Starting phenix.real_space_refine on Mon Mar 25 13:33:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w66_8776/03_2024/5w66_8776.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w66_8776/03_2024/5w66_8776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w66_8776/03_2024/5w66_8776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w66_8776/03_2024/5w66_8776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w66_8776/03_2024/5w66_8776.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w66_8776/03_2024/5w66_8776.pdb" } resolution = 3.9 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= 0.012 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 102 5.49 5 S 209 5.16 5 C 30698 2.51 5 N 8440 2.21 5 O 9402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "A PHE 1462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 280": "NH1" <-> "NH2" Residue "O ARG 407": "NH1" <-> "NH2" Residue "O ARG 419": "NH1" <-> "NH2" Residue "O ARG 472": "NH1" <-> "NH2" Residue "O ARG 484": "NH1" <-> "NH2" Residue "O ARG 542": "NH1" <-> "NH2" Residue "O GLU 664": "OE1" <-> "OE2" Residue "P TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 305": "NH1" <-> "NH2" Residue "P ARG 324": "NH1" <-> "NH2" Residue "P ARG 350": "NH1" <-> "NH2" Residue "P GLU 371": "OE1" <-> "OE2" Residue "P GLU 401": "OE1" <-> "OE2" Residue "Q PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q ARG 17": "NH1" <-> "NH2" Residue "Q ARG 30": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 166": "OE1" <-> "OE2" Residue "Q ARG 302": "NH1" <-> "NH2" Residue "Q GLU 363": "OE1" <-> "OE2" Residue "Q PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48857 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 11542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1461, 11542 Classifications: {'peptide': 1461} Link IDs: {'PTRANS': 59, 'TRANS': 1401} Chain breaks: 7 Chain: "B" Number of atoms: 9351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9351 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 58, 'TRANS': 1119} Chain breaks: 2 Chain: "C" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2431 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1070 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 479 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3131 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 21, 'TRANS': 374} Chain: "N" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1254 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "O" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5063 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 620} Chain breaks: 4 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 53 Chain: "P" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3238 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2923 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 2 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "S" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 935 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "T" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1082 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 781 SG CYS A 102 176.857 81.338 80.841 1.00 0.00 S ATOM 806 SG CYS A 105 177.076 79.029 81.287 1.00 0.00 S ATOM 1605 SG CYS A 233 178.575 81.399 83.797 1.00 0.00 S ATOM 1627 SG CYS A 236 178.926 81.068 81.453 1.00 0.00 S ATOM 461 SG CYS A 62 129.922 62.630 80.727 1.00 0.00 S ATOM 480 SG CYS A 65 129.002 60.640 82.664 1.00 0.00 S ATOM 535 SG CYS A 72 128.796 62.577 83.718 1.00 0.00 S ATOM 20196 SG CYS B1104 143.129 55.144 89.168 1.00 0.00 S ATOM 20222 SG CYS B1107 143.585 57.965 89.797 1.00 0.00 S ATOM 20369 SG CYS B1128 142.703 56.390 87.117 1.00 0.00 S ATOM 20397 SG CYS B1131 144.764 54.088 86.894 1.00 0.00 S ATOM 28945 SG CYS I 10 160.618 147.387 86.150 1.00 0.00 S ATOM 28967 SG CYS I 13 158.451 145.775 85.108 1.00 0.00 S ATOM 29087 SG CYS I 30 161.118 145.373 84.648 1.00 0.00 S ATOM 29108 SG CYS I 33 161.665 148.144 84.393 1.00 0.00 S ATOM 29415 SG CYS J 7 89.376 96.898 130.468 1.00 0.00 S ATOM 29438 SG CYS J 10 86.980 95.649 132.086 1.00 0.00 S ATOM 29718 SG CYS J 45 89.336 97.384 133.867 1.00 0.00 S ATOM 29724 SG CYS J 46 85.833 98.529 133.264 1.00 0.00 S ATOM 30790 SG CYS L 31 86.893 102.433 86.430 1.00 0.00 S ATOM 30810 SG CYS L 34 84.006 102.955 86.243 1.00 0.00 S ATOM 30914 SG CYS L 48 84.970 101.983 84.105 1.00 0.00 S ATOM 30937 SG CYS L 51 87.233 104.007 84.232 1.00 0.00 S Time building chain proxies: 25.54, per 1000 atoms: 0.52 Number of scatterers: 48857 At special positions: 0 Unit cell: (210.6, 189.8, 196.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 209 16.00 P 102 15.00 O 9402 8.00 N 8440 7.00 C 30698 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: 18.83 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 33 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 33 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11106 Finding SS restraints... Secondary structure from input PDB file: 241 helices and 64 sheets defined 44.5% alpha, 16.3% beta 29 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 17.85 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 87 through 100 removed outlier: 4.672A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLN A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 174 through 199 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.848A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.662A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.260A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 380 through 407 Processing helix chain 'A' and resid 415 through 439 removed outlier: 3.981A pdb=" N ILE A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.691A pdb=" N TYR A 657 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 Processing helix chain 'A' and resid 688 through 700 Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 802 through 825 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 862 removed outlier: 3.583A pdb=" N THR A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 885 through 912 Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 923 through 932 removed outlier: 3.619A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 991 through 1013 removed outlier: 3.543A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 4.355A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 4.119A pdb=" N SER A1061 " --> pdb=" O ILE A1057 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N HIS A1062 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A1064 " --> pdb=" O GLU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1081 through 1085 removed outlier: 3.767A pdb=" N ALA A1084 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1108 Processing helix chain 'A' and resid 1112 through 1116 removed outlier: 3.533A pdb=" N GLN A1116 " --> pdb=" O HIS A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.702A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1162 through 1176 Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1200 removed outlier: 3.660A pdb=" N MET A1200 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1247 through 1259 removed outlier: 3.506A pdb=" N SER A1259 " --> pdb=" O CYS A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1267 Processing helix chain 'A' and resid 1298 through 1307 Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1320 through 1337 Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'A' and resid 1484 through 1494 removed outlier: 3.587A pdb=" N ARG A1494 " --> pdb=" O GLU A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1531 removed outlier: 3.606A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A1531 " --> pdb=" O GLN A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.949A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.702A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1606 removed outlier: 4.133A pdb=" N THR A1605 " --> pdb=" O GLN A1601 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A1606 " --> pdb=" O GLY A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 Processing helix chain 'A' and resid 1617 through 1628 Processing helix chain 'A' and resid 1636 through 1643 Processing helix chain 'A' and resid 1649 through 1652 Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 3.590A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.716A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.554A pdb=" N LEU B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.134A pdb=" N LYS B 174 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B 175 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.835A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.601A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 404 through 433 Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.576A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.782A pdb=" N ASP B 477 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.703A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 569 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.677A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 577' Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.608A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.643A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 removed outlier: 3.601A pdb=" N ASN B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.123A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 833 through 839 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.591A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1041 through 1044 removed