Starting phenix.real_space_refine on Thu Dec 26 04:01:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jch_36162/12_2024/8jch_36162.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jch_36162/12_2024/8jch_36162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jch_36162/12_2024/8jch_36162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jch_36162/12_2024/8jch_36162.map" model { file = "/net/cci-nas-00/data/ceres_data/8jch_36162/12_2024/8jch_36162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jch_36162/12_2024/8jch_36162.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 99 5.49 5 Mg 3 5.21 5 S 210 5.16 5 C 26731 2.51 5 N 7417 2.21 5 O 8264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42732 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1419, 11132 Classifications: {'peptide': 1419} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1352} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 9193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9193 Classifications: {'peptide': 1157} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 1106} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2125 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "D" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1455 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 177} Chain breaks: 1 Chain: "E" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1704 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "H" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1104 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 138} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "I" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 871 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "J" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 895 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "L" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 364 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5834 Classifications: {'peptide': 721} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 50, 'TRANS': 670} Chain breaks: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "N" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 787 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "O" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2880 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain breaks: 1 Chain: "P" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 493 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 17} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 769 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "W" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 565 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "C" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 797 SG CYS A 107 124.898 72.972 126.026 1.00131.90 S ATOM 821 SG CYS A 110 123.595 75.595 128.364 1.00133.38 S ATOM 1126 SG CYS A 148 127.382 75.406 127.588 1.00141.59 S ATOM 1264 SG CYS A 167 125.696 72.736 129.720 1.00142.10 S ATOM 492 SG CYS A 67 80.442 75.690 106.320 1.00133.43 S ATOM 514 SG CYS A 70 80.535 79.509 106.129 1.00115.05 S ATOM 567 SG CYS A 77 82.325 77.477 103.438 1.00110.13 S ATOM 19832 SG CYS B1163 91.354 88.825 113.485 1.00105.36 S ATOM 19850 SG CYS B1166 93.362 85.876 114.890 1.00103.83 S ATOM 19975 SG CYS B1182 89.558 85.652 114.551 1.00113.98 S ATOM 19994 SG CYS B1185 91.227 87.867 117.186 1.00129.82 S ATOM 20995 SG CYS C 86 57.032 81.456 39.576 1.00107.59 S ATOM 21012 SG CYS C 88 57.085 79.224 42.678 1.00127.08 S ATOM 21045 SG CYS C 92 55.587 77.979 39.430 1.00 92.45 S ATOM 21068 SG CYS C 95 59.353 78.426 39.724 1.00 95.09 S ATOM 28778 SG CYS I 7 166.647 37.511 86.554 1.00150.85 S ATOM 28797 SG CYS I 10 163.018 36.270 87.365 1.00163.61 S ATOM 28927 SG CYS I 29 164.689 38.816 89.592 1.00160.51 S ATOM 28951 SG CYS I 32 166.100 35.293 89.444 1.00163.52 S ATOM 29278 SG CYS I 75 161.146 54.520 44.178 1.00135.09 S ATOM 29300 SG CYS I 78 161.584 51.796 41.612 1.00142.17 S ATOM 29500 SG CYS I 103 158.372 51.930 43.692 1.00126.39 S ATOM 29520 SG CYS I 106 161.710 50.948 45.292 1.00128.05 S ATOM 29648 SG CYS J 7 89.794 73.681 32.160 1.00 70.14 S ATOM 29671 SG CYS J 10 88.267 76.249 29.785 1.00 68.19 S ATOM 29951 SG CYS J 45 92.087 75.726 29.938 1.00 81.31 S ATOM 29957 SG CYS J 46 89.736 73.204 28.332 1.00 86.56 S ATOM 31084 SG CYS L 31 75.113 39.659 57.313 1.00116.97 S ATOM 31104 SG CYS L 34 74.651 37.217 54.393 1.00109.47 S ATOM 31208 SG CYS L 48 73.031 36.582 57.804 1.00126.86 S ATOM 31231 SG CYS L 51 76.785 36.170 57.229 1.00133.34 S Time building chain proxies: 21.41, per 1000 atoms: 0.50 Number of scatterers: 42732 At special positions: 0 Unit cell: (196.9, 166.1, 163.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 210 16.00 P 99 15.00 Mg 3 11.99 O 8264 8.00 N 7417 7.00 C 26731 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 - 3.00 Amino acid : True - 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: 9.23 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " 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 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 45 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9630 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 56 sheets defined 38.2% alpha, 14.9% beta 39 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 14.68 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.710A pdb=" N ARG A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 223 removed outlier: 3.520A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.510A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 305 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.806A pdb=" N CYS A 529 " --> pdb=" O GLN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.733A pdb=" N LEU A 578 " --> pdb=" O GLY A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.626A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.952A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.537A pdb=" N ILE A 878 " --> pdb=" O ALA A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.704A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 970 Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.509A pdb=" N LEU A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1014 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1127 through 1135 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1167 through 1174 Processing helix chain 'A' and resid 1199 through 1202 Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.891A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A1213 " --> pdb=" O MET A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1270 removed outlier: 3.598A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1334 through 1339 removed outlier: 3.889A pdb=" N VAL A1338 " --> pdb=" O ASP A1334 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1356 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.857A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1405 through 1415 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.857A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 4.044A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 35 removed outlier: 4.224A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.536A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 321 removed outlier: 3.524A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.758A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 390 removed outlier: 4.825A pdb=" N ARG B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 410 through 435 Processing helix chain 'B' and resid 446 through 464 removed outlier: 3.514A pdb=" N LEU B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.800A pdb=" N TRP B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 563 removed outlier: 3.518A pdb=" N GLY B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 606 removed outlier: 3.525A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 671 removed outlier: 3.551A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU B 670 " --> pdb=" O TYR B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.854A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.770A pdb=" N GLU B 711 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.534A pdb=" N ILE B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.561A pdb=" N ILE B 756 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.190A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.911A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.414A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.925A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1063 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 removed outlier: 3.549A pdb=" N LEU B1147 " --> pdb=" O ALA B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.631A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 239 through 270 Processing helix chain 'D' and resid 51 through 78 Processing helix chain 'D' and resid 118 through 131 removed outlier: 3.616A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.864A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.916A pdb=" N ILE D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.671A pdb=" N ALA D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 220 Processing helix chain 'E' and resid 2 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.575A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.592A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.613A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 