 2482 removed outlier: 3.948A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2507 removed outlier: 4.897A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2517 through 2526 Processing helix chain 'A' and resid 2537 through 2545 removed outlier: 3.845A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2554 through 2564 Processing helix chain 'A' and resid 2791 through 2799 removed outlier: 3.525A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2802 through 2819 Processing helix chain 'A' and resid 2826 through 2846 Processing helix chain 'A' and resid 2852 through 2861 Processing helix chain 'A' and resid 2867 through 2869 No H-bonds generated for 'chain 'A' and resid 2867 through 2869' Processing helix chain 'A' and resid 2873 through 2883 Processing helix chain 'A' and resid 2886 through 2896 Processing helix chain 'A' and resid 2918 through 2932 removed outlier: 4.636A pdb=" N TRP A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2940 Processing helix chain 'A' and resid 2952 through 2961 Processing helix chain 'A' and resid 2967 through 2976 Processing helix chain 'A' and resid 2988 through 3004 removed outlier: 3.828A pdb=" N PHE A2993 " --> pdb=" O ALA A2989 " (cutoff:3.500A) Processing helix chain 'A' and resid 3008 through 3017 Processing helix chain 'A' and resid 3035 through 3055 Proline residue: A3042 - end of helix removed outlier: 3.638A pdb=" N GLY A3055 " --> pdb=" O LEU A3051 " (cutoff:3.500A) Processing helix chain 'A' and resid 3061 through 3068 Processing helix chain 'A' and resid 3073 through 3081 removed outlier: 4.146A pdb=" N ILE A3077 " --> pdb=" O LEU A3073 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU A3078 " --> pdb=" O GLN A3074 " (cutoff:3.500A) Processing helix chain 'A' and resid 3085 through 3093 Processing helix chain 'A' and resid 3096 through 3114 Processing helix chain 'A' and resid 3124 through 3146 removed outlier: 3.986A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL A3132 " --> pdb=" O LYS A3128 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN A3133 " --> pdb=" O LEU A3129 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA A3134 " --> pdb=" O GLN A3130 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A3146 " --> pdb=" O ILE A3142 " (cutoff:3.500A) Processing helix chain 'A' and resid 3149 through 3151 No H-bonds generated for 'chain 'A' and resid 3149 through 3151' Processing helix chain 'A' and resid 3155 through 3166 Processing helix chain 'A' and resid 3176 through 3196 Processing helix chain 'A' and resid 3228 through 3249 Processing helix chain 'A' and resid 3252 through 3263 Processing helix chain 'A' and resid 3270 through 3288 Processing helix chain 'A' and resid 3293 through 3301 Processing helix chain 'A' and resid 3305 through 3308 No H-bonds generated for 'chain 'A' and resid 3305 through 3308' Processing helix chain 'A' and resid 3320 through 3341 Processing helix chain 'A' and resid 3354 through 3361 Processing helix chain 'A' and resid 3373 through 3390 Processing helix chain 'A' and resid 3408 through 3427 Processing helix chain 'A' and resid 3442 through 3455 removed outlier: 4.797A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) Processing helix chain 'A' and resid 3460 through 3462 No H-bonds generated for 'chain 'A' and resid 3460 through 3462' Processing helix chain 'A' and resid 3465 through 3474 Processing helix chain 'A' and resid 3481 through 3488 Processing helix chain 'A' and resid 3496 through 3507 removed outlier: 5.720A pdb=" N SER A3500 " --> pdb=" O SER A3497 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A3503 " --> pdb=" O SER A3500 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A3506 " --> pdb=" O VAL A3503 " (cutoff:3.500A) Processing helix chain 'A' and resid 3511 through 3514 Processing helix chain 'A' and resid 3516 through 3524 removed outlier: 3.825A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3536 through 3539 No H-bonds generated for 'chain 'A' and resid 3536 through 3539' Processing helix chain 'A' and resid 3548 through 3562 Processing helix chain 'A' and resid 3568 through 3578 Processing helix chain 'A' and resid 3581 through 3595 Processing helix chain 'A' and resid 3605 through 3614 removed outlier: 4.382A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3620 through 3626 removed outlier: 4.050A pdb=" N GLY A3624 " --> pdb=" O PRO A3620 " (cutoff:3.500A) Processing helix chain 'A' and resid 3631 through 3636 Processing helix chain 'A' and resid 3642 through 3649 removed outlier: 3.634A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) Processing helix chain 'A' and resid 3661 through 3673 Processing helix chain 'A' and resid 3681 through 3683 No H-bonds generated for 'chain 'A' and resid 3681 through 3683' Processing helix chain 'A' and resid 3685 through 3688 No H-bonds generated for 'chain 'A' and resid 3685 through 3688' Processing helix chain 'A' and resid 3759 through 3777 Processing helix chain 'A' and resid 3779 through 3783 Processing helix chain 'A' and resid 3812 through 3819 Processing helix chain 'A' and resid 3822 through 3829 Processing helix chain 'A' and resid 3835 through 3847 Processing helix chain 'A' and resid 3854 through 3860 removed outlier: 4.420A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3877 removed outlier: 3.908A pdb=" N LYS A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) Processing helix chain 'A' and resid 3883 through 3889 Processing helix chain 'A' and resid 3894 through 3917 Processing helix chain 'A' and resid 3925 through 3927 No H-bonds generated for 'chain 'A' and resid 3925 through 3927' Processing helix chain 'A' and resid 3965 through 3971 removed outlier: 4.167A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3982 through 3991 Processing helix chain 'A' and resid 3997 through 4006 Processing helix chain 'A' and resid 4040 through 4049 Processing helix chain 'A' and resid 4056 through 4067 Processing helix chain 'A' and resid 4074 through 4082 Processing helix chain 'A' and resid 4100 through 4111 Processing helix chain 'A' and resid 4114 through 4117 No H-bonds generated for 'chain 'A' and resid 4114 through 4117' Processing helix chain 'A' and resid 4122 through 4124 No H-bonds generated for 'chain 'A' and resid 4122 through 4124' Processing helix chain 'B' and resid 59 through 77 removed outlier: 3.855A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 removed outlier: 3.844A pdb=" N GLN B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 331 through 337 Processing helix chain 'B' and resid 378 through 391 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 481 through 494 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 522 through 529 removed outlier: 4.151A pdb=" N VAL B 529 " --> pdb=" O PHE B 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 199 through 215 Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 372 through 386 removed outlier: 4.328A pdb=" N ASP C 386 " --> pdb=" O HIS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 460 Processing helix chain 'C' and resid 485 through 499 Processing helix chain 'C' and resid 510 through 515 Processing helix chain 'C' and resid 520 through 536 removed outlier: 5.276A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing helix chain 'C' and resid 550 through 552 No H-bonds generated for 'chain 'C' and resid 550 through 552' Processing helix chain 'C' and resid 597 through 604 Processing helix chain 'C' and resid 611 through 625 Processing helix chain 'C' and resid 629 through 648 Processing helix chain 'C' and resid 653 through 668 Processing helix chain 'C' and