outlier: 3.597A pdb=" N PHE B1044 " --> pdb=" O ASN B1041 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1041 through 1044' Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1173 through 1185 Proline residue: B1179 - end of helix removed outlier: 3.716A pdb=" N TYR B1184 " --> pdb=" O PHE B1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.830A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.861A pdb=" N SER D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 27 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.793A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.509A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 142' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.817A pdb=" N THR G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.535A pdb=" N TYR G 53 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 65 through 70 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'I' and resid 19 through 23 Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.621A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.605A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.945A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 4.464A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN K 83 " --> pdb=" O VAL K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 98 Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.688A pdb=" N MET K 142 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 104 through 107 removed outlier: 3.513A pdb=" N ASN M 107 " --> pdb=" O SER M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 107' Processing helix chain 'M' and resid 118 through 132 removed outlier: 4.163A pdb=" N SER M 122 " --> pdb=" O ASP M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 147 Processing helix chain 'M' and resid 151 through 169 Processing helix chain 'M' and resid 175 through 182 removed outlier: 3.792A pdb=" N ASP M 179 " --> pdb=" O ARG M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 201 Processing helix chain 'M' and resid 203 through 208 Processing helix chain 'M' and resid 209 through 214 Processing helix chain 'M' and resid 218 through 224 Processing helix chain 'M' and resid 226 through 234 Processing helix chain 'M' and resid 241 through 250 removed outlier: 3.551A pdb=" N ASP M 248 " --> pdb=" O ALA M 244 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER M 249 " --> pdb=" O LYS M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 254 No H-bonds generated for 'chain 'M' and resid 252 through 254' Processing helix chain 'M' and resid 255 through 274 Processing helix chain 'M' and resid 279 through 285 Processing helix chain 'M' and resid 291 through 303 removed outlier: 3.527A pdb=" N VAL M 295 " --> pdb=" O PRO M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 315 removed outlier: 3.908A pdb=" N LYS M 314 " --> pdb=" O PHE M 310 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 340 Processing helix chain 'M' and resid 346 through 354 Processing helix chain 'M' and resid 356 through 367 Processing helix chain 'M' and resid 375 through 383 Processing helix chain 'M' and resid 385 through 389 Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'N' and resid 176 through 180 Processing helix chain 'O' and resid 294 through 298 removed outlier: 3.568A pdb=" N ASP O 298 " --> pdb=" O VAL O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 571 through 577 removed outlier: 3.836A pdb=" N ALA O 575 " --> pdb=" O HIS O 571 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU O 577 " --> pdb=" O GLU O 573 " (cutoff:3.500A) Processing helix chain 'O' and resid 583 through 614 Processing helix chain 'O' and resid 618 through 644 Processing helix chain 'O' and resid 671 through 686 Processing helix chain 'O' and resid 695 through 704 removed outlier: 4.046A pdb=" N LEU O 699 " --> pdb=" O GLY O 695 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 724 removed outlier: 3.908A pdb=" N TYR O 715 " --> pdb=" O LEU O 711 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN O 716 " --> pdb=" O ASP O 712 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU O 724 " --> pdb=" O GLN O 720 " (cutoff:3.500A) Processing helix chain 'O' and resid 730 through 744 removed outlier: 3.639A pdb=" N VAL O 737 " --> pdb=" O THR O 733 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE O 740 " --> pdb=" O ILE O 736 " (cutoff:3.500A) Processing helix chain 'O' and resid 752 through 764 Processing helix chain 'O' and resid 765 through 777 Processing helix chain 'P' and resid 97 through 124 Processing helix chain 'P' and resid 125 through 147 removed outlier: 3.714A pdb=" N GLU P 130 " --> pdb=" O PRO P 126 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR P 143 " --> pdb=" O LYS P 139 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP P 146 " --> pdb=" O LYS P 142 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN P 147 " --> pdb=" O THR P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 173 removed outlier: 4.037A pdb=" N THR P 161 " --> pdb=" O HIS P 157 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE P 162 " --> pdb=" O MET P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 188 Processing helix chain 'P' and resid 201 through 206 Processing helix chain 'P' and resid 211 through 215 Processing helix chain 'P' and resid 226 through 238 removed outlier: 3.875A pdb=" N ILE P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 243 Processing helix chain 'P' and resid 249 through 260 removed outlier: 4.152A pdb=" N LEU P 253 " --> pdb=" O CYS P 249 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS P 260 " --> pdb=" O LEU P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 278 removed outlier: 3.647A pdb=" N TYR P 267 " --> pdb=" O PRO P 263 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE P 268 " --> pdb=" O PRO P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 319 Processing helix chain 'P' and resid 327 through 339 removed outlier: 4.146A pdb=" N LEU P 332 " --> pdb=" O LEU P 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER P 333 " --> pdb=" O LYS P 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 355 Processing helix chain 'P' and resid 362 through 369 Processing helix chain 'P' and resid 371 through 385 Processing helix chain 'P' and resid 404 through 416 Processing helix chain 'P' and resid 437 through 449 Processing helix chain 'P' and resid 470 through 491 Processing helix chain 'P' and resid 496 through 510 removed outlier: 3.593A pdb=" N LEU P 510 " --> pdb=" O LYS P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 36 removed outlier: 3.515A pdb=" N LYS Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 159 through 167 Processing helix chain 'Q' and resid 168 through 179 removed outlier: 3.989A pdb=" N ILE Q 175 " --> pdb=" O ARG Q 171 " (cutoff:3.500A) Proline residue: Q 176 - end of helix removed outlier: 3.726A pdb=" N HIS Q 179 " --> pdb=" O ILE Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 192 Processing helix chain 'Q' and resid 207 through 225 removed outlier: 3.556A pdb=" N ASP Q 218 " --> pdb=" O VAL Q 214 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Q 219 " --> pdb=" O THR Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 242 removed outlier: 4.340A pdb=" N LYS Q 234 " --> pdb=" O SER Q 230 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 261 removed outlier: 4.450A pdb=" N GLU Q 256 " --> pdb=" O GLY Q 252 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU Q 258 " --> pdb=" O GLY Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 278 Processing helix chain 'Q' and resid 306 through 322 removed outlier: 3.502A pdb=" N LYS Q 322 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 351 Processing helix chain 'Q' and resid 362 through 382 removed outlier: 3.803A pdb=" N LEU Q 379 " --> pdb=" O LYS Q 375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 421 removed outlier: 3.742A pdb=" N ASN Q 402 " --> pdb=" O ASP Q 398 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR Q 413 " --> pdb=" O HIS Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 427 through 443 removed outlier: 3.798A pdb=" N ILE Q 431 " --> pdb=" O PRO Q 427 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG Q 441 " --> pdb=" O SER Q 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 245 removed outlier: 4.885A pdb=" N ILE A 251 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.775A pdb=" N GLU A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 475 removed outlier: 3.533A pdb=" N LYS A 474 " --> pdb=" O VAL B1071 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 5.828A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.809A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB1, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.194A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 826 through 827 removed outlier: 7.761A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP B 915 " --> pdb=" O CYS B 927 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 826 through 827 removed outlier: 4.638A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 725 through 726 removed outlier: 4.390A pdb=" N ARG B1035 " --> pdb=" O MET B 726 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS B 916 " --> pdb=" O LEU B1036 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP B 915 " --> pdb=" O CYS B 927 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB6, first strand: chain 'A' and resid 1030 through 1032 removed outlier: 6.235A pdb=" N ASP A1040 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU A1045 " --> pdb=" O ASP A1040 