75 removed outlier: 4.133A pdb=" N SER H 74 " --> pdb=" O ASN H 71 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA H 75 " --> pdb=" O ASP H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 75' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.441A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.049A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.738A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 63 removed outlier: 3.973A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.723A pdb=" N LEU K 9 " --> pdb=" O ARG K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 53 removed outlier: 4.034A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.748A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 14 Processing helix chain 'M' and resid 54 through 62 removed outlier: 3.556A pdb=" N HIS M 59 " --> pdb=" O ASN M 55 " (cutoff:3.500A) Proline residue: M 60 - end of helix Processing helix chain 'M' and resid 73 through 92 Processing helix chain 'M' and resid 106 through 137 Processing helix chain 'M' and resid 156 through 160 Processing helix chain 'M' and resid 164 through 185 removed outlier: 3.548A pdb=" N ASP M 168 " --> pdb=" O THR M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 189 removed outlier: 3.613A pdb=" N LYS M 189 " --> pdb=" O PRO M 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 186 through 189' Processing helix chain 'M' and resid 205 through 217 Processing helix chain 'M' and resid 235 through 243 removed outlier: 3.587A pdb=" N LEU M 241 " --> pdb=" O ILE M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 286 Processing helix chain 'M' and resid 294 through 303 removed outlier: 3.960A pdb=" N GLU M 299 " --> pdb=" O ASN M 295 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR M 300 " --> pdb=" O VAL M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 315 through 331 removed outlier: 3.926A pdb=" N ASP M 321 " --> pdb=" O GLU M 317 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP M 322 " --> pdb=" O ARG M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 359 removed outlier: 3.560A pdb=" N ILE M 350 " --> pdb=" O ASN M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 404 removed outlier: 4.083A pdb=" N GLY M 389 " --> pdb=" O GLY M 385 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ASP M 390 " --> pdb=" O SER M 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 604 through 613 Processing helix chain 'M' and resid 616 through 644 Processing helix chain 'M' and resid 681 through 690 Processing helix chain 'M' and resid 699 through 707 Processing helix chain 'M' and resid 710 through 717 removed outlier: 3.615A pdb=" N ILE M 714 " --> pdb=" O ASP M 710 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP M 715 " --> pdb=" O SER M 711 " (cutoff:3.500A) Processing helix chain 'M' and resid 743 through 754 Processing helix chain 'M' and resid 758 through 763 Processing helix chain 'M' and resid 780 through 790 Processing helix chain 'M' and resid 873 through 882 removed outlier: 3.604A pdb=" N LEU M 877 " --> pdb=" O THR M 873 " (cutoff:3.500A) Processing helix chain 'M' and resid 884 through 889 removed outlier: 4.174A pdb=" N ASN M 888 " --> pdb=" O TYR M 884 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR M 889 " --> pdb=" O ASN M 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 884 through 889' Processing helix chain 'M' and resid 896 through 900 Processing helix chain 'M' and resid 921 through 931 Processing helix chain 'O' and resid 49 through 55 Processing helix chain 'O' and resid 62 through 66 removed outlier: 3.737A pdb=" N PHE O 66 " --> pdb=" O PHE O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 94 Processing helix chain 'O' and resid 105 through 114 removed outlier: 3.573A pdb=" N ILE O 112 " --> pdb=" O ALA O 108 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS O 114 " --> pdb=" O LYS O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 175 Processing helix chain 'O' and resid 180 through 184 Processing helix chain 'O' and resid 185 through 194 removed outlier: 3.712A pdb=" N LYS O 194 " --> pdb=" O GLU O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 272 Processing helix chain 'O' and resid 296 through 306 removed outlier: 4.155A pdb=" N VAL O 300 " --> pdb=" O GLU O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 331 removed outlier: 3.661A pdb=" N GLY O 310 " --> pdb=" O ASN O 306 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY O 321 " --> pdb=" O ILE O 317 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS O 329 " --> pdb=" O GLU O 325 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET O 330 " --> pdb=" O TRP O 326 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE O 331 " --> pdb=" O LEU O 327 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 369 removed outlier: 3.555A pdb=" N SER O 366 " --> pdb=" O ASP O 362 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 387 Processing helix chain 'W' and resid 809 through 813 removed outlier: 3.873A pdb=" N TYR W 812 " --> pdb=" O SER W 809 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS W 813 " --> pdb=" O ALA W 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 809 through 813' Processing helix chain 'W' and resid 858 through 862 removed outlier: 3.886A pdb=" N LEU W 861 " --> pdb=" O TYR W 858 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 91 removed outlier: 11.187A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.527A pdb=" N THR A 173 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA7, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.709A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET A 487 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.829A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.614A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB2, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.165A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 3.557A pdb=" N GLN A 865 " --> pdb=" O THR A 856 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 6.468A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.541A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 87 through 89 removed outlier: 3.722A pdb=" N ARG B 135 " --> pdb=" O GLU B 89 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 95 through 97 removed outlier: 4.015A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 103 removed outlier: 3.645A pdb=" N HIS B 110 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.164A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 223 through 227 removed outlier: 4.327A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 648 through 651 Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.373A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.553A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.553A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 removed outlier: 5.797A pdb=" N GLY B1042 " --> pdb=" O THR B 805 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 821 through 827 removed outlier: 7.281A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 865 through 866 Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.901A pdb=" N LEU B 883 " --> pdb=" O LYS B 934 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP B 936 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.839A pdb=" N ILE B 911 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 3.660A pdb=" N PHE B1001 " --> pdb=" O TYR B1073 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1069 through 1070 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.468A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.935A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.822A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.666A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.767A pdb=" N PHE G 3 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 59 through 60 removed outlier: 3.526A pdb=" N SER E 59 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE8, first strand: chain 'G' and resid 86 through 94 removed outlier: 4.682A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.013A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 140 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP H 53 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 18 Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.723A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.667A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE K 71 " --> pdb=" O PHE K 35 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.742A pdb=" N ILE M 250 " --> pdb=" O LEU M 292 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N HIS M 227 " --> pdb=" O LYS M 249 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU M 251 " --> pdb=" O HIS M 227 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE M 229 " --> pdb=" O LEU M 251 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N GLU M 253 " --> pdb=" O ILE M 229 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 28 through 29 Processing sheet with id=AF6, first strand: chain 'M' and resid 49 through 53 removed outlier: 3.606A pdb=" N VAL M 98 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 367 through 368 Processing sheet with id=AF8, first strand: chain 'O' and resid 22 through 29 removed outlier: 5.985A pdb=" N GLU O 23 " --> pdb=" O ARG O 208 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG O 208 " --> pdb=" O GLU O 23 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY O 25 " --> pdb=" O VAL O 206 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG O 29 " --> pdb=" O GLU O 202 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU O 202 " --> pdb=" O ARG O 29 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR O 203 " --> pdb=" O VAL O 222 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS O 214 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE O 101 " --> pdb=" O ILE O 217 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY O 219 " --> pdb=" O ILE O 101 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR O 103 " --> pdb=" O GLY O 219 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLU O 221 " --> pdb=" O THR O 103 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 138 through 140 removed outlier: 4.438A pdb=" N ASP O 125 " --> pdb=" O VAL O 140 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU O 126 " --> pdb=" O LEU O 346 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU O 346 " --> pdb=" O LEU O 126 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE O 344 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA O 343 " --> pdb=" O ILE O 358 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER O 356 " --> pdb=" O LYS O 345 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 243 through 246 removed outlier: 6.575A pdb=" N LYS O 243 " --> pdb=" O GLY O 279 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LYS O 281 " --> pdb=" O LYS O 243 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR O 245 " --> pdb=" O LYS O 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'W' and resid 837 through 841 removed outlier: 3.554A pdb=" N ASP W 821 " --> pdb=" O THR W 828 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU W 830 " --> pdb=" O VAL W 819 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL W 819 " --> pdb=" O GLU W 830 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG W 806 " --> pdb=" O THR W 846 " (cutoff:3.500A) 1647 hydrogen bonds defined for protein. 4605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 24.46 Time building geometry restraints manager: 10.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11587 1.33 - 1.46: 8638 1.46 - 1.58: 23012 1.58 - 1.70: 195 1.70 - 1.82: 332 Bond restraints: 43764 Sorted by residual: bond pdb=" C ALA M 108 " pdb=" O ALA M 108 " ideal model delta sigma weight residual 1.236 1.288 -0.051 1.16e-02 7.43e+03 1.97e+01 bond pdb=" N ILE M 735 " pdb=" CA ILE M 735 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.39e+00 bond pdb=" C ALA M 115 " pdb=" O ALA M 115 " ideal model delta sigma weight residual 1.236 1.271 -0.035 1.21e-02 6.83e+03 8.22e+00 bond pdb=" N GLN M 112 " pdb=" CA GLN M 112 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.84e+00 bond pdb=" N LYS M 729 " pdb=" CA LYS M 729 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.16e-02 7.43e+03 7.75e+00 ... (remaining 43759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 59048 2.56 - 5.11: 471 5.11 - 7.67: 43 7.67 - 10.22: 16 10.22 - 12.78: 8 Bond angle restraints: 59586 Sorted by residual: angle pdb=" N ASN M 726 " pdb=" CA ASN M 726 " pdb=" C ASN M 726 " ideal model delta sigma weight residual 113.23 107.26 5.97 1.24e+00 6.50e-01 2.32e+01 angle pdb=" CB LYS L 49 " pdb=" CG LYS L 49 " pdb=" CD LYS L 49 " ideal model delta sigma weight residual 111.30 121.98 -10.68 2.30e+00 1.89e-01 2.15e+01 angle pdb=" N LYS M 109 " pdb=" CA LYS M 109 " pdb=" C LYS M 109 " ideal model delta sigma weight residual 111.75 105.99 5.76 1.28e+00 6.10e-01 2.02e+01 angle pdb=" CA GLN O 267 " pdb=" CB GLN O 267 " pdb=" CG GLN O 267 " ideal model delta sigma weight residual 114.10 122.97 -8.87 2.00e+00 2.50e-01 1.97e+01 angle pdb=" CA GLN J 26 " pdb=" CB GLN J 26 " pdb=" CG GLN J 26 " ideal model delta sigma weight residual 114.10 122.78 -8.68 2.00e+00 2.50e-01 1.88e+01 ... (remaining 59581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 25153 34.89 - 69.78: 1264 69.78 - 104.67: 52 104.67 - 139.56: 2 139.56 - 174.45: 4 Dihedral angle restraints: 26475 sinusoidal: 11590 harmonic: 14885 Sorted by residual: dihedral pdb=" O4' U P -18 " pdb=" C1' U P -18 " pdb=" N1 U P -18 " pdb=" C2 U P -18 " ideal model delta sinusoidal sigma weight residual -160.00 -90.96 -69.04 1 1.50e+01 4.44e-03 2.74e+01 dihedral pdb=" O4' A P -23 " pdb=" C1' A P -23 " pdb=" N9 A P -23 " pdb=" C4 A P -23 " ideal model delta sinusoidal sigma weight residual -90.00 -11.07 -78.93 1 2.00e+01 2.50e-03 1.94e+01 dihedral pdb=" CA GLN A 71 " pdb=" C GLN A 71 " pdb=" N GLU A 72 " pdb=" CA GLU A 72 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 26472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 6610 0.115 - 0.229: 54 0.229 - 0.344: 0 0.344 - 0.458: 0 0.458 - 0.573: 1 Chirality restraints: 6665 Sorted by residual: chirality pdb=" P A P -23 " pdb=" OP1 A P -23 " pdb=" OP2 A P -23 " pdb=" O5' A P -23 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" C3' A P -23 " pdb=" C4' A P -23 " pdb=" O3' A P -23 " pdb=" C2' A P -23 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU O 174 " pdb=" CB LEU O 174 " pdb=" CD1 LEU O 174 " pdb=" CD2 LEU O 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 6662 not shown) Planarity restraints: 7373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC T 2 " 0.002 2.00e-02 2.50e+03 2.26e-02 1.15e+01 pdb=" N1 DC T 2 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DC T 2 " -0.055 2.00e-02 2.50e+03 pdb=" O2 DC T 2 " 0.035 2.00e-02 2.50e+03 pdb=" N3 DC T 2 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC T 2 " -0.012 2.00e-02 2.50e+03 pdb=" N4 DC T 2 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DC T 2 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC T 2 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 381 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO A 382 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 105 " -0.013 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C ALA M 105 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA M 105 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO M 106 " -0.014 2.00e-02 2.50e+03 ... (remaining 7370 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 458 2.60 - 3.18: 35579 3.18 - 3.75: 68110 3.75 - 4.33: 90533 4.33 - 4.90: 149090 Nonbonded interactions: 343770 Sorted by model distance: nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1803 " model vdw 2.031 2.170 nonbonded pdb=" O3' U P -1 " pdb="MG MG A1803 " model vdw 2.090 2.170 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.192 2.170 nonbonded pdb=" N GLN H 35 " pdb=" OE1 GLN H 35 " model vdw 2.199 3.120 nonbonded pdb=" N GLN O 182 " pdb=" OE1 GLN O 182 " model vdw 2.212 3.120 ... (remaining 343765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.550 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 110.010 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.210 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: 0.030 Load rotamer database and sin/cos tables:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.002 0.051 43764 Z= 0.155 Angle : 0.542 12.779 59586 Z= 0.280 Chirality : 0.041 0.573 6665 Planarity : 0.003 0.062 7373 Dihedral : 18.222 174.447 16845 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.29 % Allowed : 27.64 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.88 (0.12), residues: 5065 helix: 1.89 (0.13), residues: 1755 sheet: 0.84 (0.20), residues: 749 loop : -0.41 (0.13), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 31 HIS 0.005 0.000 HIS M 396 PHE 0.018 0.001 PHE A 252 TYR 0.019 0.001 TYR I 44 ARG 0.015 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 526 time to evaluate : 4.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1411 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8252 (tp30) REVERT: B 241 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8040 (ttm110) REVERT: B 444 MET cc_start: 0.7665 (ppp) cc_final: 0.7346 (ppp) REVERT: C 155 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9370 (pp) REVERT: I 13 MET cc_start: 0.8451 (ppp) cc_final: 0.8174 (ppp) REVERT: K 24 ASP cc_start: 0.8734 (t0) cc_final: 0.8345 (t0) REVERT: M 111 ASN cc_start: -0.0213 (OUTLIER) cc_final: -0.1006 (m110) REVERT: M 281 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6876 (mm-40) REVERT: M 614 HIS cc_start: 0.4947 (OUTLIER) cc_final: 0.3344 (m170) REVERT: M 723 ILE cc_start: 0.1669 (OUTLIER) cc_final: 0.1446 (mt) REVERT: M 751 ARG cc_start: 0.5492 (mmm-85) cc_final: 0.4489 (ttm110) REVERT: M 881 MET cc_start: 0.5655 (tpp) cc_final: 0.5255 (ptp) REVERT: O 57 LEU cc_start: 0.2255 (mm) cc_final: 0.1800 (pp) REVERT: O 330 MET cc_start: 0.1087 (ppp) cc_final: 0.0295 (mpp) outliers start: 102 outliers final: 73 residues processed: 618 average time/residue: 1.5107 time to fit residues: 1163.4831 Evaluate side-chains 509 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 432 time to evaluate : 4.