resid 672 through 681 removed outlier: 3.873A pdb=" N ASP C 681 " --> pdb=" O ILE C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 704 Processing sheet with id= A, first strand: chain 'A' and resid 893 through 896 Processing sheet with id= B, first strand: chain 'A' and resid 3736 through 3738 removed outlier: 6.438A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id= D, first strand: chain 'B' and resid 198 through 201 removed outlier: 6.815A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 82 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE B 40 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 84 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL B 42 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 86 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 258 through 262 Processing sheet with id= F, first strand: chain 'B' and resid 318 through 322 Processing sheet with id= G, first strand: chain 'B' and resid 350 through 352 Processing sheet with id= H, first strand: chain 'C' and resid 53 through 59 removed outlier: 6.246A pdb=" N LYS C 129 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL C 11 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS C 131 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N CYS C 13 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU C 133 " --> pdb=" O CYS C 13 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP C 15 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE C 135 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLN C 162 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 246 through 253 removed outlier: 4.566A pdb=" N ALA C 366 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR C 264 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL C 364 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N SER C 266 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU C 362 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 364 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 392 through 395 Processing sheet with id= K, first strand: chain 'C' and resid 464 through 466 removed outlier: 4.246A pdb=" N LYS C 465 " --> pdb=" O GLU C 474 " (cutoff:3.500A) 1618 hydrogen bonds defined for protein. 4746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 23.04 Time building geometry restraints manager: 18.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12162 1.34 - 1.46: 8810 1.46 - 1.59: 18203 1.59 - 1.71: 102 1.71 - 1.83: 359 Bond restraints: 39636 Sorted by residual: bond pdb=" C11 1IX A4201 " pdb="CL1 1IX A4201 " ideal model delta sigma weight residual 1.728 1.833 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C24 1IX A4201 " pdb=" N26 1IX A4201 " ideal model delta sigma weight residual 1.371 1.475 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C12 1IX A4201 " pdb=" C13 1IX A4201 " ideal model delta sigma weight residual 1.379 1.471 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C14 1IX A4201 " pdb=" C16 1IX A4201 " ideal model delta sigma weight residual 1.480 1.565 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C ASP A2289 " pdb=" N PRO A2290 " ideal model delta sigma weight residual 1.331 1.365 -0.033 7.90e-03 1.60e+04 1.76e+01 ... (remaining 39631 not shown) Histogram of bond angle deviations from ideal: 95.57 - 103.38: 554 103.38 - 111.19: 15645 111.19 - 119.00: 16875 119.00 - 126.81: 20154 126.81 - 134.62: 569 Bond angle restraints: 53797 Sorted by residual: angle pdb=" C SER A2547 " pdb=" N PRO A2548 " pdb=" CA PRO A2548 " ideal model delta sigma weight residual 119.84 134.62 -14.78 1.25e+00 6.40e-01 1.40e+02 angle pdb=" N VAL A 407 " pdb=" CA VAL A 407 " pdb=" C VAL A 407 " ideal model delta sigma weight residual 113.53 107.38 6.15 9.80e-01 1.04e+00 3.94e+01 angle pdb=" N ARG A3965 " pdb=" CA ARG A3965 " pdb=" C ARG A3965 " ideal model delta sigma weight residual 111.33 118.64 -7.31 1.21e+00 6.83e-01 3.65e+01 angle pdb=" N VAL A 976 " pdb=" CA VAL A 976 " pdb=" C VAL A 976 " ideal model delta sigma weight residual 110.62 115.78 -5.16 1.02e+00 9.61e-01 2.56e+01 angle pdb=" C LEU A1639 " pdb=" N GLU A1640 " pdb=" CA GLU A1640 " ideal model delta sigma weight residual 122.08 129.68 -7.60 1.53e+00 4.27e-01 2.47e+01 ... (remaining 53792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.04: 22706 28.04 - 56.08: 1224 56.08 - 84.12: 122 84.12 - 112.17: 10 112.17 - 140.21: 2 Dihedral angle restraints: 24064 sinusoidal: 10096 harmonic: 13968 Sorted by residual: dihedral pdb=" CA PRO A1020 " pdb=" C PRO A1020 " pdb=" N VAL A1021 " pdb=" CA VAL A1021 " ideal model delta harmonic sigma weight residual -180.00 -141.07 -38.93 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA ARG A3462 " pdb=" C ARG A3462 " pdb=" N LEU A3463 " pdb=" CA LEU A3463 " ideal model delta harmonic sigma weight residual -180.00 -146.48 -33.52 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CA ARG B 252 " pdb=" C ARG B 252 " pdb=" N LYS B 253 " pdb=" CA LYS B 253 " ideal model delta harmonic sigma weight residual 180.00 147.20 32.80 0 5.00e+00 4.00e-02 4.30e+01 ... (remaining 24061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 5095 0.063 - 0.127: 918 0.127 - 0.190: 105 0.190 - 0.253: 12 0.253 - 0.317: 5 Chirality restraints: 6135 Sorted by residual: chirality pdb=" CG LEU A3005 " pdb=" CB LEU A3005 " pdb=" CD1 LEU A3005 " pdb=" CD2 LEU A3005 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE A2336 " pdb=" CA ILE A2336 " pdb=" CG1 ILE A2336 " pdb=" CG2 ILE A2336 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA TYR A3531 " pdb=" N TYR A3531 " pdb=" C TYR A3531 " pdb=" CB TYR A3531 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 6132 not shown) Planarity restraints: 6660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A4055 " 0.075 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A4056 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO A4056 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A4056 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 634 " -0.063 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO A 635 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 635 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 635 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A4005 " 0.025 2.00e-02 2.50e+03 2.89e-02 1.47e+01 pdb=" CG PHE A4005 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A4005 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A4005 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A4005 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A4005 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A4005 " 0.003 2.00e-02 2.50e+03 ... (remaining 6657 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1915 2.71 - 3.26: 42274 3.26 - 3.80: 64533 3.80 - 4.35: 83236 4.35 - 4.90: 130967 Nonbonded interactions: 322925 Sorted by model distance: nonbonded pdb=" OE1 GLU A3478 " pdb=" OG1 THR A3479 " model vdw 2.160 2.440 nonbonded pdb=" OD2 ASP B 505 " pdb=" OH TYR C 333 " model vdw 2.195 2.440 nonbonded pdb=" O GLU A1769 " pdb=" NH2 ARG A1822 " model vdw 2.203 2.520 nonbonded pdb=" O CYS A 931 " pdb=" OH TYR A 984 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR A3828 " pdb=" OE1 GLU A4125 " model vdw 2.215 2.440 ... (remaining 322920 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 individual isotropic 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: 2.080 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: 0.030 Extract box with map and model: 11.270 Check model and map are aligned: 0.590 Set scattering table: 0.350 Process input model: 120.970 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 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 : 0.005 0.105 39636 Z= 0.336 Angle : 0.917 14.776 53797 Z= 0.500 Chirality : 0.050 0.317 6135 Planarity : 0.006 0.111 6660 Dihedral : 16.275 140.207 14952 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.29 % Favored : 88.62 % Rotamer: Outliers : 0.19 % Allowed : 0.55 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.11), residues: 4694 helix: -1.29 (0.09), residues: 2710 sheet: -2.56 (0.32), residues: 212 loop : -3.47 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 300 HIS 0.021 0.002 HIS B 360 PHE 0.067 0.002 PHE A4005 TYR 0.032 0.002 TYR A3531 ARG 0.020 0.001 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 690 time to evaluate : 4.