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 4.035A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.287A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1461 through 1462 removed outlier: 3.572A pdb=" N GLU A1274 " --> pdb=" O VAL I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.057A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 15.333A pdb=" N HIS G 119 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 16.855A pdb=" N GLU G 102 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.057A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.503A pdb=" N VAL B 97 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC5, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC6, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.725A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.603A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC9, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD1, first strand: chain 'B' and resid 571 through 572 removed outlier: 3.573A pdb=" N ALA B 571 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP B 595 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.649A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.649A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD5, first strand: chain 'B' and resid 824 through 825 removed outlier: 3.843A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 863 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD7, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD8, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD9, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AE1, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.421A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 10.812A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 76 through 88 removed outlier: 4.751A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.212A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE5, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.629A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AE7, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.349A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.531A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AF1, first strand: chain 'G' and resid 153 through 158 removed outlier: 6.934A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR G 136 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP G 246 " --> pdb=" O ARG G 234 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AF3, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.298A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF5, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF6, first strand: chain 'M' and resid 10 through 11 Processing sheet with id=AF7, first strand: chain 'M' and resid 14 through 16 removed outlier: 3.576A pdb=" N LYS M 92 " --> pdb=" O GLN M 16 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 37 through 40 removed outlier: 4.720A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU M 56 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA M 22 " --> pdb=" O LEU N 110 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 43 through 45 Processing sheet with id=AG1, first strand: chain 'M' and resid 304 through 305 removed outlier: 3.527A pdb=" N PHE M 319 " --> pdb=" O VAL M 304 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 343 through 345 Processing sheet with id=AG3, first strand: chain 'O' and resid 57 through 60 removed outlier: 3.550A pdb=" N TYR O 548 " --> pdb=" O VAL O 539 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP O 536 " --> pdb=" O THR O 510 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR O 510 " --> pdb=" O ASP O 536 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU O 538 " --> pdb=" O ILE O 508 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE O 508 " --> pdb=" O LEU O 538 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS O 540 " --> pdb=" O THR O 506 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 201 through 205 removed outlier: 3.991A pdb=" N GLU O 201 " --> pdb=" O LEU O 219 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.629A pdb=" N ILE O 264 " --> pdb=" O LYS O 243 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 305 through 306 Processing sheet with id=AG7, first strand: chain 'O' and resid 362 through 365 removed outlier: 3.989A pdb=" N ILE O 372 " --> pdb=" O ILE O 383 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 402 through 405 removed outlier: 6.878A pdb=" N THR O 417 " --> pdb=" O ARG O 403 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 452 through 457 Processing sheet with id=AH1, first strand: chain 'O' and resid 452 through 457 2133 hydrogen bonds defined for protein. 5853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 27.49 Time building geometry restraints manager: 20.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8232 1.32 - 1.44: 13429 1.44 - 1.57: 27797 1.57 - 1.70: 244 1.70 - 1.82: 333 Bond restraints: 50035 Sorted by residual: bond pdb=" CA MET P 402 " pdb=" C MET P 402 " ideal model delta sigma weight residual 1.523 1.637 -0.114 1.34e-02 5.57e+03 7.17e+01 bond pdb=" CA ILE O 736 " pdb=" C ILE O 736 " ideal model delta sigma weight residual 1.523 1.627 -0.104 1.27e-02 6.20e+03 6.66e+01 bond pdb=" N PRO B 78 " pdb=" CD PRO B 78 " ideal model delta sigma weight residual 1.473 1.361 0.112 1.40e-02 5.10e+03 6.46e+01 bond pdb=" CA ILE O 297 " pdb=" C ILE O 297 " ideal model delta sigma weight residual 1.523 1.620 -0.097 1.27e-02 6.20e+03 5.78e+01 bond pdb=" CA HIS P 511 " pdb=" C HIS P 511 " ideal model delta sigma weight residual 1.524 1.629 -0.105 1.40e-02 5.10e+03 5.60e+01 ... (remaining 50030 not shown) Histogram of bond angle deviations from ideal: 86.75 - 97.53: 22 97.53 - 108.31: 4438 108.31 - 119.09: 38041 119.09 - 129.88: 25246 129.88 - 140.66: 321 Bond angle restraints: 68068 Sorted by residual: angle pdb=" N LYS I 39 " pdb=" CA LYS I 39 " pdb=" C LYS I 39 " ideal model delta sigma weight residual 111.28 87.60 23.68 1.09e+00 8.42e-01 4.72e+02 angle pdb=" N HIS O 705 " pdb=" CA HIS O 705 " pdb=" C HIS O 705 " ideal model delta sigma weight residual 113.15 92.30 20.85 1.19e+00 7.06e-01 3.07e+02 angle pdb=" C LYS Q 133 " pdb=" N PRO Q 134 " pdb=" CA PRO Q 134 " ideal model delta sigma weight residual 119.84 140.66 -20.82 1.25e+00 6.40e-01 2.77e+02 angle pdb=" C PHE P 125 " pdb=" N PRO P 126 " pdb=" CA PRO P 126 " ideal model delta sigma weight residual 119.84 140.15 -20.31 1.25e+00 6.40e-01 2.64e+02 angle pdb=" N THR Q 217 " pdb=" CA THR Q 217 " pdb=" C THR Q 217 " ideal model delta sigma weight residual 111.02 129.24 -18.22 1.22e+00 6.72e-01 2.23e+02 ... (remaining 68063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 29419 34.80 - 69.60: 772 69.60 - 104.39: 46 104.39 - 139.19: 2 139.19 - 173.99: 1 Dihedral angle restraints: 30240 sinusoidal: 13122 harmonic: 17118 Sorted by residual: dihedral pdb=" C LYS A 410 " pdb=" N LYS A 410 " pdb=" CA LYS A 410 " pdb=" CB LYS A 410 " ideal model delta harmonic sigma weight residual -122.60 -157.49 34.89 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" N LYS A 410 " pdb=" C LYS A 410 " pdb=" CA LYS A 410 " pdb=" CB LYS A 410 " ideal model delta harmonic sigma weight residual 122.80 157.10 -34.30 0 2.50e+00 1.60e-01 1.88e+02 dihedral pdb=" C LEU O 654 " pdb=" N LEU O 654 " pdb=" CA LEU O 654 " pdb=" CB LEU O 654 " ideal model delta harmonic sigma weight residual -122.60 -148.47 25.87 0 2.50e+00 1.60e-01 1.07e+02 ... (remaining 30237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 7507 0.296 - 0.591: 117 0.591 - 0.887: 9 0.887 - 1.182: 2 1.182 - 1.478: 1 Chirality restraints: 7636 Sorted by residual: chirality pdb=" CA LYS A 410 " pdb=" N LYS A 410 " pdb=" C LYS A 410 " pdb=" CB LYS A 410 " both_signs ideal model delta sigma weight residual False 2.51 1.03 1.48 2.00e-01 2.50e+01 5.46e+01 chirality pdb=" CA LEU O 654 " pdb=" N LEU O 654 " pdb=" C LEU O 654 " pdb=" CB LEU O 654 " both_signs ideal model delta sigma weight residual False 2.51 1.34 1.17 2.00e-01 2.50e+01 3.42e+01 chirality pdb=" CA GLU P 246 " pdb=" N GLU P 246 " pdb=" C GLU P 246 " pdb=" CB GLU P 246 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 ... (remaining 7633 not shown) Planarity restraints: 8374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 188 " 0.100 2.00e-02 2.50e+03 6.15e-02 6.61e+01 pdb=" CG PHE Q 188 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 188 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 188 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 188 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 188 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE Q 188 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 270 " 0.083 2.00e-02 2.50e+03 5.20e-02 4.73e+01 pdb=" CG PHE Q 270 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 270 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 270 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 270 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 270 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE Q 270 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP O 770 " -0.032 2.00e-02 2.50e+03 6.86e-02 4.70e+01 pdb=" CG ASP O 770 " 0.119 2.00e-02 2.50e+03 pdb=" OD1 ASP O 770 " -0.044 2.00e-02 2.50e+03 pdb=" OD2 ASP O 770 " -0.043 2.00e-02 2.50e+03 ... (remaining 8371 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.79: 204 1.79 - 2.57: 2068 2.57 - 3.34: 68813 3.34 - 4.12: 127743 4.12 - 4.90: 220909 Nonbonded interactions: 419737 Sorted by model distance: nonbonded pdb=" CD LYS Q 136 " pdb=" CG HIS