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1383 SER Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 111 ASN Chi-restraints excluded: chain M residue 614 HIS Chi-restraints excluded: chain M residue 723 ILE Chi-restraints excluded: chain M residue 800 VAL Chi-restraints excluded: chain M residue 906 VAL Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 309 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 434 optimal weight: 20.0000 chunk 390 optimal weight: 3.9990 chunk 216 optimal weight: 0.0980 chunk 133 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 403 optimal weight: 0.0370 chunk 156 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 300 optimal weight: 7.9990 chunk 467 optimal weight: 5.9990 overall best weight: 1.6264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 118 HIS A 160 GLN A 399 HIS A 451 HIS A 471 ASN A 576 GLN A 587 HIS A 589 GLN A 650 GLN A 741 ASN A 802 ASN A 903 ASN A1011 GLN A1278 ASN A1367 HIS A1390 ASN A1432 GLN B 215 GLN B 236 HIS B 657 HIS B 716 ASN B 719 ASN B 733 HIS B 762 ASN B 776 GLN B1013 ASN B1062 HIS B1074 ASN B1117 GLN B1141 HIS B1176 ASN C 135 GLN C 151 GLN C 195 GLN D 34 GLN D 132 GLN D 137 ASN G 10 ASN G 96 GLN G 122 ASN H 43 ASN H 71 ASN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN I 89 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN K 2 ASN K 40 HIS K 96 ASN K 104 ASN K 110 ASN M 25 GLN ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN M 112 GLN M 227 HIS M 287 GLN M 373 ASN M 383 HIS ** M 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 886 ASN M 901 GLN O 42 ASN O 132 ASN ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 305 ASN O 308 GLN W 863 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 43764 Z= 0.293 Angle : 0.575 10.225 59586 Z= 0.299 Chirality : 0.043 0.182 6665 Planarity : 0.004 0.060 7373 Dihedral : 14.081 173.378 6867 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.88 % Allowed : 24.11 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.67 (0.12), residues: 5065 helix: 1.80 (0.13), residues: 1773 sheet: 0.48 (0.19), residues: 759 loop : -0.53 (0.13), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 192 HIS 0.005 0.001 HIS A 399 PHE 0.021 0.001 PHE A 219 TYR 0.018 0.001 TYR I 44 ARG 0.010 0.001 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 446 time to evaluate : 5.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8560 (t0) cc_final: 0.8175 (t0) REVERT: A 329 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8001 (pp) REVERT: A 618 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: A 678 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: A 1411 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8256 (tp30) REVERT: B 40 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: B 239 GLU cc_start: 0.8109 (pm20) cc_final: 0.7841 (pm20) REVERT: B 241 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8378 (ttm110) REVERT: B 296 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: B 473 MET cc_start: 0.8807 (mpt) cc_final: 0.8601 (mpm) REVERT: B 1124 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8137 (ptm160) REVERT: D 132 GLN cc_start: 0.5953 (OUTLIER) cc_final: 0.5686 (pm20) REVERT: E 152 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8088 (tptt) REVERT: F 116 ASP cc_start: 0.9052 (t0) cc_final: 0.8650 (t0) REVERT: F 144 GLU cc_start: 0.9059 (pt0) cc_final: 0.8767 (pt0) REVERT: G 44 TYR cc_start: 0.7010 (m-80) cc_final: 0.6604 (m-80) REVERT: G 46 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7664 (mm) REVERT: G 71 ASN cc_start: 0.8977 (t0) cc_final: 0.8728 (t0) REVERT: G 131 GLN cc_start: 0.6996 (mm-40) cc_final: 0.5838 (pm20) REVERT: G 144 ARG cc_start: 0.5061 (mtt90) cc_final: 0.4770 (mtt90) REVERT: H 77 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7734 (mmm-85) REVERT: H 106 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7696 (tp30) REVERT: I 47 GLU cc_start: 0.8142 (tp30) cc_final: 0.7779 (tp30) REVERT: J 26 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8149 (tm-30) REVERT: K 1 MET cc_start: 0.7688 (tpp) cc_final: 0.7480 (tpp) REVERT: K 24 ASP cc_start: 0.8797 (t0) cc_final: 0.8438 (t0) REVERT: L 34 CYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7950 (m) REVERT: M 25 GLN cc_start: 0.6643 (mm110) cc_final: 0.6334 (mm110) REVERT: M 54 MET cc_start: 0.6313 (tpp) cc_final: 0.5919 (tpp) REVERT: M 239 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7975 (mt) REVERT: M 294 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6880 (tp) REVERT: M 614 HIS cc_start: 0.5081 (OUTLIER) cc_final: 0.3492 (m-70) REVERT: M 730 MET cc_start: 0.1063 (pmt) cc_final: -0.0255 (tpp) REVERT: M 751 ARG cc_start: 0.5424 (mmm-85) cc_final: 0.4483 (ttm110) REVERT: M 881 MET cc_start: 0.5629 (tpp) cc_final: 0.5269 (ptp) REVERT: O 57 LEU cc_start: 0.2251 (OUTLIER) cc_final: 0.1739 (pp) REVERT: O 259 ARG cc_start: 0.4930 (OUTLIER) cc_final: 0.4680 (mtm-85) REVERT: O 330 MET cc_start: 0.0829 (ppp) cc_final: -0.0215 (mmm) outliers start: 173 outliers final: 64 residues processed: 567 average time/residue: 1.6414 time to fit residues: 1166.1487 Evaluate side-chains 495 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 416 time to evaluate : 5.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain M residue 614 HIS Chi-restraints excluded: chain M residue 800 VAL Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 259 ARG Chi-restraints excluded: chain O residue 294 SER Chi-restraints excluded: chain O residue 309 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 259 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 389 optimal weight: 0.3980 chunk 318 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 468 optimal weight: 10.0000 chunk 506 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 chunk 464 optimal weight: 50.0000 chunk 159 optimal weight: 5.9990 chunk 375 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 517 ASN A 741 ASN A1390 ASN A1432 GLN B1179 GLN B1205 GLN G 10 ASN H 128 ASN I 87 GLN I 89 GLN I 90 GLN ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 222 ASN ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 43764 Z= 0.256 Angle : 0.547 13.110 59586 Z= 0.283 Chirality : 0.042 0.208 6665 Planarity : 0.004 0.060 7373 Dihedral : 13.902 176.862 6787 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.59 % Allowed : 24.09 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.57 (0.12), residues: 5065 helix: 1.75 (0.13), residues: 1775 sheet: 0.34 (0.19), residues: 743 loop : -0.59 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 291 HIS 0.004 0.001 HIS A 659 PHE 0.021 0.001 PHE A 219 TYR 0.018 0.001 TYR M 882 ARG 0.009 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 431 time to evaluate : 4.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8943 (t80) REVERT: A 72 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: A 329 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8343 (pp) REVERT: A 510 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8432 (mt0) REVERT: A 618 GLU cc_start: 0.8466 (pt0) cc_final: 0.7707 (pm20) REVERT: A 678 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: A 1112 LYS cc_start: 0.9161 (mtpt) cc_final: 0.8905 (tppt) REVERT: A 1142 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7473 (p) REVERT: A 1411 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8217 (tp30) REVERT: B 239 GLU cc_start: 0.8278 (pm20) cc_final: 0.7937 (pm20) REVERT: B 241 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8372 (ttm110) REVERT: B 296 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: B 473 MET cc_start: 0.8835 (mpt) cc_final: 0.8624 (mpm) REVERT: B 884 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7898 (ttm-80) REVERT: B 1124 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8124 (ptm160) REVERT: C 155 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9289 (pp) REVERT: E 152 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8062 (tptt) REVERT: E 179 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8432 (mm110) REVERT: F 116 ASP cc_start: 0.9123 (t0) cc_final: 0.8734 (t0) REVERT: F 144 GLU cc_start: 0.9041 (pt0) cc_final: 0.8703 (pt0) REVERT: G 46 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7775 (mm) REVERT: G 131 GLN cc_start: 0.7026 (mm-40) cc_final: 0.5966 (pm20) REVERT: G 136 VAL cc_start: 0.5186 (OUTLIER) cc_final: 0.4902 (p) REVERT: H 77 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.7729 (mmm-85) REVERT: H 106 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7837 (tm-30) REVERT: I 30 ARG cc_start: 0.7651 (mmm-85) cc_final: 0.7371 (ttp80) REVERT: I 47 GLU cc_start: 0.8141 (tp30) cc_final: 0.7883 (tp30) REVERT: J 27 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7961 (mp0) REVERT: K 24 ASP cc_start: 0.8811 (t0) cc_final: 0.8504 (t0) REVERT: L 34 CYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7888 (m) REVERT: M 239 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8051 (mt) REVERT: M 614 HIS cc_start: 0.5084 (OUTLIER) cc_final: 0.3403 (m-70) REVERT: M 730 MET cc_start: 0.1175 (pmt) cc_final: 0.0091 (tpp) REVERT: M 751 ARG cc_start: 0.5524 (mmm-85) cc_final: 0.4525 (ttm110) REVERT: O 57 LEU cc_start: 0.2000 (OUTLIER) cc_final: 0.1632 (pp) REVERT: O 196 ILE cc_start: 0.2092 (OUTLIER) cc_final: 0.1888 (mm) REVERT: O 259 ARG cc_start: 0.5037 (OUTLIER) cc_final: 0.4719 (mtm-85) REVERT: O 330 MET cc_start: 0.0578 (ppp) cc_final: -0.0516 (mmm) outliers start: 160 outliers final: 66 residues processed: 554 average time/residue: 1.5723 time to fit residues: 1079.3203 Evaluate side-chains 498 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 413 time to evaluate : 4.