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 PHE cc_start: 0.5882 (t80) cc_final: 0.5428 (t80) REVERT: A 321 LYS cc_start: 0.6074 (ttmt) cc_final: 0.5680 (mttp) REVERT: A 343 GLU cc_start: 0.4615 (pt0) cc_final: 0.4388 (pt0) REVERT: A 862 LEU cc_start: 0.7500 (pp) cc_final: 0.7057 (pp) REVERT: A 901 MET cc_start: 0.6048 (ptm) cc_final: 0.5536 (ttp) REVERT: A 976 VAL cc_start: 0.6813 (OUTLIER) cc_final: 0.6438 (t) REVERT: A 1136 ARG cc_start: 0.6700 (mtt90) cc_final: 0.6208 (mtt180) REVERT: A 1382 ILE cc_start: 0.8100 (pt) cc_final: 0.7792 (pt) REVERT: A 1592 MET cc_start: 0.6560 (mmm) cc_final: 0.6139 (mmm) REVERT: A 2087 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6284 (mm-30) REVERT: A 2439 ILE cc_start: 0.8634 (tt) cc_final: 0.8387 (tt) REVERT: A 2540 LEU cc_start: 0.7379 (mm) cc_final: 0.7171 (mm) REVERT: A 2935 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 3729 MET cc_start: 0.7473 (ppp) cc_final: 0.6989 (ppp) REVERT: A 3808 ASN cc_start: 0.6896 (m-40) cc_final: 0.6490 (m-40) REVERT: A 3885 ARG cc_start: 0.6168 (mtm-85) cc_final: 0.5948 (mtm-85) REVERT: A 4046 TYR cc_start: 0.6117 (m-10) cc_final: 0.5805 (m-10) REVERT: A 4062 ASP cc_start: 0.6067 (m-30) cc_final: 0.5407 (m-30) REVERT: B 204 HIS cc_start: 0.4749 (t-90) cc_final: 0.4200 (t-90) REVERT: B 328 ILE cc_start: 0.8402 (tp) cc_final: 0.8166 (tp) REVERT: B 493 LEU cc_start: 0.8255 (tp) cc_final: 0.7929 (tt) REVERT: C 428 GLU cc_start: 0.6464 (tt0) cc_final: 0.6106 (tt0) REVERT: C 514 ASN cc_start: 0.5980 (m-40) cc_final: 0.5401 (m-40) outliers start: 8 outliers final: 2 residues processed: 697 average time/residue: 0.5432 time to fit residues: 612.4859 Evaluate side-chains 589 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 586 time to evaluate : 4.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 4090 ARG Chi-restraints excluded: chain B residue 296 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 403 optimal weight: 1.9990 chunk 362 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 193 optimal weight: 0.0770 chunk 374 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 278 optimal weight: 1.9990 chunk 434 optimal weight: 1.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 GLN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 GLN ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3924 HIS B 158 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 39636 Z= 0.311 Angle : 0.779 11.043 53797 Z= 0.395 Chirality : 0.047 0.247 6135 Planarity : 0.005 0.076 6660 Dihedral : 12.682 141.520 5664 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.97 % Favored : 87.94 % Rotamer: Outliers : 1.47 % Allowed : 10.78 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.70 (0.12), residues: 4694 helix: -0.81 (0.10), residues: 2728 sheet: -2.37 (0.33), residues: 196 loop : -3.28 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1633 HIS 0.017 0.001 HIS B 360 PHE 0.037 0.002 PHE A2260 TYR 0.023 0.002 TYR A 527 ARG 0.007 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 628 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.6876 (ttpt) cc_final: 0.6619 (ttpp) REVERT: A 294 PHE cc_start: 0.5833 (t80) cc_final: 0.5536 (t80) REVERT: A 628 GLU cc_start: 0.5945 (OUTLIER) cc_final: 0.5610 (mp0) REVERT: A 1038 LYS cc_start: 0.6664 (mtpp) cc_final: 0.6218 (mttm) REVERT: A 1066 LEU cc_start: 0.8397 (tp) cc_final: 0.7898 (mt) REVERT: A 1136 ARG cc_start: 0.6613 (mtt90) cc_final: 0.6084 (mtt-85) REVERT: A 1382 ILE cc_start: 0.8123 (pt) cc_final: 0.7781 (pt) REVERT: A 2042 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7500 (mp-120) REVERT: A 2085 MET cc_start: 0.2295 (OUTLIER) cc_final: 0.1903 (tpp) REVERT: A 2087 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6243 (mm-30) REVERT: A 2331 MET cc_start: 0.7356 (mmt) cc_final: 0.6846 (tpt) REVERT: A 2439 ILE cc_start: 0.8488 (tt) cc_final: 0.8115 (tt) REVERT: A 3708 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.4714 (mmt-90) REVERT: A 3729 MET cc_start: 0.7515 (ppp) cc_final: 0.7208 (ppp) REVERT: A 3808 ASN cc_start: 0.6806 (m-40) cc_final: 0.6427 (m-40) REVERT: A 3820 MET cc_start: 0.7176 (ptm) cc_final: 0.6891 (ptp) REVERT: A 4062 ASP cc_start: 0.6040 (m-30) cc_final: 0.5667 (m-30) REVERT: B 204 HIS cc_start: 0.4445 (t-90) cc_final: 0.3850 (t-90) REVERT: B 328 ILE cc_start: 0.8483 (tp) cc_final: 0.8218 (tp) REVERT: B 493 LEU cc_start: 0.8281 (tp) cc_final: 0.7934 (tt) REVERT: C 514 ASN cc_start: 0.5878 (m-40) cc_final: 0.5448 (m-40) outliers start: 61 outliers final: 40 residues processed: 650 average time/residue: 0.5760 time to fit residues: 610.6047 Evaluate side-chains 640 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 596 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1954 CYS Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2243 GLU Chi-restraints excluded: chain A residue 2307 MET Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 3136 THR Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 414 HIS Chi-restraints excluded: chain C residue 418 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 241 optimal weight: 0.0970 chunk 134 optimal weight: 5.9990 chunk 361 optimal weight: 0.7980 chunk 295 optimal weight: 4.9990 chunk 119 optimal weight: 0.2980 chunk 434 optimal weight: 2.9990 chunk 469 optimal weight: 7.9990 chunk 387 optimal weight: 0.5980 chunk 431 optimal weight: 2.9990 chunk 148 optimal weight: 0.0870 chunk 348 optimal weight: 0.5980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 827 ASN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3743 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39636 Z= 0.196 Angle : 0.670 10.508 53797 Z= 0.340 Chirality : 0.042 0.241 6135 Planarity : 0.005 0.062 6660 Dihedral : 12.363 142.260 5659 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.97 % Favored : 89.97 % Rotamer: Outliers : 2.24 % Allowed : 14.19 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.08 (0.12), residues: 4694 helix: -0.25 (0.10), residues: 2730 sheet: -1.97 (0.34), residues: 191 loop : -3.15 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1633 HIS 0.011 0.001 HIS B 360 PHE 0.028 0.001 PHE A4005 TYR 0.021 0.001 TYR A1675 ARG 0.005 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 643 time to evaluate : 4.