Q 304 " model vdw 1.010 3.660 nonbonded pdb=" OE2 GLU Q 124 " pdb=" NH2 ARG Q 291 " model vdw 1.015 2.520 nonbonded pdb=" N VAL Q 353 " pdb=" CZ PHE Q 358 " model vdw 1.026 3.420 nonbonded pdb=" CD GLN A 407 " pdb=" NH2 ARG M 166 " model vdw 1.033 3.350 nonbonded pdb=" N VAL Q 353 " pdb=" CE2 PHE Q 358 " model vdw 1.052 3.420 ... (remaining 419732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 4.840 Check model and map are aligned: 0.760 Set scattering table: 0.460 Process input model: 153.630 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.190 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 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 : 0.010 0.114 50035 Z= 0.623 Angle : 1.618 24.048 68068 Z= 0.992 Chirality : 0.093 1.478 7636 Planarity : 0.011 0.144 8374 Dihedral : 14.972 173.990 19134 Min Nonbonded Distance : 1.010 Molprobity Statistics. All-atom Clashscore : 70.90 Ramachandran Plot: Outliers : 4.19 % Allowed : 8.51 % Favored : 87.29 % Rotamer: Outliers : 4.84 % Allowed : 4.92 % Favored : 90.24 % Cbeta Deviations : 0.99 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.09), residues: 5722 helix: -1.80 (0.09), residues: 2092 sheet: -1.63 (0.17), residues: 748 loop : -2.75 (0.10), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP Q 273 HIS 0.028 0.003 HIS A 580 PHE 0.100 0.005 PHE Q 188 TYR 0.096 0.008 TYR Q 443 ARG 0.097 0.011 ARG J 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1857 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1605 time to evaluate : 5.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 219 LEU cc_start: 0.7110 (tp) cc_final: 0.6861 (tp) REVERT: A 243 PHE cc_start: 0.6276 (m-80) cc_final: 0.6039 (m-10) REVERT: A 471 MET cc_start: 0.5881 (mtp) cc_final: 0.5642 (mtt) REVERT: A 1018 TYR cc_start: 0.5234 (t80) cc_final: 0.4978 (t80) REVERT: A 1030 VAL cc_start: 0.8374 (t) cc_final: 0.8173 (t) REVERT: A 1272 VAL cc_start: 0.6445 (t) cc_final: 0.6160 (t) REVERT: A 1623 THR cc_start: 0.5098 (m) cc_final: 0.4866 (m) REVERT: B 91 LEU cc_start: 0.2101 (OUTLIER) cc_final: -0.0014 (mt) REVERT: B 229 TYR cc_start: 0.5793 (m-80) cc_final: 0.5496 (m-80) REVERT: B 462 GLN cc_start: 0.6672 (tt0) cc_final: 0.6445 (tt0) REVERT: B 524 SER cc_start: 0.7331 (m) cc_final: 0.7006 (t) REVERT: B 664 VAL cc_start: 0.8747 (t) cc_final: 0.8175 (p) REVERT: B 821 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.6958 (mm) REVERT: B 845 LEU cc_start: 0.7153 (mt) cc_final: 0.6881 (mp) REVERT: B 954 PHE cc_start: 0.7820 (m-80) cc_final: 0.7525 (m-10) REVERT: B 1046 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.8963 (m) REVERT: B 1194 ILE cc_start: 0.3727 (OUTLIER) cc_final: 0.2921 (mp) REVERT: C 192 LEU cc_start: 0.7439 (tp) cc_final: 0.7170 (tp) REVERT: C 204 LEU cc_start: 0.4779 (pp) cc_final: 0.4532 (pp) REVERT: E 111 VAL cc_start: 0.6018 (t) cc_final: 0.5710 (t) REVERT: H 102 TYR cc_start: 0.5149 (p90) cc_final: 0.4944 (p90) REVERT: L 67 PHE cc_start: 0.5721 (m-80) cc_final: 0.5129 (m-80) REVERT: N 131 LEU cc_start: 0.6863 (pp) cc_final: 0.6269 (pp) REVERT: O 443 ASP cc_start: 0.5108 (m-30) cc_final: 0.4895 (m-30) REVERT: O 481 PHE cc_start: 0.3789 (m-80) cc_final: 0.2786 (m-80) REVERT: P 351 ASN cc_start: 0.5681 (m-40) cc_final: 0.5402 (m110) REVERT: P 352 ILE cc_start: 0.6047 (mm) cc_final: 0.5376 (mm) REVERT: P 512 ARG cc_start: 0.1953 (OUTLIER) cc_final: -0.0307 (mtt90) REVERT: Q 204 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.3906 (pm20) REVERT: Q 205 VAL cc_start: 0.6579 (t) cc_final: 0.6267 (m) REVERT: Q 271 LEU cc_start: 0.7520 (mt) cc_final: 0.7165 (mt) REVERT: Q 385 ASN cc_start: 0.5049 (OUTLIER) cc_final: 0.4777 (p0) outliers start: 252 outliers final: 107 residues processed: 1816 average time/residue: 0.6413 time to fit residues: 1879.6013 Evaluate side-chains 1012 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 898 time to evaluate : 6.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 463 LYS Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1174 THR Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain E residue 125 PRO Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 237 GLU Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain O residue 351 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 439 LYS Chi-restraints excluded: chain O residue 568 ILE Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 620 ASP Chi-restraints excluded: chain O residue 650 LEU Chi-restraints excluded: chain O residue 655 SER Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain O residue 665 ASN Chi-restraints excluded: chain O residue 671 SER Chi-restraints excluded: chain O residue 689 GLN Chi-restraints excluded: chain O residue 712 ASP Chi-restraints excluded: chain O residue 714 PHE Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 747 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 151 GLU Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 198 ILE Chi-restraints excluded: chain P residue 279 THR Chi-restraints excluded: chain P residue 281 ILE Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 284 LEU Chi-restraints excluded: chain P residue 341 ARG Chi-restraints excluded: chain P residue 355 VAL Chi-restraints excluded: chain P residue 365 ASP Chi-restraints excluded: chain P residue 371 GLU Chi-restraints excluded: chain P residue 386 LEU Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 453 PHE Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 495 LYS Chi-restraints excluded: chain P residue 497 GLN Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 147 GLN Chi-restraints excluded: chain Q residue 148 ASN Chi-restraints excluded: chain Q residue 150 GLN Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 180 CYS Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 203 SER Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 246 GLN Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 250 LEU Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 277 ILE Chi-restraints excluded: chain Q residue 292 SER Chi-restraints excluded: chain Q residue 293 ILE Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 303 THR Chi-restraints excluded: chain Q residue 364 VAL Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 385 ASN Chi-restraints excluded: chain Q residue 388 LYS Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 395 LEU Chi-restraints excluded: chain Q residue 397 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 493 optimal weight: 30.0000 chunk 443 optimal weight: 30.0000 chunk 246 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 458 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 531 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 332 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN A 998 HIS A1020 GLN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 147 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 183 HIS B 197 ASN B 248 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN B 555 GLN B 575 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN B 715 ASN B1010 ASN ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 61 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN M 71 GLN M 74 ASN ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 324 ASN ** M 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS O 215 ASN O 239 HIS O 267 ASN ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 401 ASN ** O 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 HIS ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 490 GLN O 579 ASN ** O 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 486 GLN P 497 GLN P 511 HIS Q 184 ASN Q 246 GLN ** Q 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 50035 Z= 0.366 Angle : 1.036 32.848 68068 Z= 0.532 Chirality : 0.053 0.344 7636 Planarity : 0.007 0.093 8374 Dihedral : 15.383 159.287 7743 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 29.66 Ramachandran Plot: Outliers : 1.56 % Allowed : 7.25 % Favored : 91.19 % Rotamer: Outliers : 5.82 % Allowed : 14.16 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.27 % 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: -1.92 (0.10), residues: 5722 helix: -0.48 (0.10), residues: 2163 sheet: -1.09 (0.17), residues: 720 loop : -1.96 (0.11), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP O 399 HIS 0.020 0.002 HIS M 351 PHE 0.054 0.003 PHE P 110 TYR 0.047 0.003 TYR B1184 ARG 0.013 0.001 ARG P 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1382 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1079 time to evaluate : 5.