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain M residue 614 HIS Chi-restraints excluded: chain M residue 800 VAL Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 217 ILE Chi-restraints excluded: chain O residue 259 ARG Chi-restraints excluded: chain O residue 294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 462 optimal weight: 4.9990 chunk 352 optimal weight: 4.9990 chunk 243 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 314 optimal weight: 2.9990 chunk 470 optimal weight: 50.0000 chunk 497 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 445 optimal weight: 50.0000 chunk 134 optimal weight: 0.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS A 451 HIS A 741 ASN A1390 ASN A1432 GLN B 363 HIS B 776 GLN D 132 GLN G 10 ASN I 87 GLN I 89 GLN ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 43764 Z= 0.304 Angle : 0.566 12.675 59586 Z= 0.291 Chirality : 0.043 0.264 6665 Planarity : 0.004 0.059 7373 Dihedral : 13.894 176.158 6777 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.80 % Favored : 95.18 % Rotamer: Outliers : 4.40 % Allowed : 23.42 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.49 (0.12), residues: 5065 helix: 1.69 (0.13), residues: 1784 sheet: 0.28 (0.19), residues: 727 loop : -0.64 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 31 HIS 0.007 0.001 HIS A 975 PHE 0.030 0.001 PHE G 2 TYR 0.020 0.001 TYR I 44 ARG 0.010 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 427 time to evaluate : 4.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.9022 (t80) REVERT: A 510 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8384 (mt0) REVERT: A 618 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: A 626 ASN cc_start: 0.8317 (p0) cc_final: 0.8057 (p0) REVERT: A 712 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8310 (mt-10) REVERT: A 1112 LYS cc_start: 0.9186 (mtpt) cc_final: 0.8938 (tppt) REVERT: A 1142 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7468 (p) REVERT: A 1337 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8660 (mp0) REVERT: A 1411 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8202 (tp30) REVERT: B 239 GLU cc_start: 0.8398 (pm20) cc_final: 0.7939 (pm20) REVERT: B 296 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: B 444 MET cc_start: 0.8132 (ppp) cc_final: 0.7778 (ppp) REVERT: B 473 MET cc_start: 0.8866 (mpt) cc_final: 0.8636 (mpm) REVERT: B 729 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8797 (pt) REVERT: B 884 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7991 (ttm-80) REVERT: B 935 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7818 (ttm-80) REVERT: B 1124 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8142 (ptm160) REVERT: B 1125 ASP cc_start: 0.8517 (t0) cc_final: 0.8225 (t0) REVERT: B 1219 ASP cc_start: 0.8687 (p0) cc_final: 0.8482 (p0) REVERT: C 147 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8957 (pp) REVERT: D 132 GLN cc_start: 0.5896 (OUTLIER) cc_final: 0.5592 (pm20) REVERT: E 152 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8013 (tptt) REVERT: E 179 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8421 (mm110) REVERT: F 114 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: F 116 ASP cc_start: 0.9109 (t0) cc_final: 0.8617 (t70) REVERT: G 44 TYR cc_start: 0.7125 (m-80) cc_final: 0.6838 (m-80) REVERT: G 131 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6223 (pm20) REVERT: G 136 VAL cc_start: 0.5164 (OUTLIER) cc_final: 0.4871 (p) REVERT: H 77 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7710 (mmm-85) REVERT: H 106 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7805 (tm-30) REVERT: I 30 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7376 (tmm160) REVERT: I 47 GLU cc_start: 0.8037 (tp30) cc_final: 0.7692 (tp30) REVERT: J 27 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7968 (mp0) REVERT: K 24 ASP cc_start: 0.8804 (t0) cc_final: 0.8481 (t0) REVERT: K 54 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7778 (tmt170) REVERT: L 33 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8521 (pp20) REVERT: L 34 CYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7718 (m) REVERT: M 54 MET cc_start: 0.6463 (tpp) cc_final: 0.5943 (tpp) REVERT: M 237 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8619 (pp) REVERT: M 239 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8099 (mt) REVERT: M 253 GLU cc_start: 0.5889 (tp30) cc_final: 0.5536 (pm20) REVERT: M 614 HIS cc_start: 0.4820 (OUTLIER) cc_final: 0.2818 (m-70) REVERT: M 730 MET cc_start: 0.1101 (pmt) cc_final: 0.0123 (tpp) REVERT: M 751 ARG cc_start: 0.5475 (mmm-85) cc_final: 0.4475 (ttm110) REVERT: M 883 LYS cc_start: 0.3299 (OUTLIER) cc_final: 0.2801 (pptt) REVERT: O 57 LEU cc_start: 0.2062 (OUTLIER) cc_final: 0.1737 (pp) REVERT: O 196 ILE cc_start: 0.1902 (OUTLIER) cc_final: 0.1636 (mm) REVERT: O 259 ARG cc_start: 0.5044 (OUTLIER) cc_final: 0.4686 (mtm-85) REVERT: O 330 MET cc_start: 0.0440 (ppp) cc_final: -0.0739 (mmm) outliers start: 196 outliers final: 80 residues processed: 581 average time/residue: 1.6056 time to fit residues: 1154.8449 Evaluate side-chains 513 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 407 time to evaluate : 5.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 741 ASN Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 935 ARG Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 305 LEU Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain M residue 614 HIS Chi-restraints excluded: chain M residue 800 VAL Chi-restraints excluded: chain M residue 813 VAL Chi-restraints excluded: chain M residue 883 LYS Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 217 ILE Chi-restraints excluded: chain O residue 259 ARG Chi-restraints excluded: chain O residue 294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 414 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 370 optimal weight: 7.9990 chunk 205 optimal weight: 0.6980 chunk 424 optimal weight: 50.0000 chunk 344 optimal weight: 30.0000 chunk 0 optimal weight: 4.9990 chunk 254 optimal weight: 0.7980 chunk 446 optimal weight: 50.0000 chunk 125 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS A 451 HIS A 741 ASN A1171 GLN A1278 ASN A1390 ASN A1432 GLN E 99 HIS G 10 ASN G 97 HIS ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 837 ASN ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 43764 Z= 0.441 Angle : 0.623 13.066 59586 Z= 0.321 Chirality : 0.045 0.195 6665 Planarity : 0.004 0.058 7373 Dihedral : 13.906 174.905 6770 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 4.24 % Allowed : 23.62 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.32 (0.12), residues: 5065 helix: 1.56 (0.12), residues: 1788 sheet: 0.15 (0.19), residues: 726 loop : -0.74 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 31 HIS 0.008 0.001 HIS A 399 PHE 0.025 0.001 PHE A 219 TYR 0.025 0.001 TYR M 882 ARG 0.014 0.001 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 415 time to evaluate : 5.302 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: A 66 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8514 (mmmm) REVERT: A 408 ASP cc_start: 0.8051 (m-30) cc_final: 0.7652 (p0) REVERT: A 510 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: A 618 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: A 626 ASN cc_start: 0.8358 (p0) cc_final: 0.8122 (p0) REVERT: A 712 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8325 (mt-10) REVERT: A 1074 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: A 1112 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8952 (tppt) REVERT: A 1142 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7511 (p) REVERT: A 1337 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8727 (mp0) REVERT: A 1411 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8238 (tp30) REVERT: A 1448 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: B 40 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: B 96 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6287 (p90) REVERT: B 133 LYS cc_start: 0.8818 (tppt) cc_final: 0.8574 (tppt) REVERT: B 239 GLU cc_start: 0.8480 (pm20) cc_final: 0.8019 (pm20) REVERT: B 296 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: B 473 MET cc_start: 0.8894 (mpt) cc_final: 0.8672 (mpm) REVERT: B 729 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8834 (pt) REVERT: B 884 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7975 (ttm-80) REVERT: B 1124 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8135 (ptm160) REVERT: B 1125 ASP cc_start: 0.8598 (t0) cc_final: 0.8234 (t0) REVERT: C 147 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8995 (pp) REVERT: E 32 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8155 (mm-40) REVERT: E 152 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8054 (tptt) REVERT: E 179 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8561 (mm110) REVERT: F 114 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: F 116 ASP cc_start: 0.9127 (t0) cc_final: 0.8790 (t0) REVERT: G 44 TYR cc_start: 0.7081 (m-80) cc_final: 0.6751 (m-80) REVERT: G 46 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8106 (mm) REVERT: G 131 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6147 (pm20) REVERT: G 136 VAL cc_start: 0.5163 (OUTLIER) cc_final: 0.4873 (p) REVERT: H 77 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.7751 (mmm-85) REVERT: H 105 GLU cc_start: 0.8240 (tt0) cc_final: 0.7841 (tm-30) REVERT: H 106 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7537 (tm-30) REVERT: I 15 TYR cc_start: 0.7900 (m-10) cc_final: 0.7694 (m-10) REVERT: I 47 GLU cc_start: 0.8073 (tp30) cc_final: 0.7856 (tp30) REVERT: I 48 LEU cc_start: 0.9408 (mm) cc_final: 0.9157 (mm) REVERT: J 27 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8077 (mt-10) REVERT: K 24 ASP cc_start: 0.8851 (t0) cc_final: 0.8525 (t0) REVERT: K 54 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8014 (tpt90) REVERT: L 34 CYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7745 (m) REVERT: M 90 MET cc_start: 0.6562 (pp-130) cc_final: 0.5656 (pp-130) REVERT: M 227 HIS cc_start: 0.4940 (OUTLIER) cc_final: 0.4000 (m90) REVERT: M 239 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7849 (mt) REVERT: M 614 HIS cc_start: 0.4874 (OUTLIER) cc_final: 0.2842 (m-70) REVERT: M 730 MET cc_start: 0.1146 (pmt) cc_final: 0.0186 (tpp) REVERT: M 751 ARG cc_start: 0.5508 (mmm-85) cc_final: 0.4498 (ttm110) REVERT: O 48 LEU cc_start: 0.4053 (OUTLIER) cc_final: 0.3844 (tm) REVERT: O 57 LEU cc_start: 0.1905 (OUTLIER) cc_final: 0.1698 (pt) REVERT: O 196 ILE cc_start: 0.1893 (OUTLIER) cc_final: 0.1600 (mm) REVERT: O 259 ARG cc_start: 0.5017 (OUTLIER) cc_final: 0.4680 (mtm-85) outliers start: 189 outliers final: 83 residues processed: 565 average time/residue: 1.6426 time to fit residues: 1152.6515 Evaluate side-chains 518 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 407 time to evaluate : 4.