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.5681 (mt-10) cc_final: 0.5375 (mt-10) REVERT: A 294 PHE cc_start: 0.5751 (t80) cc_final: 0.5482 (t80) REVERT: A 384 MET cc_start: 0.5838 (mtt) cc_final: 0.5559 (mtp) REVERT: A 396 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6438 (p90) REVERT: A 628 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5585 (mp0) REVERT: A 754 MET cc_start: 0.7112 (ttm) cc_final: 0.6754 (tpp) REVERT: A 853 ILE cc_start: 0.8010 (mt) cc_final: 0.7551 (mm) REVERT: A 1066 LEU cc_start: 0.8199 (tp) cc_final: 0.7669 (mt) REVERT: A 1136 ARG cc_start: 0.6498 (mtt90) cc_final: 0.6056 (mtt180) REVERT: A 1382 ILE cc_start: 0.8069 (pt) cc_final: 0.7694 (pt) REVERT: A 1428 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6358 (mp) REVERT: A 1592 MET cc_start: 0.6591 (mmm) cc_final: 0.5973 (mmm) REVERT: A 1760 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.5937 (mm-30) REVERT: A 2042 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7267 (mm-40) REVERT: A 2085 MET cc_start: 0.2289 (OUTLIER) cc_final: 0.1828 (tpp) REVERT: A 2087 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6242 (mm-30) REVERT: A 2220 MET cc_start: 0.7595 (mtt) cc_final: 0.7320 (mtt) REVERT: A 2331 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6719 (tpt) REVERT: A 2881 LEU cc_start: 0.7907 (mt) cc_final: 0.7699 (mt) REVERT: A 3808 ASN cc_start: 0.6674 (m-40) cc_final: 0.6302 (m-40) REVERT: B 217 TYR cc_start: 0.3295 (OUTLIER) cc_final: 0.2248 (m-10) REVERT: B 261 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6709 (tp) REVERT: B 328 ILE cc_start: 0.8543 (tp) cc_final: 0.8307 (tp) REVERT: B 493 LEU cc_start: 0.8241 (tp) cc_final: 0.7894 (tt) REVERT: B 514 MET cc_start: 0.2959 (mpp) cc_final: 0.2694 (mpp) outliers start: 93 outliers final: 46 residues processed: 694 average time/residue: 0.5322 time to fit residues: 603.7088 Evaluate side-chains 661 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 606 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1888 ASP Chi-restraints excluded: chain A residue 1954 CYS Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2243 GLU Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 414 HIS Chi-restraints excluded: chain C residue 418 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 429 optimal weight: 4.9990 chunk 326 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 436 optimal weight: 0.0270 chunk 462 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 413 optimal weight: 20.0000 chunk 124 optimal weight: 0.0570 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1772 HIS ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 GLN A2234 ASN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3074 GLN ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3660 ASN A3924 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 39636 Z= 0.231 Angle : 0.671 10.344 53797 Z= 0.340 Chirality : 0.043 0.230 6135 Planarity : 0.005 0.079 6660 Dihedral : 12.323 143.047 5659 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.65 % Favored : 89.28 % Rotamer: Outliers : 3.04 % Allowed : 16.26 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.12), residues: 4694 helix: -0.12 (0.10), residues: 2736 sheet: -1.94 (0.35), residues: 194 loop : -3.03 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1633 HIS 0.010 0.001 HIS B 360 PHE 0.027 0.002 PHE A2260 TYR 0.028 0.002 TYR C 416 ARG 0.007 0.000 ARG A3289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 621 time to evaluate : 4.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.5776 (m-10) REVERT: A 294 PHE cc_start: 0.5932 (t80) cc_final: 0.5539 (t80) REVERT: A 396 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6613 (p90) REVERT: A 628 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5693 (mp0) REVERT: A 754 MET cc_start: 0.7164 (ttm) cc_final: 0.6838 (tpp) REVERT: A 757 LYS cc_start: 0.8563 (tmmt) cc_final: 0.8323 (tmmt) REVERT: A 853 ILE cc_start: 0.8045 (mt) cc_final: 0.7559 (mm) REVERT: A 883 TYR cc_start: 0.6930 (m-80) cc_final: 0.6144 (m-10) REVERT: A 961 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7106 (mt) REVERT: A 1066 LEU cc_start: 0.8214 (tp) cc_final: 0.7664 (mt) REVERT: A 1382 ILE cc_start: 0.8073 (pt) cc_final: 0.7693 (pt) REVERT: A 1428 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6773 (mp) REVERT: A 1592 MET cc_start: 0.6713 (mmm) cc_final: 0.5995 (mmm) REVERT: A 1760 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6484 (mt-10) REVERT: A 1878 ASP cc_start: 0.5871 (OUTLIER) cc_final: 0.5362 (t0) REVERT: A 2042 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7386 (mp-120) REVERT: A 2085 MET cc_start: 0.2400 (OUTLIER) cc_final: 0.1597 (pmm) REVERT: A 2087 GLU cc_start: 0.6581 (mm-30) cc_final: 0.6141 (mm-30) REVERT: A 2331 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6723 (tpt) REVERT: A 2341 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.4974 (pt) REVERT: A 3708 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.4193 (mmt-90) REVERT: A 3729 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7236 (ptp) REVERT: A 3808 ASN cc_start: 0.6714 (m-40) cc_final: 0.6371 (m-40) REVERT: B 217 TYR cc_start: 0.3395 (OUTLIER) cc_final: 0.2485 (m-10) REVERT: B 261 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6762 (tp) REVERT: B 281 LEU cc_start: 0.7331 (pt) cc_final: 0.6148 (mt) REVERT: B 294 GLU cc_start: 0.5583 (tp30) cc_final: 0.5332 (tp30) REVERT: B 328 ILE cc_start: 0.8524 (tp) cc_final: 0.8316 (tp) REVERT: B 409 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6856 (t80) REVERT: B 470 ARG cc_start: 0.6846 (ttp-170) cc_final: 0.6368 (ttm170) REVERT: B 514 MET cc_start: 0.3036 (mpp) cc_final: 0.2689 (mpp) REVERT: C 43 GLN cc_start: 0.5903 (pt0) cc_final: 0.5480 (pt0) outliers start: 126 outliers final: 70 residues processed: 695 average time/residue: 0.5432 time to fit residues: 615.0807 Evaluate side-chains 689 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 603 time to evaluate : 4.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1888 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1954 CYS Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain A residue 2308 SER Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3729 MET Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 414 HIS Chi-restraints excluded: chain C residue 418 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 384 optimal weight: 1.9990 chunk 262 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 344 optimal weight: 0.9990 chunk 190 optimal weight: 0.0980 chunk 394 optimal weight: 0.6980 chunk 319 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 235 optimal weight: 0.9990 chunk 414 optimal weight: 30.0000 chunk 116 optimal weight: 0.0470 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 625 ASN A 960 GLN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 GLN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3185 ASN ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39636 Z= 0.192 Angle : 0.645 11.198 53797 Z= 0.326 Chirality : 0.041 0.215 6135 Planarity : 0.004 0.063 6660 Dihedral : 12.206 143.680 5659 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.78 % Favored : 90.16 % Rotamer: Outliers : 2.94 % Allowed : 17.90 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.12), residues: 4694 helix: 0.05 (0.10), residues: 2731 sheet: -1.77 (0.35), residues: 194 loop : -2.98 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3842 HIS 0.009 0.001 HIS A3743 PHE 0.026 0.001 PHE A4005 TYR 0.025 0.001 TYR C 416 ARG 0.015 0.000 ARG A3763 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 636 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.5734 (m-10) REVERT: A 294 PHE cc_start: 0.5885 (t80) cc_final: 0.5655 (t80) REVERT: A 364 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6940 (mtm-85) REVERT: A 384 MET cc_start: 0.5924 (mtt) cc_final: 0.5609 (mtp) REVERT: A 396 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6438 (p90) REVERT: A 628 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5678 (mp0) REVERT: A 754 MET cc_start: 0.7031 (ttm) cc_final: 0.6785 (tpp) REVERT: A 757 LYS cc_start: 0.8566 (tmmt) cc_final: 0.8314 (tmmt) REVERT: A 853 ILE cc_start: 0.7968 (mt) cc_final: 0.7453 (mm) REVERT: A 883 TYR cc_start: 0.6840 (m-80) cc_final: 0.6106 (m-10) REVERT: A 961 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6980 (mt) REVERT: A 1066 LEU cc_start: 0.8209 (tp) cc_final: 0.7692 (mt) REVERT: A 1382 ILE cc_start: 0.8063 (pt) cc_final: 0.7661 (pt) REVERT: A 1428 ILE cc_start: 0.6968 (OUTLIER) cc_final: 0.6369 (mp) REVERT: A 1592 MET cc_start: 0.6352 (mmm) cc_final: 0.5702 (mmm) REVERT: A 1760 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6512 (mt-10) REVERT: A 1878 ASP cc_start: 0.5619 (OUTLIER) cc_final: 0.5153 (t0) REVERT: A 2085 MET cc_start: 0.2433 (OUTLIER) cc_final: 0.1655 (pmm) REVERT: A 2087 GLU cc_start: 0.6485 (mm-30) cc_final: 0.6105 (mm-30) REVERT: A 2331 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6685 (tpt) REVERT: A 2341 LEU cc_start: 0.5009 (OUTLIER) cc_final: 0.4621 (pt) REVERT: A 2351 GLN cc_start: 0.6260 (OUTLIER) cc_final: 0.5997 (tp40) REVERT: A 2937 ASP cc_start: 0.7416 (m-30) cc_final: 0.7131 (m-30) REVERT: A 3708 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.4060 (mmt-90) REVERT: A 3729 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7212 (ptp) REVERT: A 3808 ASN cc_start: 0.6663 (m-40) cc_final: 0.6321 (m-40) REVERT: A 3889 ARG cc_start: 0.7258 (tmt-80) cc_final: 0.6950 (ttt-90) REVERT: A 3933 GLU cc_start: 0.7088 (pp20) cc_final: 0.6865 (pp20) REVERT: B 156 ASP cc_start: 0.6739 (m-30) cc_final: 0.6524 (m-30) REVERT: B 217 TYR cc_start: 0.3385 (OUTLIER) cc_final: 0.2588 (m-10) REVERT: B 261 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6640 (tp) REVERT: B 281 LEU cc_start: 0.7376 (pt) cc_final: 0.6287 (mt) REVERT: B 294 GLU cc_start: 0.5733 (tp30) cc_final: 0.5493 (tp30) REVERT: B 328 ILE cc_start: 0.8524 (tp) cc_final: 0.8302 (tp) REVERT: B 409 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6796 (t80) REVERT: B 514 MET cc_start: 0.3065 (mpp) cc_final: 0.2641 (mpp) outliers start: 122 outliers final: 74 residues processed: 707 average time/residue: 0.5319 time to fit residues: 617.9739 Evaluate side-chains 693 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 603 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1888 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3729 MET Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 155 optimal weight: 0.7980 chunk 416 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 114 optimal weight: 0.0770 chunk 462 optimal weight: 0.9990 chunk 383 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 152 optimal weight: 0.2980 chunk 242 optimal weight: 0.0970 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 ASN A 960 GLN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 GLN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3660 ASN B 101 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 ASN ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39636 Z= 0.196 Angle : 0.641 9.632 53797 Z= 0.324 Chirality : 0.041 0.279 6135 Planarity : 0.004 0.062 6660 Dihedral : 12.152 144.110 5658 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.88 % Favored : 90.05 % Rotamer: Outliers : 3.55 % Allowed : 18.38 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 4694 helix: 0.13 (0.10), residues: 2727 sheet: -1.70 (0.35), residues: 194 loop : -2.94 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1633 HIS 0.009 0.001 HIS A3743 PHE 0.024 0.001 PHE B 49 TYR 0.024 0.001 TYR C 416 ARG 0.006 0.000 ARG A3289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 626 time to evaluate : 4.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.5739 (m-10) REVERT: A 290 TYR cc_start: 0.4736 (p90) cc_final: 0.4483 (p90) REVERT: A 396 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6243 (p90) REVERT: A 628 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5670 (mp0) REVERT: A 762 TYR cc_start: 0.7656 (t80) cc_final: 0.7262 (t80) REVERT: A 853 ILE cc_start: 0.7925 (mt) cc_final: 0.7432 (mm) REVERT: A 883 TYR cc_start: 0.6741 (m-80) cc_final: 0.6147 (m-10) REVERT: A 961 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.6977 (mt) REVERT: A 1066 LEU cc_start: 0.8219 (tp) cc_final: 0.7698 (mt) REVERT: A 1189 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.5975 (mp0) REVERT: A 1382 ILE cc_start: 0.7998 (pt) cc_final: 0.7626 (pt) REVERT: A 1428 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6188 (mp) REVERT: A 1592 MET cc_start: 0.6261 (mmm) cc_final: 0.5627 (mmm) REVERT: A 1754 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6215 (mt0) REVERT: A 1760 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6605 (mt-10) REVERT: A 1878 ASP cc_start: 0.5756 (OUTLIER) cc_final: 0.5288 (t0) REVERT: A 2042 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7058 (mp-120) REVERT: A 2085 MET cc_start: 0.2434 (OUTLIER) cc_final: 0.1632 (pmm) REVERT: A 2087 GLU cc_start: 0.6627 (mm-30) cc_final: 0.6177 (mm-30) REVERT: A 2162 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6506 (ttpt) REVERT: A 2331 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6693 (tpt) REVERT: A 2341 LEU cc_start: 0.5167 (OUTLIER) cc_final: 0.4813 (pt) REVERT: A 2351 GLN cc_start: 0.6262 (OUTLIER) cc_final: 0.5960 (tp40) REVERT: A 2821 ASP cc_start: 0.5831 (OUTLIER) cc_final: 0.5348 (m-30) REVERT: A 2937 ASP cc_start: 0.7392 (m-30) cc_final: 0.7117 (m-30) REVERT: A 3178 ILE cc_start: 0.5891 (mp) cc_final: 0.5286 (mm) REVERT: A 3414 MET cc_start: 0.5270 (mmt) cc_final: 0.4921 (mmp) REVERT: A 3708 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.4071 (mmt-90) REVERT: A 3808 ASN cc_start: 0.6671 (m-40) cc_final: 0.6338 (m-40) REVERT: A 3888 VAL cc_start: 0.8290 (p) cc_final: 0.8078 (p) REVERT: A 3889 ARG cc_start: 0.7256 (tmt-80) cc_final: 0.6943 (ttt-90) REVERT: B 156 ASP cc_start: 0.6726 (m-30) cc_final: 0.6446 (m-30) REVERT: B 217 TYR cc_start: 0.3274 (OUTLIER) cc_final: 0.2549 (m-10) REVERT: B 254 ARG cc_start: 0.6354 (ttp-170) cc_final: 0.5965 (ttp-170) REVERT: B 261 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6619 (tp) REVERT: B 281 LEU cc_start: 0.7349 (pt) cc_final: 0.6285 (mt) REVERT: B 294 GLU cc_start: 0.5708 (tp30) cc_final: 0.5478 (tp30) REVERT: B 328 ILE cc_start: 0.8511 (tp) cc_final: 0.8282 (tp) REVERT: B 409 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6807 (t80) REVERT: B 514 MET cc_start: 0.3355 (mpp) cc_final: 0.2902 (mpp) REVERT: C 479 THR cc_start: 0.7895 (p) cc_final: 0.7247 (t) outliers start: 147 outliers final: 99 residues processed: 715 average time/residue: 0.5328 time to fit residues: 623.5982 Evaluate side-chains 728 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 609 time to evaluate : 4.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1385 ASN Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1754 GLN Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1888 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2183 HIS Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2308 SER Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2821 ASP Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2884 LEU Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3333 THR Chi-restraints excluded: chain A residue 3460 GLU Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 445 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 389 optimal weight: 0.5980 chunk 258 optimal weight: 1.9990 chunk 460 optimal weight: 0.0070 chunk 288 optimal weight: 0.6980 chunk 280 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 ASN A 960 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2163 HIS ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39636 Z= 0.229 Angle : 0.666 11.001 53797 Z= 0.335 Chirality : 0.042 0.275 6135 Planarity : 0.005 0.063 6660 Dihedral : 12.157 144.086 5658 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.46 % Favored : 89.48 % Rotamer: Outliers : 3.59 % Allowed : 18.91 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.12), residues: 4694 helix: 0.13 (0.10), residues: 2731 sheet: -1.68 (0.35), residues: 194 loop : -2.87 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A3493 HIS 0.010 0.001 HIS A3743 PHE 0.025 0.001 PHE A2260 TYR 0.025 0.001 TYR C 416 ARG 0.015 0.000 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 614 time to evaluate : 4.