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 501 PHE cc_start: 0.6144 (m-10) cc_final: 0.5933 (m-10) REVERT: A 1063 MET cc_start: 0.5887 (mmm) cc_final: 0.5615 (tpp) REVERT: B 91 LEU cc_start: 0.0299 (OUTLIER) cc_final: -0.1505 (mp) REVERT: B 96 SER cc_start: 0.6048 (OUTLIER) cc_final: 0.5599 (p) REVERT: B 364 LYS cc_start: 0.6681 (mttt) cc_final: 0.6477 (mttt) REVERT: B 966 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7583 (p) REVERT: B 1040 VAL cc_start: 0.6428 (OUTLIER) cc_final: 0.6218 (t) REVERT: B 1194 ILE cc_start: 0.3402 (OUTLIER) cc_final: 0.2450 (mp) REVERT: C 70 ILE cc_start: 0.6820 (pt) cc_final: 0.6442 (pt) REVERT: E 74 ASP cc_start: 0.6038 (OUTLIER) cc_final: 0.5557 (p0) REVERT: E 187 TYR cc_start: 0.5907 (t80) cc_final: 0.5651 (t80) REVERT: F 120 ILE cc_start: 0.6884 (mt) cc_final: 0.6656 (mm) REVERT: G 238 THR cc_start: 0.4879 (OUTLIER) cc_final: 0.4565 (p) REVERT: L 43 THR cc_start: 0.6513 (p) cc_final: 0.6281 (m) REVERT: N 93 THR cc_start: 0.4980 (m) cc_final: 0.4761 (m) REVERT: N 107 MET cc_start: 0.5363 (mmp) cc_final: 0.5093 (mmp) REVERT: P 306 VAL cc_start: 0.6482 (t) cc_final: 0.6243 (t) REVERT: P 512 ARG cc_start: 0.2018 (OUTLIER) cc_final: 0.1268 (mtm180) REVERT: Q 204 GLU cc_start: 0.5133 (OUTLIER) cc_final: 0.4525 (pm20) REVERT: Q 205 VAL cc_start: 0.5963 (t) cc_final: 0.5496 (m) outliers start: 303 outliers final: 150 residues processed: 1286 average time/residue: 0.5925 time to fit residues: 1263.2750 Evaluate side-chains 977 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 818 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1174 THR Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 25 ARG Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 333 LEU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 178 GLU Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 274 ILE Chi-restraints excluded: chain O residue 312 LEU Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 379 LYS Chi-restraints excluded: chain O residue 436 ILE Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 468 VAL Chi-restraints excluded: chain O residue 492 LEU Chi-restraints excluded: chain O residue 571 HIS Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain O residue 664 GLU Chi-restraints excluded: chain O residue 665 ASN Chi-restraints excluded: chain O residue 672 ILE Chi-restraints excluded: chain O residue 689 GLN Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 747 LEU Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 289 ARG Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 365 ASP Chi-restraints excluded: chain P residue 371 GLU Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 497 GLN Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 142 ARG Chi-restraints excluded: chain Q residue 157 MET Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 160 HIS Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 180 CYS Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 211 ARG Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 302 ARG Chi-restraints excluded: chain Q residue 303 THR Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 388 LYS Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 410 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 295 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 442 optimal weight: 50.0000 chunk 361 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 532 optimal weight: 5.9990 chunk 574 optimal weight: 6.9990 chunk 473 optimal weight: 10.0000 chunk 527 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 426 optimal weight: 0.5980 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS A 344 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 ASN ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN F 100 GLN F 104 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 GLN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 395 GLN ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 613 HIS ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 GLN ** P 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 300 ASN ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 339 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 385 ASN ** Q 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 50035 Z= 0.317 Angle : 0.903 28.090 68068 Z= 0.460 Chirality : 0.049 0.348 7636 Planarity : 0.006 0.103 8374 Dihedral : 14.861 159.509 7577 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 29.13 Ramachandran Plot: Outliers : 1.05 % Allowed : 7.41 % Favored : 91.54 % Rotamer: Outliers : 5.65 % Allowed : 16.90 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.05 % 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 (0.11), residues: 5722 helix: -0.01 (0.10), residues: 2159 sheet: -0.90 (0.18), residues: 721 loop : -1.76 (0.12), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 595 HIS 0.012 0.002 HIS P 131 PHE 0.042 0.003 PHE C 67 TYR 0.044 0.002 TYR Q 278 ARG 0.011 0.001 ARG Q 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 897 time to evaluate : 6.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.6603 (p) cc_final: 0.6347 (p) REVERT: A 92 ASN cc_start: 0.5914 (OUTLIER) cc_final: 0.5391 (p0) REVERT: B 46 ILE cc_start: 0.7871 (mm) cc_final: 0.7590 (mm) REVERT: B 91 LEU cc_start: 0.0069 (OUTLIER) cc_final: -0.1340 (mt) REVERT: B 188 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: B 712 SER cc_start: 0.6487 (p) cc_final: 0.6281 (p) REVERT: B 787 MET cc_start: 0.6496 (ppp) cc_final: 0.6049 (ppp) REVERT: B 788 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8407 (mm) REVERT: B 807 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6641 (mt-10) REVERT: C 70 ILE cc_start: 0.6645 (pt) cc_final: 0.6306 (mm) REVERT: E 74 ASP cc_start: 0.5841 (OUTLIER) cc_final: 0.5459 (p0) REVERT: H 25 ARG cc_start: 0.4148 (OUTLIER) cc_final: 0.3012 (ttp80) REVERT: J 49 MET cc_start: 0.7329 (tpp) cc_final: 0.6198 (tpp) REVERT: J 55 ASP cc_start: 0.5515 (OUTLIER) cc_final: 0.5209 (t0) REVERT: L 67 PHE cc_start: 0.6476 (m-80) cc_final: 0.6050 (m-80) REVERT: O 386 MET cc_start: 0.3630 (ptt) cc_final: 0.3326 (mtm) REVERT: P 306 VAL cc_start: 0.6089 (t) cc_final: 0.5754 (t) REVERT: Q 204 GLU cc_start: 0.5593 (OUTLIER) cc_final: 0.4948 (pm20) REVERT: Q 339 ASN cc_start: 0.6991 (OUTLIER) cc_final: 0.6421 (p0) outliers start: 294 outliers final: 184 residues processed: 1086 average time/residue: 0.5804 time to fit residues: 1055.2980 Evaluate side-chains 947 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 753 time to evaluate : 5.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1623 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 807 GLU Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 924 LYS Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1161 ASP Chi-restraints excluded: chain B residue 1174 THR Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 25 ARG Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 330 CYS Chi-restraints excluded: chain M residue 333 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 263 ILE Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 421 ILE Chi-restraints excluded: chain O residue 422 ILE Chi-restraints excluded: chain O residue 436 ILE Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 453 VAL Chi-restraints excluded: chain O residue 468 VAL Chi-restraints excluded: chain O residue 492 LEU Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain O residue 664 GLU Chi-restraints excluded: chain O residue 691 VAL Chi-restraints excluded: chain O residue 747 LEU Chi-restraints excluded: chain O residue 770 ASP Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 280 ASP Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 289 ARG Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 365 ASP Chi-restraints excluded: chain P residue 371 GLU Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 488 LEU Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 160 HIS Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 211 ARG Chi-restraints excluded: chain Q residue 215 THR Chi-restraints excluded: chain Q residue 229 TRP Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 302 ARG Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 339 ASN Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 410 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 525 optimal weight: 7.9990 chunk 400 optimal weight: 30.0000 chunk 276 optimal weight: 6.9990 chunk 58 optimal weight: 0.0050 chunk 253 optimal weight: 5.9990 chunk 357 optimal weight: 20.0000 chunk 534 optimal weight: 20.0000 chunk 565 optimal weight: 20.0000 chunk 279 optimal weight: 4.9990 chunk 506 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 HIS E 3 GLN E 61 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 324 ASN ** M 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 487 ASN ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 300 ASN ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 GLN ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 50035 Z= 0.294 Angle : 0.836 21.152 68068 Z= 0.426 Chirality : 0.047 0.290 7636 Planarity : 0.006 0.086 8374 Dihedral : 14.645 157.113 7552 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 28.00 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.27 % Favored : 91.75 % Rotamer: Outliers : 5.69 % Allowed : 18.44 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.05 % 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: -1.23 (0.11), residues: 5722 helix: 0.24 (0.11), residues: 2153 sheet: -0.93 (0.18), residues: 736 loop : -1.63 (0.12), residues: 2833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 54 HIS 0.017 0.001 HIS M 351 PHE 0.047 0.002 PHE B 464 TYR 0.038 0.002 TYR B1184 ARG 0.008 0.001 ARG B1130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 830 time to evaluate : 5.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.6174 (OUTLIER) cc_final: 0.5371 (p0) REVERT: A 438 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.7020 (mm) REVERT: A 708 THR cc_start: 0.6228 (m) cc_final: 0.6024 (m) REVERT: A 1223 ARG cc_start: 0.5166 (OUTLIER) cc_final: 0.4186 (ptp-110) REVERT: B 46 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7441 (tp) REVERT: B 91 LEU cc_start: 0.0386 (OUTLIER) cc_final: -0.0743 (mt) REVERT: B 188 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6602 (m-30) REVERT: B 513 LYS cc_start: 0.5189 (OUTLIER) cc_final: 0.4878 (mtmt) REVERT: B 589 ASP cc_start: 0.5596 (OUTLIER) cc_final: 0.5342 (t0) REVERT: C 192 LEU cc_start: 0.8032 (tp) cc_final: 0.7652 (tt) REVERT: D 37 LEU cc_start: 0.5508 (pp) cc_final: 0.4955 (pp) REVERT: J 49 MET cc_start: 0.7570 (tpp) cc_final: 0.6597 (tpp) REVERT: J 55 ASP cc_start: 0.5262 (OUTLIER) cc_final: 0.4812 (t0) REVERT: Q 204 GLU cc_start: 0.5482 (OUTLIER) cc_final: 0.5008 (pm20) outliers start: 296 outliers final: 197 residues processed: 1027 average time/residue: 0.5723 time to fit residues: 993.7500 Evaluate side-chains 935 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 728 time to evaluate : 5.