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1448 GLU Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain M residue 614 HIS Chi-restraints excluded: chain M residue 800 VAL Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 217 ILE Chi-restraints excluded: chain O residue 259 ARG Chi-restraints excluded: chain O residue 275 ARG Chi-restraints excluded: chain O residue 294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 167 optimal weight: 3.9990 chunk 448 optimal weight: 50.0000 chunk 98 optimal weight: 0.4980 chunk 292 optimal weight: 30.0000 chunk 122 optimal weight: 4.9990 chunk 498 optimal weight: 9.9990 chunk 413 optimal weight: 30.0000 chunk 230 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS A 451 HIS A1171 GLN A1278 ASN A1390 ASN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN G 10 ASN H 128 ASN I 89 GLN J 53 HIS ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 43764 Z= 0.242 Angle : 0.573 12.944 59586 Z= 0.294 Chirality : 0.042 0.249 6665 Planarity : 0.004 0.060 7373 Dihedral : 13.846 174.416 6767 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.44 % Allowed : 24.72 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.38 (0.12), residues: 5065 helix: 1.63 (0.12), residues: 1782 sheet: 0.18 (0.19), residues: 724 loop : -0.71 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 31 HIS 0.005 0.001 HIS A 399 PHE 0.021 0.001 PHE A 219 TYR 0.025 0.001 TYR B 259 ARG 0.012 0.000 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 425 time to evaluate : 5.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8515 (mmmm) REVERT: A 510 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8384 (mt0) REVERT: A 618 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: A 626 ASN cc_start: 0.8350 (p0) cc_final: 0.8126 (p0) REVERT: A 1074 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: A 1112 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8955 (tppt) REVERT: A 1142 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7478 (p) REVERT: A 1337 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: A 1411 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8201 (tp30) REVERT: B 96 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.6290 (p90) REVERT: B 133 LYS cc_start: 0.8835 (tppt) cc_final: 0.8611 (tppt) REVERT: B 239 GLU cc_start: 0.8456 (pm20) cc_final: 0.7961 (pm20) REVERT: B 296 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: B 444 MET cc_start: 0.8124 (ppp) cc_final: 0.7641 (ppp) REVERT: B 473 MET cc_start: 0.8934 (mpt) cc_final: 0.8714 (mpm) REVERT: B 729 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8757 (pt) REVERT: B 884 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7982 (ttm-80) REVERT: B 1124 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8120 (ptm160) REVERT: B 1125 ASP cc_start: 0.8591 (t0) cc_final: 0.8185 (t0) REVERT: C 147 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8927 (pp) REVERT: E 152 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8031 (tptt) REVERT: E 179 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8403 (mm110) REVERT: F 114 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8126 (mm-30) REVERT: F 116 ASP cc_start: 0.9110 (t0) cc_final: 0.8734 (t0) REVERT: G 44 TYR cc_start: 0.7127 (m-80) cc_final: 0.6852 (m-80) REVERT: G 131 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6128 (pm20) REVERT: G 136 VAL cc_start: 0.5213 (OUTLIER) cc_final: 0.4926 (p) REVERT: H 77 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.7739 (mmm-85) REVERT: H 105 GLU cc_start: 0.8198 (tt0) cc_final: 0.7838 (tm-30) REVERT: H 106 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7490 (tm-30) REVERT: I 47 GLU cc_start: 0.8064 (tp30) cc_final: 0.7728 (tp30) REVERT: I 48 LEU cc_start: 0.9427 (mm) cc_final: 0.9172 (mm) REVERT: I 81 ARG cc_start: 0.8801 (mmm-85) cc_final: 0.8348 (mmm-85) REVERT: J 27 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8099 (mt-10) REVERT: J 31 ASP cc_start: 0.8628 (p0) cc_final: 0.8422 (p0) REVERT: K 24 ASP cc_start: 0.8840 (t0) cc_final: 0.8523 (t0) REVERT: K 54 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7991 (tpt90) REVERT: L 34 CYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7818 (m) REVERT: M 54 MET cc_start: 0.6286 (ttt) cc_final: 0.6079 (ttt) REVERT: M 208 ILE cc_start: 0.6281 (mm) cc_final: 0.5932 (tp) REVERT: M 227 HIS cc_start: 0.4941 (OUTLIER) cc_final: 0.3998 (m90) REVERT: M 239 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8010 (mt) REVERT: M 730 MET cc_start: 0.1143 (pmt) cc_final: 0.0216 (tpp) REVERT: M 751 ARG cc_start: 0.5537 (mmm-85) cc_final: 0.4531 (ttm110) REVERT: O 57 LEU cc_start: 0.1971 (OUTLIER) cc_final: 0.1763 (pt) REVERT: O 196 ILE cc_start: 0.2004 (OUTLIER) cc_final: 0.1702 (mm) REVERT: O 259 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4683 (mtm-85) REVERT: O 278 TYR cc_start: -0.0377 (OUTLIER) cc_final: -0.1500 (m-80) REVERT: O 330 MET cc_start: 0.0095 (ppp) cc_final: -0.0416 (tpp) outliers start: 153 outliers final: 71 residues processed: 549 average time/residue: 1.6353 time to fit residues: 1109.7277 Evaluate side-chains 500 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 405 time to evaluate : 5.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain M residue 800 VAL Chi-restraints excluded: chain M residue 813 VAL Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 259 ARG Chi-restraints excluded: chain O residue 278 TYR Chi-restraints excluded: chain O residue 294 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 480 optimal weight: 30.0000 chunk 56 optimal weight: 0.5980 chunk 283 optimal weight: 40.0000 chunk 363 optimal weight: 4.9990 chunk 281 optimal weight: 0.7980 chunk 419 optimal weight: 30.0000 chunk 278 optimal weight: 0.6980 chunk 496 optimal weight: 50.0000 chunk 310 optimal weight: 6.9990 chunk 302 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS A 451 HIS A1278 ASN A1390 ASN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 128 ASN I 89 GLN ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 43764 Z= 0.293 Angle : 0.595 13.382 59586 Z= 0.303 Chirality : 0.043 0.231 6665 Planarity : 0.004 0.052 7373 Dihedral : 13.829 174.187 6764 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.94 % Favored : 95.04 % Rotamer: Outliers : 3.75 % Allowed : 24.52 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.35 (0.12), residues: 5065 helix: 1.60 (0.12), residues: 1786 sheet: 0.13 (0.19), residues: 732 loop : -0.71 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 31 HIS 0.005 0.001 HIS A 399 PHE 0.022 0.001 PHE A 219 TYR 0.016 0.001 TYR B 259 ARG 0.015 0.000 ARG I 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 411 time to evaluate : 4.991 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: A 66 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8572 (mmmm) REVERT: A 510 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8391 (mt0) REVERT: A 618 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: A 626 ASN cc_start: 0.8331 (p0) cc_final: 0.8115 (p0) REVERT: A 1074 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: A 1112 LYS cc_start: 0.9183 (mtpt) cc_final: 0.8959 (tppt) REVERT: A 1142 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7427 (p) REVERT: A 1337 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8707 (mp0) REVERT: A 1411 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8223 (tp30) REVERT: A 1448 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8280 (pm20) REVERT: B 96 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6367 (p90) REVERT: B 239 GLU cc_start: 0.8464 (pm20) cc_final: 0.7947 (pm20) REVERT: B 296 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: B 444 MET cc_start: 0.8325 (ppp) cc_final: 0.7933 (ppp) REVERT: B 473 MET cc_start: 0.8985 (mpt) cc_final: 0.8765 (mpm) REVERT: B 729 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8744 (pt) REVERT: B 884 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7927 (ttm-80) REVERT: B 1124 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8131 (ptm160) REVERT: B 1125 ASP cc_start: 0.8637 (t0) cc_final: 0.8219 (t0) REVERT: C 147 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8913 (pp) REVERT: D 117 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5772 (tm-30) REVERT: E 152 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8038 (tptt) REVERT: F 114 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: F 116 ASP cc_start: 0.9102 (t0) cc_final: 0.8721 (t0) REVERT: G 44 TYR cc_start: 0.7157 (m-80) cc_final: 0.6877 (m-80) REVERT: G 131 GLN cc_start: 0.7305 (mm-40) cc_final: 0.6133 (pm20) REVERT: G 136 VAL cc_start: 0.5219 (OUTLIER) cc_final: 0.4931 (p) REVERT: H 77 ARG cc_start: 0.8336 (mmm-85) cc_final: 0.7748 (mmm-85) REVERT: H 105 GLU cc_start: 0.8245 (tt0) cc_final: 0.7867 (tm-30) REVERT: H 106 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7503 (tm-30) REVERT: I 47 GLU cc_start: 0.8096 (tp30) cc_final: 0.7887 (tp30) REVERT: I 48 LEU cc_start: 0.9425 (mm) cc_final: 0.9165 (mm) REVERT: I 81 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8309 (mmm-85) REVERT: J 27 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8076 (mt-10) REVERT: J 31 ASP cc_start: 0.8583 (p0) cc_final: 0.8364 (p0) REVERT: K 24 ASP cc_start: 0.8840 (t0) cc_final: 0.8526 (t0) REVERT: K 54 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7775 (tmt170) REVERT: L 34 CYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7697 (m) REVERT: M 90 MET cc_start: 0.6751 (pp-130) cc_final: 0.5880 (pp-130) REVERT: M 208 ILE cc_start: 0.6281 (mm) cc_final: 0.5945 (tp) REVERT: M 227 HIS cc_start: 0.4936 (OUTLIER) cc_final: 0.3932 (m90) REVERT: M 239 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7981 (mt) REVERT: M 292 LEU cc_start: 0.4219 (mm) cc_final: 0.3699 (mm) REVERT: M 614 HIS cc_start: 0.4818 (OUTLIER) cc_final: 0.2872 (m-70) REVERT: M 730 MET cc_start: 0.1108 (pmt) cc_final: 0.0238 (tpp) REVERT: M 751 ARG cc_start: 0.5542 (mmm-85) cc_final: 0.4533 (ttm110) REVERT: O 196 ILE cc_start: 0.1963 (OUTLIER) cc_final: 0.1678 (mm) REVERT: O 259 ARG cc_start: 0.5028 (OUTLIER) cc_final: 0.4688 (mtm-85) outliers start: 167 outliers final: 85 residues processed: 547 average time/residue: 1.6345 time to fit residues: 1108.3583 Evaluate side-chains 513 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 404 time to evaluate : 4.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1448 GLU Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain M residue 614 HIS Chi-restraints excluded: chain M residue 800 VAL Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 259 ARG Chi-restraints excluded: chain O residue 294 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 307 optimal weight: 3.9990 chunk 198 optimal weight: 0.1980 chunk 296 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 315 optimal weight: 1.9990 chunk 338 optimal weight: 20.0000 chunk 245 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 390 optimal weight: 5.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A1278 ASN A1390 ASN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 128 ASN I 89 GLN ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43764 Z= 0.200 Angle : 0.584 13.812 59586 Z= 0.296 Chirality : 0.042 0.219 6665 Planarity : 0.004 0.058 7373 Dihedral : 13.788 174.236 6764 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.36 % Allowed : 25.71 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.42 (0.12), residues: 5065 helix: 1.64 (0.13), residues: 1784 sheet: 0.16 (0.19), residues: 738 loop : -0.66 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 561 HIS 0.003 0.001 HIS A 399 PHE 0.021 0.001 PHE A 219 TYR 0.025 0.001 TYR M 882 ARG 0.013 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 422 time to evaluate : 5.240 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: A 22 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8982 (t80) REVERT: A 66 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8531 (mmmm) REVERT: A 510 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8410 (mt0) REVERT: A 618 GLU cc_start: 0.8540 (pt0) cc_final: 0.7762 (pm20) REVERT: A 626 ASN cc_start: 0.8314 (p0) cc_final: 0.8088 (p0) REVERT: A 995 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: A 1112 LYS cc_start: 0.9182 (mtpt) cc_final: 0.8950 (tppt) REVERT: A 1142 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7443 (p) REVERT: A 1337 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8719 (mp0) REVERT: A 1411 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8227 (tp30) REVERT: A 1448 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: B 40 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: B 96 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6372 (p90) REVERT: B 239 GLU cc_start: 0.8442 (pm20) cc_final: 0.7872 (pm20) REVERT: B 296 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: B 398 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8413 (ttp-170) REVERT: B 444 MET cc_start: 0.8396 (ppp) cc_final: 0.8092 (ppp) REVERT: B 729 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8756 (pt) REVERT: B 884 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7885 (ttm-80) REVERT: B 1124 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8116 (ptm160) REVERT: B 1125 ASP cc_start: 0.8582 (t0) cc_final: 0.8139 (t0) REVERT: C 147 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8911 (pp) REVERT: D 117 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5672 (tm-30) REVERT: F 114 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: F 116 ASP cc_start: 0.9045 (t0) cc_final: 0.8670 (t0) REVERT: G 44 TYR cc_start: 0.7140 (m-80) cc_final: 0.6877 (m-80) REVERT: G 131 GLN cc_start: 0.7277 (mm-40) cc_final: 0.6127 (pm20) REVERT: G 136 VAL cc_start: 0.5210 (OUTLIER) cc_final: 0.4921 (p) REVERT: H 77 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.7741 (mmm-85) REVERT: H 105 GLU cc_start: 0.8216 (tt0) cc_final: 0.7848 (tm-30) REVERT: H 106 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7479 (tm-30) REVERT: I 45 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8480 (tpp80) REVERT: I 47 GLU cc_start: 0.8074 (tp30) cc_final: 0.7791 (tp30) REVERT: I 48 LEU cc_start: 0.9439 (mm) cc_final: 0.9179 (mm) REVERT: J 27 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8031 (mt-10) REVERT: J 31 ASP cc_start: 0.8539 (p0) cc_final: 0.8300 (p0) REVERT: K 24 ASP cc_start: 0.8802 (t0) cc_final: 0.8496 (t0) REVERT: L 34 CYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7796 (m) REVERT: M 208 ILE cc_start: 0.6254 (mm) cc_final: 0.5920 (tp) REVERT: M 227 HIS cc_start: 0.4918 (OUTLIER) cc_final: 0.3917 (m90) REVERT: M 239 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8052 (mt) REVERT: M 292 LEU cc_start: 0.4289 (mm) cc_final: 0.3782 (mm) REVERT: M 730 MET cc_start: 0.1118 (pmt) cc_final: 0.0294 (tpp) REVERT: M 751 ARG cc_start: 0.5560 (mmm-85) cc_final: 0.4559 (ttm110) REVERT: O 196 ILE cc_start: 0.1972 (OUTLIER) cc_final: 0.1693 (mm) REVERT: O 259 ARG cc_start: 0.5035 (OUTLIER) cc_final: 0.4690 (mtm-85) REVERT: O 278 TYR cc_start: -0.0306 (OUTLIER) cc_final: -0.1479 (m-80) REVERT: O 330 MET cc_start: 0.0061 (ppp) cc_final: -0.0308 (mmt) outliers start: 105 outliers final: 65 residues processed: 510 average time/residue: 1.6465 time to fit residues: 1038.7201 Evaluate side-chains 498 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 409 time to evaluate : 5.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1448 GLU Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain M residue 800 VAL Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 259 ARG Chi-restraints excluded: chain O residue 278 TYR Chi-restraints excluded: chain O residue 294 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 451 optimal weight: 10.0000 chunk 475 optimal weight: 10.0000 chunk 433 optimal weight: 3.9990 chunk 462 optimal weight: 40.0000 chunk 278 optimal weight: 0.8980 chunk 201 optimal weight: 0.2980 chunk 363 optimal weight: 4.9990 chunk 141 optimal weight: 0.2980 chunk 417 optimal weight: 30.0000 chunk 437 optimal weight: 40.0000 chunk 460 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS A 451 HIS A1278 ASN A1390 ASN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 128 ASN I 89 GLN ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 43764 Z= 0.255 Angle : 0.610 13.773 59586 Z= 0.307 Chirality : 0.043 0.212 6665 Planarity : 0.004 0.064 7373 Dihedral : 13.771 174.079 6763 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.47 % Allowed : 25.82 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.39 (0.12), residues: 5065 helix: 1.64 (0.12), residues: 1784 sheet: 0.11 (0.19), residues: 743 loop : -0.68 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 31 HIS 0.005 0.001 HIS A 399 PHE 0.022 0.001 PHE A 219 TYR 0.015 0.001 TYR O 365 ARG 0.014 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 413 time to evaluate : 5.