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.5808 (m-10) REVERT: A 290 TYR cc_start: 0.4640 (p90) cc_final: 0.4399 (p90) REVERT: A 294 PHE cc_start: 0.5632 (t80) cc_final: 0.5334 (t80) REVERT: A 396 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6303 (p90) REVERT: A 628 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5708 (mp0) REVERT: A 757 LYS cc_start: 0.8487 (tmmt) cc_final: 0.8206 (ttpp) REVERT: A 853 ILE cc_start: 0.7955 (mt) cc_final: 0.7465 (mm) REVERT: A 883 TYR cc_start: 0.6696 (m-80) cc_final: 0.6070 (m-10) REVERT: A 961 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7136 (mt) REVERT: A 1066 LEU cc_start: 0.8251 (tp) cc_final: 0.7717 (mt) REVERT: A 1189 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5966 (mp0) REVERT: A 1382 ILE cc_start: 0.8009 (pt) cc_final: 0.7646 (pt) REVERT: A 1428 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6610 (mp) REVERT: A 1748 ASP cc_start: 0.5364 (t0) cc_final: 0.4992 (m-30) REVERT: A 1760 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6632 (mt-10) REVERT: A 1802 TYR cc_start: 0.6998 (t80) cc_final: 0.6770 (t80) REVERT: A 1878 ASP cc_start: 0.5652 (OUTLIER) cc_final: 0.5219 (t0) REVERT: A 2085 MET cc_start: 0.2414 (OUTLIER) cc_final: 0.1654 (pmm) REVERT: A 2087 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6140 (mm-30) REVERT: A 2162 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6513 (ttpt) REVERT: A 2220 MET cc_start: 0.7657 (mtt) cc_final: 0.7361 (mtt) REVERT: A 2331 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6685 (tpt) REVERT: A 2341 LEU cc_start: 0.5154 (OUTLIER) cc_final: 0.4799 (pt) REVERT: A 2423 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7880 (t) REVERT: A 2821 ASP cc_start: 0.5901 (OUTLIER) cc_final: 0.5459 (m-30) REVERT: A 2937 ASP cc_start: 0.7411 (m-30) cc_final: 0.7127 (m-30) REVERT: A 3178 ILE cc_start: 0.5804 (mp) cc_final: 0.5323 (mm) REVERT: A 3708 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.4121 (mmt-90) REVERT: A 3808 ASN cc_start: 0.6645 (m-40) cc_final: 0.6332 (m-40) REVERT: A 3888 VAL cc_start: 0.8332 (p) cc_final: 0.8125 (p) REVERT: A 3889 ARG cc_start: 0.7313 (tmt-80) cc_final: 0.6919 (ttp80) REVERT: B 156 ASP cc_start: 0.6751 (m-30) cc_final: 0.6488 (m-30) REVERT: B 217 TYR cc_start: 0.3430 (OUTLIER) cc_final: 0.2850 (m-10) REVERT: B 254 ARG cc_start: 0.6398 (ttp-170) cc_final: 0.6038 (ttp-170) REVERT: B 261 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6664 (tp) REVERT: B 281 LEU cc_start: 0.7383 (pt) cc_final: 0.6250 (mt) REVERT: B 294 GLU cc_start: 0.5737 (tp30) cc_final: 0.5503 (tp30) REVERT: B 328 ILE cc_start: 0.8519 (tp) cc_final: 0.8278 (tp) REVERT: B 409 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6861 (t80) REVERT: B 514 MET cc_start: 0.3417 (mpp) cc_final: 0.2946 (mpp) REVERT: C 271 ARG cc_start: 0.6574 (ttm-80) cc_final: 0.6165 (mtm-85) outliers start: 149 outliers final: 114 residues processed: 707 average time/residue: 0.5283 time to fit residues: 611.1480 Evaluate side-chains 737 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 605 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1385 ASN Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1455 CYS Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1888 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2183 HIS Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2304 VAL Chi-restraints excluded: chain A residue 2308 SER Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2380 ASN Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2821 ASP Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3333 THR Chi-restraints excluded: chain A residue 3460 GLU Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 285 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 292 optimal weight: 2.9990 chunk 313 optimal weight: 0.4980 chunk 227 optimal weight: 0.5980 chunk 42 optimal weight: 0.0000 chunk 362 optimal weight: 0.5980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 GLN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39636 Z= 0.191 Angle : 0.648 10.200 53797 Z= 0.326 Chirality : 0.041 0.264 6135 Planarity : 0.004 0.064 6660 Dihedral : 12.056 144.366 5658 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.86 % Favored : 90.07 % Rotamer: Outliers : 3.69 % Allowed : 19.30 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.12), residues: 4694 helix: 0.23 (0.10), residues: 2722 sheet: -1.60 (0.35), residues: 194 loop : -2.86 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1633 HIS 0.010 0.001 HIS A3743 PHE 0.023 0.001 PHE B 49 TYR 0.025 0.001 TYR C 416 ARG 0.008 0.000 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 628 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.5858 (m-10) REVERT: A 396 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6731 (p90) REVERT: A 628 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5730 (mp0) REVERT: A 757 LYS cc_start: 0.8491 (tmmt) cc_final: 0.8200 (ttpp) REVERT: A 853 ILE cc_start: 0.7916 (mt) cc_final: 0.7426 (mm) REVERT: A 883 TYR cc_start: 0.6665 (m-80) cc_final: 0.6073 (m-10) REVERT: A 961 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.6981 (mt) REVERT: A 1066 LEU cc_start: 0.8217 (tp) cc_final: 0.7689 (mt) REVERT: A 1189 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5964 (mp0) REVERT: A 1382 ILE cc_start: 0.8027 (pt) cc_final: 0.7618 (pt) REVERT: A 1428 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6618 (mp) REVERT: A 1592 MET cc_start: 0.6406 (mmm) cc_final: 0.5755 (mmm) REVERT: A 1748 ASP cc_start: 0.5242 (OUTLIER) cc_final: 0.4930 (m-30) REVERT: A 1760 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6529 (mt-10) REVERT: A 1802 TYR cc_start: 0.6789 (t80) cc_final: 0.6567 (t80) REVERT: A 1849 ASP cc_start: 0.8011 (t0) cc_final: 0.6941 (p0) REVERT: A 1878 ASP cc_start: 0.5696 (OUTLIER) cc_final: 0.5263 (t0) REVERT: A 2085 MET cc_start: 0.2337 (OUTLIER) cc_final: 0.1608 (pmm) REVERT: A 2087 GLU cc_start: 0.6490 (mm-30) cc_final: 0.6124 (mm-30) REVERT: A 2162 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6646 (tttp) REVERT: A 2331 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6671 (tpt) REVERT: A 2341 LEU cc_start: 0.4969 (OUTLIER) cc_final: 0.4632 (pt) REVERT: A 2347 LYS cc_start: 0.6653 (mmtt) cc_final: 0.6337 (mttp) REVERT: A 2821 ASP cc_start: 0.5890 (OUTLIER) cc_final: 0.5452 (m-30) REVERT: A 2937 ASP cc_start: 0.7379 (m-30) cc_final: 0.7087 (m-30) REVERT: A 3178 ILE cc_start: 0.5709 (mp) cc_final: 0.5259 (mm) REVERT: A 3414 MET cc_start: 0.5363 (mmt) cc_final: 0.4946 (mmp) REVERT: A 3708 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.4338 (mmt-90) REVERT: A 3763 ARG cc_start: 0.6284 (ttt180) cc_final: 0.5917 (ttt180) REVERT: A 3808 ASN cc_start: 0.6669 (m-40) cc_final: 0.6329 (m-40) REVERT: A 3889 ARG cc_start: 0.7224 (tmt-80) cc_final: 0.6901 (ttp80) REVERT: B 156 ASP cc_start: 0.6722 (m-30) cc_final: 0.6439 (m-30) REVERT: B 195 ASP cc_start: 0.6418 (m-30) cc_final: 0.6152 (m-30) REVERT: B 217 TYR cc_start: 0.3343 (OUTLIER) cc_final: 0.2772 (m-10) REVERT: B 254 ARG cc_start: 0.6320 (ttp-170) cc_final: 0.5939 (ttp-170) REVERT: B 261 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6591 (tp) REVERT: B 281 LEU cc_start: 0.7341 (pt) cc_final: 0.6307 (mt) REVERT: B 294 GLU cc_start: 0.5671 (tp30) cc_final: 0.5460 (tp30) REVERT: B 310 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5369 (tp) REVERT: B 328 ILE cc_start: 0.8512 (tp) cc_final: 0.8267 (tp) REVERT: B 409 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.6840 (t80) REVERT: B 514 MET cc_start: 0.3985 (mpp) cc_final: 0.3489 (mpp) REVERT: C 271 ARG cc_start: 0.6538 (ttm-80) cc_final: 0.6090 (mtm-85) outliers start: 153 outliers final: 113 residues processed: 724 average time/residue: 0.5355 time to fit residues: 640.6094 Evaluate side-chains 742 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 610 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1385 ASN Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1748 ASP Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1888 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2183 HIS Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2304 VAL Chi-restraints excluded: chain A residue 2308 SER Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2821 ASP Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2884 LEU Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3333 THR Chi-restraints excluded: chain A residue 3460 GLU Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain A residue 4004 VAL Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 419 optimal weight: 7.9990 chunk 441 optimal weight: 2.9990 chunk 402 optimal weight: 0.9980 chunk 429 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 337 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 387 optimal weight: 0.6980 chunk 406 optimal weight: 0.9990 chunk 427 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 GLN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2432 GLN ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3185 ASN ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 39636 Z= 0.359 Angle : 0.752 11.689 53797 Z= 0.379 Chirality : 0.046 0.286 6135 Planarity : 0.005 0.085 6660 Dihedral : 12.295 143.765 5658 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.18 % Favored : 88.75 % Rotamer: Outliers : 3.86 % Allowed : 19.52 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.12), residues: 4694 helix: -0.09 (0.10), residues: 2731 sheet: -1.79 (0.35), residues: 193 loop : -2.88 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A4127 HIS 0.011 0.001 HIS A1830 PHE 0.030 0.002 PHE A2260 TYR 0.027 0.002 TYR C 416 ARG 0.009 0.001 ARG A3289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 609 time to evaluate : 4.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.3875 (ppp) cc_final: 0.3438 (ptp) REVERT: A 282 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6078 (m-10) REVERT: A 294 PHE cc_start: 0.6181 (t80) cc_final: 0.5853 (t80) REVERT: A 396 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6714 (p90) REVERT: A 628 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5782 (mp0) REVERT: A 757 LYS cc_start: 0.8544 (tmmt) cc_final: 0.8264 (ttpp) REVERT: A 853 ILE cc_start: 0.8106 (mt) cc_final: 0.7597 (mm) REVERT: A 883 TYR cc_start: 0.6986 (m-80) cc_final: 0.6333 (m-10) REVERT: A 961 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7059 (mt) REVERT: A 1066 LEU cc_start: 0.8334 (tp) cc_final: 0.7753 (mt) REVERT: A 1175 HIS cc_start: 0.5255 (OUTLIER) cc_final: 0.3623 (p90) REVERT: A 1189 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: A 1382 ILE cc_start: 0.7968 (pt) cc_final: 0.7608 (pt) REVERT: A 1428 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6642 (mm) REVERT: A 1748 ASP cc_start: 0.5358 (t0) cc_final: 0.4945 (m-30) REVERT: A 1760 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6651 (mt-10) REVERT: A 1802 TYR cc_start: 0.7066 (t80) cc_final: 0.6820 (t80) REVERT: A 1878 ASP cc_start: 0.6128 (OUTLIER) cc_final: 0.5758 (t0) REVERT: A 2085 MET cc_start: 0.2417 (OUTLIER) cc_final: 0.1676 (pmm) REVERT: A 2087 GLU cc_start: 0.6537 (mm-30) cc_final: 0.6151 (mm-30) REVERT: A 2162 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6553 (ttpt) REVERT: A 2331 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6778 (tpt) REVERT: A 2341 LEU cc_start: 0.4792 (OUTLIER) cc_final: 0.4507 (pt) REVERT: A 2423 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.7893 (t) REVERT: A 2821 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5533 (m-30) REVERT: A 2937 ASP cc_start: 0.7417 (m-30) cc_final: 0.7019 (m-30) REVERT: A 3069 MET cc_start: 0.6013 (mmp) cc_final: 0.5655 (mmp) REVERT: A 3414 MET cc_start: 0.5273 (mmt) cc_final: 0.4771 (mmp) REVERT: A 3708 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.4182 (mmt-90) REVERT: A 3763 ARG cc_start: 0.6233 (ttt180) cc_final: 0.5928 (ttt180) REVERT: A 3808 ASN cc_start: 0.6694 (m-40) cc_final: 0.6349 (m-40) REVERT: A 3889 ARG cc_start: 0.7330 (tmt-80) cc_final: 0.7033 (ttp80) REVERT: A 3933 GLU cc_start: 0.7213 (pp20) cc_final: 0.6924 (pp20) REVERT: B 102 ILE cc_start: 0.6755 (mm) cc_final: 0.6484 (mm) REVERT: B 156 ASP cc_start: 0.6836 (m-30) cc_final: 0.6521 (m-30) REVERT: B 217 TYR cc_start: 0.3307 (OUTLIER) cc_final: 0.2782 (m-10) REVERT: B 254 ARG cc_start: 0.6613 (ttp-170) cc_final: 0.6036 (ttp-170) REVERT: B 261 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6772 (tp) REVERT: B 281 LEU cc_start: 0.7349 (pt) cc_final: 0.6168 (mt) REVERT: B 310 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5722 (tp) REVERT: B 328 ILE cc_start: 0.8544 (tp) cc_final: 0.8277 (tp) REVERT: B 409 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6886 (t80) REVERT: B 514 MET cc_start: 0.3871 (mpp) cc_final: 0.3441 (mpp) REVERT: C 271 ARG cc_start: 0.6972 (ttm-80) cc_final: 0.6448 (mmt180) outliers start: 160 outliers final: 123 residues processed: 706 average time/residue: 0.5327 time to fit residues: 619.4524 Evaluate side-chains 747 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 604 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1175 HIS Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1284 THR Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1385 ASN Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1455 CYS Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1888 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2183 HIS Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2304 VAL Chi-restraints excluded: chain A residue 2308 SER Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2380 ASN Chi-restraints excluded: chain A residue 2386 LEU Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2821 ASP Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3460 GLU Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain A residue 4004 VAL Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 281 optimal weight: 1.9990 chunk 453 optimal weight: 4.9990 chunk 277 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 315 optimal weight: 0.0000 chunk 476 optimal weight: 1.9990 chunk 438 optimal weight: 0.5980 chunk 379 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 292 optimal weight: 2.9990 chunk 232 optimal weight: 0.3980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 GLN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1457 GLN A1754 GLN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39636 Z= 0.196 Angle : 0.671 12.420 53797 Z= 0.337 Chirality : 0.042 0.265 6135 Planarity : 0.004 0.068 6660 Dihedral : 12.091 144.570 5658 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.71 % Favored : 90.22 % Rotamer: Outliers : 3.28 % Allowed : 20.22 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.12), residues: 4694 helix: 0.14 (0.10), residues: 2733 sheet: -1.62 (0.35), residues: 194 loop : -2.82 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A4127 HIS 0.010 0.001 HIS A3743 PHE 0.025 0.001 PHE B 49 TYR 0.024 0.001 TYR C 416 ARG 0.009 0.000 ARG A3289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 614 time to evaluate : 4.