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1223 ARG Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1070 ARG Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1174 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 44 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain M residue 330 CYS Chi-restraints excluded: chain M residue 333 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 422 ILE Chi-restraints excluded: chain O residue 436 ILE Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 453 VAL Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain O residue 691 VAL Chi-restraints excluded: chain O residue 747 LEU Chi-restraints excluded: chain O residue 770 ASP Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 280 ASP Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 289 ARG Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 365 ASP Chi-restraints excluded: chain P residue 371 GLU Chi-restraints excluded: chain P residue 406 GLN Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 488 LEU Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 142 ARG Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 211 ARG Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 229 TRP Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 275 CYS Chi-restraints excluded: chain Q residue 285 VAL Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 409 HIS Chi-restraints excluded: chain Q residue 410 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 470 optimal weight: 6.9990 chunk 320 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 421 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 482 optimal weight: 50.0000 chunk 390 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 507 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 HIS B 979 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 HIS E 61 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 617 HIS ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 207 ASN ** Q 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 263 ASN ** Q 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 50035 Z= 0.319 Angle : 0.830 18.068 68068 Z= 0.423 Chirality : 0.047 0.298 7636 Planarity : 0.006 0.092 8374 Dihedral : 14.622 156.154 7549 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 28.73 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.43 % Favored : 91.66 % Rotamer: Outliers : 5.80 % Allowed : 19.61 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.07 % 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: -1.16 (0.11), residues: 5722 helix: 0.28 (0.11), residues: 2160 sheet: -0.87 (0.18), residues: 734 loop : -1.57 (0.12), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 595 HIS 0.009 0.001 HIS P 131 PHE 0.044 0.002 PHE B 464 TYR 0.043 0.002 TYR J 21 ARG 0.007 0.001 ARG O 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 770 time to evaluate : 6.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.6165 (OUTLIER) cc_final: 0.5477 (p0) REVERT: B 46 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7412 (tp) REVERT: B 91 LEU cc_start: 0.0513 (OUTLIER) cc_final: -0.0672 (mt) REVERT: B 268 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7015 (tm-30) REVERT: B 409 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.7135 (t80) REVERT: B 589 ASP cc_start: 0.5699 (OUTLIER) cc_final: 0.5416 (t0) REVERT: C 192 LEU cc_start: 0.8039 (tp) cc_final: 0.7711 (tt) REVERT: I 64 LYS cc_start: 0.5547 (pttt) cc_final: 0.5208 (pttm) REVERT: J 49 MET cc_start: 0.7510 (tpp) cc_final: 0.6686 (tpp) REVERT: J 55 ASP cc_start: 0.5360 (OUTLIER) cc_final: 0.4854 (t0) REVERT: Q 204 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.4967 (pm20) outliers start: 302 outliers final: 217 residues processed: 973 average time/residue: 0.5754 time to fit residues: 951.9879 Evaluate side-chains 916 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 692 time to evaluate : 5.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1622 LEU Chi-restraints excluded: chain A residue 1623 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 44 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 330 CYS Chi-restraints excluded: chain M residue 333 LEU Chi-restraints excluded: chain M residue 362 SER Chi-restraints excluded: chain N residue 66 LYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 263 ILE Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain O residue 379 LYS Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 422 ILE Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 512 LEU Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 538 LEU Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain O residue 693 PHE Chi-restraints excluded: chain O residue 746 ARG Chi-restraints excluded: chain O residue 747 LEU Chi-restraints excluded: chain O residue 770 ASP Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 177 TYR Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 211 TYR Chi-restraints excluded: chain P residue 280 ASP Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 323 ASP Chi-restraints excluded: chain P residue 365 ASP Chi-restraints excluded: chain P residue 371 GLU Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 488 LEU Chi-restraints excluded: chain P residue 510 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 229 TRP Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 253 ILE Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 264 SER Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 275 CYS Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 364 VAL Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 409 HIS Chi-restraints excluded: chain Q residue 410 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 190 optimal weight: 2.9990 chunk 509 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 331 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 566 optimal weight: 9.9990 chunk 469 optimal weight: 10.0000 chunk 262 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 297 optimal weight: 9.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1438 ASN B 87 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 HIS E 61 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 665 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 ASN Q 221 HIS ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 287 ASN ** Q 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 434 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 50035 Z= 0.237 Angle : 0.812 16.249 68068 Z= 0.408 Chirality : 0.047 0.292 7636 Planarity : 0.005 0.100 8374 Dihedral : 14.437 154.584 7534 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.83 % Favored : 92.31 % Rotamer: Outliers : 4.76 % Allowed : 21.86 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: -0.96 (0.11), residues: 5722 helix: 0.45 (0.11), residues: 2163 sheet: -0.91 (0.18), residues: 739 loop : -1.42 (0.12), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 595 HIS 0.018 0.001 HIS Q 407 PHE 0.039 0.002 PHE B 464 TYR 0.032 0.002 TYR B1184 ARG 0.010 0.001 ARG O 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 799 time to evaluate : 5.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.5080 (t80) cc_final: 0.4879 (t80) REVERT: A 92 ASN cc_start: 0.6148 (OUTLIER) cc_final: 0.5635 (p0) REVERT: A 592 GLN cc_start: 0.6882 (tm-30) cc_final: 0.6665 (tm-30) REVERT: A 818 THR cc_start: 0.7066 (p) cc_final: 0.6720 (t) REVERT: B 46 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7490 (tp) REVERT: B 91 LEU cc_start: 0.0176 (OUTLIER) cc_final: -0.0887 (mp) REVERT: B 155 VAL cc_start: 0.7878 (m) cc_final: 0.7662 (m) REVERT: B 268 GLU cc_start: 0.7572 (tm-30) cc_final: 0.6960 (tm-30) REVERT: B 589 ASP cc_start: 0.5713 (OUTLIER) cc_final: 0.5401 (t0) REVERT: C 192 LEU cc_start: 0.7902 (tp) cc_final: 0.7637 (tt) REVERT: E 74 ASP cc_start: 0.5756 (OUTLIER) cc_final: 0.5278 (p0) REVERT: H 38 LEU cc_start: 0.4588 (tp) cc_final: 0.4304 (tt) REVERT: I 64 LYS cc_start: 0.5466 (pttt) cc_final: 0.5103 (pttp) REVERT: J 9 SER cc_start: 0.6717 (m) cc_final: 0.6492 (m) REVERT: J 49 MET cc_start: 0.7391 (tpp) cc_final: 0.6620 (tpp) REVERT: J 55 ASP cc_start: 0.5272 (OUTLIER) cc_final: 0.4931 (t0) REVERT: N 80 MET cc_start: 0.5105 (mmt) cc_final: 0.4826 (mmt) REVERT: O 747 LEU cc_start: 0.3623 (OUTLIER) cc_final: 0.3351 (mp) REVERT: P 246 GLU cc_start: 0.3211 (OUTLIER) cc_final: 0.2771 (pm20) REVERT: Q 204 GLU cc_start: 0.5070 (OUTLIER) cc_final: 0.4607 (pm20) outliers start: 248 outliers final: 185 residues processed: 967 average time/residue: 0.5707 time to fit residues: 942.9446 Evaluate side-chains 912 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 718 time to evaluate : 5.