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8954 (t80) REVERT: A 66 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8490 (mmmm) REVERT: A 455 MET cc_start: 0.9227 (mtp) cc_final: 0.9015 (mtt) REVERT: A 510 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8399 (mt0) REVERT: A 618 GLU cc_start: 0.8541 (pt0) cc_final: 0.7809 (pm20) REVERT: A 626 ASN cc_start: 0.8308 (p0) cc_final: 0.8086 (p0) REVERT: A 1112 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8960 (tppt) REVERT: A 1337 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: A 1411 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8254 (tp30) REVERT: B 40 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: B 96 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6455 (p90) REVERT: B 167 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8845 (pt) REVERT: B 239 GLU cc_start: 0.8450 (pm20) cc_final: 0.7893 (pm20) REVERT: B 296 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: B 398 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8465 (ttp-170) REVERT: B 444 MET cc_start: 0.8421 (ppp) cc_final: 0.8162 (ppp) REVERT: B 729 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8738 (pt) REVERT: B 884 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7920 (ttm-80) REVERT: B 1124 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8116 (ptm160) REVERT: B 1125 ASP cc_start: 0.8635 (t0) cc_final: 0.8188 (t0) REVERT: C 147 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8903 (pp) REVERT: D 117 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5851 (tm-30) REVERT: E 122 LYS cc_start: 0.8965 (ttpp) cc_final: 0.8680 (pttm) REVERT: F 114 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: F 116 ASP cc_start: 0.9048 (t0) cc_final: 0.8670 (t0) REVERT: G 44 TYR cc_start: 0.7112 (m-80) cc_final: 0.6907 (m-80) REVERT: G 131 GLN cc_start: 0.7308 (mm-40) cc_final: 0.6095 (pm20) REVERT: G 136 VAL cc_start: 0.5211 (OUTLIER) cc_final: 0.4927 (p) REVERT: H 77 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.7744 (mmm-85) REVERT: H 105 GLU cc_start: 0.8232 (tt0) cc_final: 0.7861 (tm-30) REVERT: H 106 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7510 (tm-30) REVERT: I 45 ARG cc_start: 0.8777 (tpp80) cc_final: 0.8458 (tpp80) REVERT: I 47 GLU cc_start: 0.8071 (tp30) cc_final: 0.7829 (tp30) REVERT: I 48 LEU cc_start: 0.9429 (mm) cc_final: 0.9163 (mm) REVERT: I 81 ARG cc_start: 0.8728 (mmm-85) cc_final: 0.8269 (mmm-85) REVERT: J 27 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8091 (mt-10) REVERT: K 24 ASP cc_start: 0.8816 (t0) cc_final: 0.8502 (t0) REVERT: L 34 CYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7782 (m) REVERT: M 90 MET cc_start: 0.6787 (pp-130) cc_final: 0.5909 (pp-130) REVERT: M 208 ILE cc_start: 0.6257 (mm) cc_final: 0.5927 (tp) REVERT: M 227 HIS cc_start: 0.4818 (OUTLIER) cc_final: 0.3906 (m90) REVERT: M 239 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8067 (mt) REVERT: M 292 LEU cc_start: 0.4278 (mm) cc_final: 0.3768 (mm) REVERT: M 614 HIS cc_start: 0.4856 (OUTLIER) cc_final: 0.2897 (m-70) REVERT: M 730 MET cc_start: 0.1215 (pmt) cc_final: 0.0299 (tpp) REVERT: M 751 ARG cc_start: 0.5563 (mmm-85) cc_final: 0.4562 (ttm110) REVERT: O 196 ILE cc_start: 0.2006 (OUTLIER) cc_final: 0.1744 (mm) REVERT: O 259 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.4709 (mtm-85) outliers start: 110 outliers final: 76 residues processed: 500 average time/residue: 1.6671 time to fit residues: 1040.0985 Evaluate side-chains 503 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 405 time to evaluate : 5.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain M residue 614 HIS Chi-restraints excluded: chain M residue 737 LEU Chi-restraints excluded: chain M residue 800 VAL Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 259 ARG Chi-restraints excluded: chain O residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 303 optimal weight: 0.7980 chunk 489 optimal weight: 10.0000 chunk 298 optimal weight: 0.0670 chunk 232 optimal weight: 1.9990 chunk 340 optimal weight: 8.9990 chunk 513 optimal weight: 5.9990 chunk 472 optimal weight: 6.9990 chunk 408 optimal weight: 40.0000 chunk 42 optimal weight: 0.9980 chunk 315 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A1278 ASN A1390 ASN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 128 ASN I 89 GLN ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 43764 Z= 0.238 Angle : 0.605 13.501 59586 Z= 0.306 Chirality : 0.042 0.219 6665 Planarity : 0.004 0.086 7373 Dihedral : 13.765 174.029 6760 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.33 % Allowed : 26.07 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.41 (0.12), residues: 5065 helix: 1.64 (0.13), residues: 1785 sheet: 0.12 (0.19), residues: 745 loop : -0.66 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 31 HIS 0.004 0.001 HIS A 399 PHE 0.022 0.001 PHE A 219 TYR 0.027 0.001 TYR M 875 ARG 0.015 0.000 ARG B 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10130 Ramachandran restraints generated. 5065 Oldfield, 0 Emsley, 5065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 409 time to evaluate : 4.798 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: A 22 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8956 (t80) REVERT: A 66 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8498 (mmmm) REVERT: A 510 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8411 (mt0) REVERT: A 618 GLU cc_start: 0.8536 (pt0) cc_final: 0.7781 (pm20) REVERT: A 626 ASN cc_start: 0.8299 (p0) cc_final: 0.8080 (p0) REVERT: A 995 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: A 1112 LYS cc_start: 0.9187 (mtpt) cc_final: 0.8959 (tppt) REVERT: A 1337 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8668 (mp0) REVERT: A 1411 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8255 (tp30) REVERT: B 40 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: B 96 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.6483 (p90) REVERT: B 167 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8857 (pt) REVERT: B 239 GLU cc_start: 0.8439 (pm20) cc_final: 0.7848 (pm20) REVERT: B 296 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: B 444 MET cc_start: 0.8407 (ppp) cc_final: 0.8169 (ppp) REVERT: B 729 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8730 (pt) REVERT: B 884 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7921 (ttm-80) REVERT: B 1124 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8112 (ptm160) REVERT: B 1125 ASP cc_start: 0.8606 (t0) cc_final: 0.8149 (t0) REVERT: C 147 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8900 (pp) REVERT: D 117 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5857 (tm-30) REVERT: E 152 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8120 (tptt) REVERT: F 114 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8149 (mm-30) REVERT: F 116 ASP cc_start: 0.9051 (t0) cc_final: 0.8669 (t0) REVERT: G 44 TYR cc_start: 0.7041 (m-80) cc_final: 0.6762 (m-80) REVERT: G 131 GLN cc_start: 0.7300 (mm-40) cc_final: 0.6092 (pm20) REVERT: G 136 VAL cc_start: 0.5208 (OUTLIER) cc_final: 0.4924 (p) REVERT: H 77 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.7617 (mmm-85) REVERT: H 105 GLU cc_start: 0.8346 (tt0) cc_final: 0.7933 (tm-30) REVERT: H 106 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7503 (tm-30) REVERT: I 45 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8465 (tpp80) REVERT: I 47 GLU cc_start: 0.8078 (tp30) cc_final: 0.7806 (tp30) REVERT: I 48 LEU cc_start: 0.9447 (mm) cc_final: 0.9209 (mm) REVERT: I 81 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8281 (mmm-85) REVERT: J 27 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8105 (mt-10) REVERT: K 24 ASP cc_start: 0.8812 (t0) cc_final: 0.8502 (t0) REVERT: L 34 CYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7856 (m) REVERT: M 90 MET cc_start: 0.6794 (pp-130) cc_final: 0.5908 (pp-130) REVERT: M 208 ILE cc_start: 0.6294 (mm) cc_final: 0.5959 (tp) REVERT: M 227 HIS cc_start: 0.4812 (OUTLIER) cc_final: 0.3905 (m90) REVERT: M 239 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8089 (mt) REVERT: M 292 LEU cc_start: 0.4263 (mm) cc_final: 0.3757 (mm) REVERT: M 730 MET cc_start: 0.1298 (pmt) cc_final: 0.0331 (tpp) REVERT: M 751 ARG cc_start: 0.5659 (mmm-85) cc_final: 0.4664 (ttm110) REVERT: O 196 ILE cc_start: 0.2011 (OUTLIER) cc_final: 0.1747 (mm) REVERT: O 259 ARG cc_start: 0.5050 (OUTLIER) cc_final: 0.4711 (mtm-85) outliers start: 104 outliers final: 71 residues processed: 491 average time/residue: 1.6608 time to fit residues: 1003.7735 Evaluate side-chains 498 residues out of total 4519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 405 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1232 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain M residue 800 VAL Chi-restraints excluded: chain O residue 35 TYR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 259 ARG Chi-restraints excluded: chain O residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 324 optimal weight: 0.9990 chunk 435 optimal weight: 30.0000 chunk 125 optimal weight: 0.7980 chunk 376 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 409 optimal weight: 50.0000 chunk 171 optimal weight: 0.5980 chunk 420 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A1278 ASN A1390 ASN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 128 ASN I 89 GLN ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.160434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.090007 restraints weight = 75610.070| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.28 r_work: 0.2923 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 43764 Z= 0.201 Angle : 0.606 13.328 59586 Z= 0.305 Chirality : 0.042 0.216 6665 Planarity : 0.004 0.067 7373 Dihedral : 13.751 174.132 6760 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.29 % Allowed : 26.18 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: 0.44 (0.12), residues: 5065 helix: 1.65 (0.13), residues: 1785 sheet: 0.15 (0.19), residues: 741 loop : -0.64 (0.13), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 31 HIS 0.003 0.001 HIS A 399 PHE 0.021 0.001 PHE A 219 TYR 0.015 0.001 TYR O 365 ARG 0.014 0.000 ARG A 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17108.58 seconds wall clock time: 308 minutes 17.30 seconds (18497.30 seconds total)