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.3798 (ppp) cc_final: 0.3189 (ptp) REVERT: A 189 MET cc_start: 0.7147 (ptm) cc_final: 0.6522 (ppp) REVERT: A 282 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.5798 (m-10) REVERT: A 294 PHE cc_start: 0.5860 (t80) cc_final: 0.5461 (t80) REVERT: A 396 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6565 (p90) REVERT: A 628 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5594 (mp0) REVERT: A 757 LYS cc_start: 0.8518 (tmmt) cc_final: 0.8217 (ttpp) REVERT: A 853 ILE cc_start: 0.8022 (mt) cc_final: 0.7527 (mm) REVERT: A 883 TYR cc_start: 0.6863 (m-80) cc_final: 0.6170 (m-10) REVERT: A 961 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7137 (mt) REVERT: A 1066 LEU cc_start: 0.8206 (tp) cc_final: 0.7663 (mt) REVERT: A 1175 HIS cc_start: 0.5037 (OUTLIER) cc_final: 0.3454 (p90) REVERT: A 1189 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5893 (mp0) REVERT: A 1382 ILE cc_start: 0.7909 (pt) cc_final: 0.7551 (pt) REVERT: A 1428 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6595 (mm) REVERT: A 1457 GLN cc_start: 0.7388 (mt0) cc_final: 0.7109 (mt0) REVERT: A 1592 MET cc_start: 0.6401 (mmm) cc_final: 0.5757 (mmm) REVERT: A 1708 GLU cc_start: 0.5252 (tm-30) cc_final: 0.5042 (tm-30) REVERT: A 1748 ASP cc_start: 0.5256 (t0) cc_final: 0.4948 (m-30) REVERT: A 1760 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: A 1802 TYR cc_start: 0.6791 (t80) cc_final: 0.6554 (t80) REVERT: A 1878 ASP cc_start: 0.6007 (OUTLIER) cc_final: 0.5572 (t0) REVERT: A 2085 MET cc_start: 0.2778 (OUTLIER) cc_final: 0.2290 (pmm) REVERT: A 2087 GLU cc_start: 0.6486 (mm-30) cc_final: 0.6116 (mm-30) REVERT: A 2162 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6638 (tttp) REVERT: A 2331 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6763 (tpt) REVERT: A 2341 LEU cc_start: 0.5109 (OUTLIER) cc_final: 0.4826 (pt) REVERT: A 2343 GLU cc_start: 0.5437 (mt-10) cc_final: 0.5112 (mt-10) REVERT: A 2347 LYS cc_start: 0.6553 (mmtt) cc_final: 0.6276 (mttp) REVERT: A 2540 LEU cc_start: 0.7536 (mm) cc_final: 0.7165 (mm) REVERT: A 2821 ASP cc_start: 0.5828 (OUTLIER) cc_final: 0.5378 (m-30) REVERT: A 2937 ASP cc_start: 0.7384 (m-30) cc_final: 0.6984 (m-30) REVERT: A 2964 ASP cc_start: 0.6364 (m-30) cc_final: 0.6019 (m-30) REVERT: A 3069 MET cc_start: 0.6129 (mmp) cc_final: 0.5746 (mmp) REVERT: A 3178 ILE cc_start: 0.5781 (mp) cc_final: 0.5316 (mm) REVERT: A 3414 MET cc_start: 0.5348 (mmt) cc_final: 0.4893 (mmp) REVERT: A 3708 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.4329 (mmt-90) REVERT: A 3763 ARG cc_start: 0.6137 (ttt180) cc_final: 0.5792 (ttt180) REVERT: A 3808 ASN cc_start: 0.6635 (m-40) cc_final: 0.6302 (m-40) REVERT: A 3889 ARG cc_start: 0.7325 (tmt-80) cc_final: 0.7094 (ttp80) REVERT: B 156 ASP cc_start: 0.6772 (m-30) cc_final: 0.6475 (m-30) REVERT: B 217 TYR cc_start: 0.3395 (OUTLIER) cc_final: 0.2693 (m-10) REVERT: B 254 ARG cc_start: 0.6496 (ttp-170) cc_final: 0.6018 (ttp-170) REVERT: B 261 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6699 (tp) REVERT: B 281 LEU cc_start: 0.7448 (pt) cc_final: 0.6272 (mt) REVERT: B 310 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5465 (tp) REVERT: B 328 ILE cc_start: 0.8494 (tp) cc_final: 0.8225 (tp) REVERT: B 514 MET cc_start: 0.3807 (mpp) cc_final: 0.3434 (mpp) REVERT: C 271 ARG cc_start: 0.6806 (ttm-80) cc_final: 0.6134 (mtm-85) REVERT: C 352 GLN cc_start: 0.5477 (OUTLIER) cc_final: 0.5173 (mt0) outliers start: 136 outliers final: 104 residues processed: 699 average time/residue: 0.5320 time to fit residues: 613.1384 Evaluate side-chains 733 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 610 time to evaluate : 4.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 783 HIS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1175 HIS Chi-restraints excluded: chain A residue 1180 GLN Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1284 THR Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1392 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1428 ILE Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1643 MET Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1824 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1888 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2162 LYS Chi-restraints excluded: chain A residue 2183 HIS Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2297 SER Chi-restraints excluded: chain A residue 2304 VAL Chi-restraints excluded: chain A residue 2308 SER Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2331 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2353 GLN Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2439 ILE Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2462 VAL Chi-restraints excluded: chain A residue 2476 ILE Chi-restraints excluded: chain A residue 2792 THR Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2821 ASP Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2859 GLN Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3333 THR Chi-restraints excluded: chain A residue 3460 GLU Chi-restraints excluded: chain A residue 3531 TYR Chi-restraints excluded: chain A residue 3567 VAL Chi-restraints excluded: chain A residue 3708 ARG Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3984 MET Chi-restraints excluded: chain A residue 4004 VAL Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 352 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 301 optimal weight: 0.6980 chunk 403 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 349 optimal weight: 0.0050 chunk 55 optimal weight: 0.0980 chunk 105 optimal weight: 0.0060 chunk 379 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 390 optimal weight: 0.0870 chunk 48 optimal weight: 0.0020 chunk 69 optimal weight: 1.9990 overall best weight: 0.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN A 960 GLN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1898 GLN A2183 HIS ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2353 GLN A2365 ASN A2574 ASN ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2864 GLN A2865 HIS ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.242277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.210895 restraints weight = 42997.389| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.94 r_work: 0.3984 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39636 Z= 0.162 Angle : 0.639 13.530 53797 Z= 0.320 Chirality : 0.040 0.259 6135 Planarity : 0.004 0.063 6660 Dihedral : 11.822 145.595 5658 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.46 % Favored : 90.50 % Rotamer: Outliers : 2.29 % Allowed : 21.38 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.12), residues: 4694 helix: 0.36 (0.10), residues: 2731 sheet: -1.31 (0.36), residues: 188 loop : -2.76 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A4127 HIS 0.009 0.001 HIS A3743 PHE 0.024 0.001 PHE B 49 TYR 0.025 0.001 TYR A1675 ARG 0.010 0.000 ARG A3289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10935.21 seconds wall clock time: 198 minutes 51.05 seconds (11931.05 seconds total)