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 924 LYS Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain M residue 333 LEU Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 263 ILE Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain O residue 365 TRP Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 379 LYS Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 422 ILE Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 512 LEU Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 538 LEU Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain O residue 693 PHE Chi-restraints excluded: chain O residue 746 ARG Chi-restraints excluded: chain O residue 747 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 192 TYR Chi-restraints excluded: chain P residue 246 GLU Chi-restraints excluded: chain P residue 280 ASP Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 365 ASP Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 488 LEU Chi-restraints excluded: chain P residue 510 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 133 LYS Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 264 SER Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 367 ILE Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 410 TYR Chi-restraints excluded: chain Q residue 434 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 545 optimal weight: 50.0000 chunk 63 optimal weight: 0.0770 chunk 322 optimal weight: 20.0000 chunk 413 optimal weight: 40.0000 chunk 320 optimal weight: 3.9990 chunk 476 optimal weight: 7.9990 chunk 316 optimal weight: 20.0000 chunk 563 optimal weight: 4.9990 chunk 352 optimal weight: 40.0000 chunk 343 optimal weight: 40.0000 chunk 260 optimal weight: 20.0000 overall best weight: 7.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 ASN ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN B 168 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 GLN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 665 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 50035 Z= 0.361 Angle : 0.842 17.427 68068 Z= 0.431 Chirality : 0.048 0.322 7636 Planarity : 0.006 0.099 8374 Dihedral : 14.484 154.193 7529 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 31.10 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.04 % Favored : 91.14 % Rotamer: Outliers : 5.47 % Allowed : 22.30 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.07 (0.11), residues: 5722 helix: 0.35 (0.11), residues: 2162 sheet: -0.90 (0.18), residues: 750 loop : -1.50 (0.12), residues: 2810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP O 438 HIS 0.014 0.002 HIS Q 407 PHE 0.044 0.002 PHE B 464 TYR 0.045 0.002 TYR E 211 ARG 0.007 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 712 time to evaluate : 5.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.6292 (OUTLIER) cc_final: 0.5638 (p0) REVERT: A 105 CYS cc_start: 0.5644 (OUTLIER) cc_final: 0.5186 (p) REVERT: A 495 ILE cc_start: 0.8855 (tp) cc_final: 0.8631 (tt) REVERT: A 1439 MET cc_start: 0.3837 (mpp) cc_final: 0.3611 (mpp) REVERT: B 91 LEU cc_start: 0.0671 (OUTLIER) cc_final: -0.0387 (mt) REVERT: B 155 VAL cc_start: 0.7936 (OUTLIER) cc_final: 0.7706 (m) REVERT: B 268 GLU cc_start: 0.7590 (tm-30) cc_final: 0.6988 (tm-30) REVERT: B 589 ASP cc_start: 0.5860 (OUTLIER) cc_final: 0.5585 (t0) REVERT: B 625 GLU cc_start: 0.5304 (tt0) cc_final: 0.5055 (tt0) REVERT: H 38 LEU cc_start: 0.4695 (tp) cc_final: 0.4447 (tt) REVERT: J 49 MET cc_start: 0.7333 (tpp) cc_final: 0.6543 (tpp) REVERT: J 55 ASP cc_start: 0.5593 (OUTLIER) cc_final: 0.5046 (t0) REVERT: P 246 GLU cc_start: 0.3090 (OUTLIER) cc_final: 0.2167 (pm20) REVERT: Q 204 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.4889 (pm20) outliers start: 285 outliers final: 219 residues processed: 908 average time/residue: 0.5617 time to fit residues: 873.6925 Evaluate side-chains 894 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 667 time to evaluate : 5.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1036 ASN Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 924 LYS Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain M residue 330 CYS Chi-restraints excluded: chain M residue 333 LEU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 376 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 263 ILE Chi-restraints excluded: chain O residue 302 VAL Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain O residue 365 TRP Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 379 LYS Chi-restraints excluded: chain O residue 422 ILE Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 538 LEU Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 665 ASN Chi-restraints excluded: chain O residue 691 VAL Chi-restraints excluded: chain O residue 693 PHE Chi-restraints excluded: chain O residue 746 ARG Chi-restraints excluded: chain O residue 747 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 177 TYR Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 211 TYR Chi-restraints excluded: chain P residue 246 GLU Chi-restraints excluded: chain P residue 280 ASP Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 323 ASP Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 488 LEU Chi-restraints excluded: chain P residue 510 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 229 TRP Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 264 SER Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 313 LEU Chi-restraints excluded: chain Q residue 316 SER Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 364 VAL Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 409 HIS Chi-restraints excluded: chain Q residue 410 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 348 optimal weight: 0.5980 chunk 225 optimal weight: 9.9990 chunk 336 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 358 optimal weight: 6.9990 chunk 384 optimal weight: 7.9990 chunk 278 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 443 optimal weight: 30.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 ASN ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 GLN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN E 115 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN M 238 ASN ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 665 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 50035 Z= 0.228 Angle : 0.825 16.008 68068 Z= 0.411 Chirality : 0.047 0.303 7636 Planarity : 0.005 0.100 8374 Dihedral : 14.388 155.587 7521 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.13 % Favored : 92.03 % Rotamer: Outliers : 4.36 % Allowed : 23.90 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: -0.93 (0.11), residues: 5722 helix: 0.46 (0.11), residues: 2162 sheet: -0.88 (0.18), residues: 738 loop : -1.40 (0.12), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP O 438 HIS 0.017 0.001 HIS P 131 PHE 0.033 0.002 PHE N 58 TYR 0.028 0.002 TYR B1184 ARG 0.011 0.001 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 775 time to evaluate : 5.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.6109 (OUTLIER) cc_final: 0.5562 (p0) REVERT: A 105 CYS cc_start: 0.5474 (OUTLIER) cc_final: 0.5028 (p) REVERT: A 495 ILE cc_start: 0.8935 (tp) cc_final: 0.8726 (tt) REVERT: A 818 THR cc_start: 0.6949 (p) cc_final: 0.6683 (t) REVERT: A 1038 ILE cc_start: 0.6585 (mp) cc_final: 0.6366 (mt) REVERT: B 57 ASP cc_start: 0.4517 (OUTLIER) cc_final: 0.4262 (t0) REVERT: B 91 LEU cc_start: 0.1596 (OUTLIER) cc_final: 0.0450 (mt) REVERT: B 110 ASN cc_start: 0.5175 (OUTLIER) cc_final: 0.4709 (p0) REVERT: B 155 VAL cc_start: 0.7854 (OUTLIER) cc_final: 0.7613 (m) REVERT: B 589 ASP cc_start: 0.5704 (OUTLIER) cc_final: 0.5347 (t0) REVERT: H 38 LEU cc_start: 0.4602 (tp) cc_final: 0.4363 (tt) REVERT: J 49 MET cc_start: 0.7451 (tpp) cc_final: 0.6845 (tpp) REVERT: P 246 GLU cc_start: 0.3328 (OUTLIER) cc_final: 0.2548 (pm20) REVERT: Q 204 GLU cc_start: 0.4924 (OUTLIER) cc_final: 0.4540 (pm20) outliers start: 227 outliers final: 182 residues processed: 923 average time/residue: 0.5765 time to fit residues: 901.8799 Evaluate side-chains 900 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 709 time to evaluate : 5.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 924 LYS Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 127 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 238 ASN Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain M residue 333 LEU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 263 ILE Chi-restraints excluded: chain O residue 302 VAL Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain O residue 365 TRP Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 379 LYS Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 422 ILE Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 665 ASN Chi-restraints excluded: chain O residue 691 VAL Chi-restraints excluded: chain O residue 693 PHE Chi-restraints excluded: chain O residue 746 ARG Chi-restraints excluded: chain O residue 747 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 177 TYR Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 192 TYR Chi-restraints excluded: chain P residue 246 GLU Chi-restraints excluded: chain P residue 280 ASP Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 323 ASP Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 488 LEU Chi-restraints excluded: chain P residue 510 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 219 LEU Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 264 SER Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 285 VAL Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 364 VAL Chi-restraints excluded: chain Q residue 367 ILE Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 410 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 512 optimal weight: 10.0000 chunk 540 optimal weight: 20.0000 chunk 492 optimal weight: 30.0000 chunk 525 optimal weight: 5.9990 chunk 316 optimal weight: 20.0000 chunk 228 optimal weight: 4.9990 chunk 412 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 474 optimal weight: 5.9990 chunk 496 optimal weight: 7.9990 chunk 523 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN M 238 ASN ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 665 ASN ** O 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 228 ASN ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 50035 Z= 0.311 Angle : 0.848 16.800 68068 Z= 0.427 Chirality : 0.047 0.297 7636 Planarity : 0.006 0.098 8374 Dihedral : 14.410 155.102 7521 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.97 % Favored : 91.26 % Rotamer: Outliers : 4.48 % Allowed : 24.09 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.01 (0.11), residues: 5722 helix: 0.38 (0.11), residues: 2173 sheet: -0.97 (0.18), residues: 747 loop : -1.41 (0.12), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 595 HIS 0.017 0.001 HIS P 131 PHE 0.028 0.002 PHE B1167 TYR 0.031 0.002 TYR G 73 ARG 0.011 0.001 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 721 time to evaluate : 5.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.5217 (t80) cc_final: 0.5003 (t80) REVERT: A 92 ASN cc_start: 0.6268 (OUTLIER) cc_final: 0.5620 (p0) REVERT: A 105 CYS cc_start: 0.5813 (OUTLIER) cc_final: 0.5411 (p) REVERT: B 57 ASP cc_start: 0.4424 (OUTLIER) cc_final: 0.4198 (t0) REVERT: B 155 VAL cc_start: 0.7920 (OUTLIER) cc_final: 0.7695 (m) REVERT: B 589 ASP cc_start: 0.5897 (OUTLIER) cc_final: 0.5568 (t0) REVERT: H 38 LEU cc_start: 0.4702 (tp) cc_final: 0.4492 (tt) REVERT: J 49 MET cc_start: 0.7333 (tpp) cc_final: 0.6561 (tpp) REVERT: J 55 ASP cc_start: 0.5830 (OUTLIER) cc_final: 0.5310 (t0) REVERT: L 67 PHE cc_start: 0.6034 (OUTLIER) cc_final: 0.5749 (m-10) REVERT: N 63 ASP cc_start: 0.4207 (p0) cc_final: 0.3870 (p0) REVERT: P 246 GLU cc_start: 0.2956 (OUTLIER) cc_final: 0.2005 (pm20) REVERT: P 287 TRP cc_start: 0.2110 (OUTLIER) cc_final: 0.1473 (m100) REVERT: Q 204 GLU cc_start: 0.5316 (OUTLIER) cc_final: 0.4733 (pm20) outliers start: 233 outliers final: 189 residues processed: 873 average time/residue: 0.5913 time to fit residues: 887.1650 Evaluate side-chains 875 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 676 time to evaluate : 5.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1000 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 769 PHE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 924 LYS Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 127 LEU Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 263 ILE Chi-restraints excluded: chain O residue 302 VAL Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain O residue 365 TRP Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 379 LYS Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 422 ILE Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 665 ASN Chi-restraints excluded: chain O residue 691 VAL Chi-restraints excluded: chain O residue 693 PHE Chi-restraints excluded: chain O residue 746 ARG Chi-restraints excluded: chain O residue 747 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 177 TYR Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 192 TYR Chi-restraints excluded: chain P residue 211 TYR Chi-restraints excluded: chain P residue 246 GLU Chi-restraints excluded: chain P residue 280 ASP Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 287 TRP Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 323 ASP Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 510 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 179 HIS Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 264 SER Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 276 GLN Chi-restraints excluded: chain Q residue 285 VAL Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 316 SER Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 364 VAL Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 409 HIS Chi-restraints excluded: chain Q residue 410 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 345 optimal weight: 8.9990 chunk 555 optimal weight: 7.9990 chunk 339 optimal weight: 9.9990 chunk 263 optimal weight: 0.6980 chunk 386 optimal weight: 20.0000 chunk 582 optimal weight: 30.0000 chunk 536 optimal weight: 30.0000 chunk 464 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 358 optimal weight: 30.0000 chunk 284 optimal weight: 5.9990 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 ASN ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 0.7292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 50035 Z= 0.285 Angle : 0.855 17.029 68068 Z= 0.428 Chirality : 0.047 0.297 7636 Planarity : 0.005 0.098 8374 Dihedral : 14.435 156.592 7521 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 27.74 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.71 % Favored : 91.56 % Rotamer: Outliers : 4.21 % Allowed : 24.59 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: -0.99 (0.11), residues: 5722 helix: 0.36 (0.11), residues: 2172 sheet: -0.92 (0.18), residues: 735 loop : -1.39 (0.12), residues: 2815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 595 HIS 0.016 0.001 HIS P 131 PHE 0.033 0.002 PHE B 963 TYR 0.033 0.002 TYR J 21 ARG 0.013 0.001 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11444 Ramachandran restraints generated. 5722 Oldfield, 0 Emsley, 5722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 718 time to evaluate : 6.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.5260 (t80) cc_final: 0.5033 (t80) REVERT: A 92 ASN cc_start: 0.6254 (OUTLIER) cc_final: 0.5570 (p0) REVERT: A 105 CYS cc_start: 0.5879 (OUTLIER) cc_final: 0.5430 (p) REVERT: B 91 LEU cc_start: 0.1280 (OUTLIER) cc_final: 0.0521 (mt) REVERT: B 155 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7667 (m) REVERT: B 589 ASP cc_start: 0.5923 (OUTLIER) cc_final: 0.5549 (t0) REVERT: J 49 MET cc_start: 0.7286 (tpp) cc_final: 0.6569 (tpp) REVERT: J 54 VAL cc_start: 0.9009 (t) cc_final: 0.8766 (p) REVERT: J 55 ASP cc_start: 0.6162 (OUTLIER) cc_final: 0.5625 (t0) REVERT: K 125 MET cc_start: 0.3248 (ptp) cc_final: 0.3035 (mtt) REVERT: L 67 PHE cc_start: 0.5976 (OUTLIER) cc_final: 0.5690 (m-10) REVERT: O 380 MET cc_start: 0.3953 (tpp) cc_final: 0.3594 (tpt) REVERT: P 287 TRP cc_start: 0.2241 (OUTLIER) cc_final: 0.1687 (m100) outliers start: 219 outliers final: 188 residues processed: 867 average time/residue: 0.5668 time to fit residues: 840.2860 Evaluate side-chains 885 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 689 time to evaluate : 6.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1000 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 547 HIS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 769 PHE Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 924 LYS Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 127 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain M residue 376 VAL Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 263 ILE Chi-restraints excluded: chain O residue 266 GLU Chi-restraints excluded: chain O residue 302 VAL Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain O residue 365 TRP Chi-restraints excluded: chain O residue 379 LYS Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 691 VAL Chi-restraints excluded: chain O residue 693 PHE Chi-restraints excluded: chain O residue 747 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 177 TYR Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 192 TYR Chi-restraints excluded: chain P residue 211 TYR Chi-restraints excluded: chain P residue 280 ASP Chi-restraints excluded: chain P residue 282 ARG Chi-restraints excluded: chain P residue 287 TRP Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 323 ASP Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 510 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 220 LEU Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 264 SER Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 276 GLN Chi-restraints excluded: chain Q residue 285 VAL Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 364 VAL Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 409 HIS Chi-restraints excluded: chain Q residue 410 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 368 optimal weight: 10.0000 chunk 494 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 427 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 464 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 477 optimal weight: 50.0000 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 ASN ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 238 ASN ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 701 HIS O 716 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.078330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057660 restraints weight = 248345.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059577 restraints weight = 132233.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.060813 restraints weight = 86311.190| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 50035 Z= 0.306 Angle : 0.867 17.476 68068 Z= 0.434 Chirality : 0.048 0.284 7636 Planarity : 0.005 0.098 8374 Dihedral : 14.423 157.477 7514 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 29.05 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.30 % Favored : 90.98 % Rotamer: Outliers : 4.26 % Allowed : 24.61 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.01 (0.11), residues: 5722 helix: 0.36 (0.11), residues: 2164 sheet: -0.88 (0.18), residues: 768 loop : -1.42 (0.12), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 595 HIS 0.015 0.001 HIS P 131 PHE 0.036 0.002 PHE B 963 TYR 0.032 0.002 TYR J 21 ARG 0.013 0.001 ARG A 591 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15269.81 seconds wall clock time: 274 minutes 12.18 seconds (16452.18 seconds total)