Starting phenix.real_space_refine on Fri Oct 30 14:57:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6h68_0147/10_2026/6h68_0147.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h68_0147/10_2026/6h68_0147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6h68_0147/10_2026/6h68_0147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h68_0147/10_2026/6h68_0147.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6h68_0147/10_2026/6h68_0147.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6h68_0147/10_2026/6h68_0147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6h68_0147/10_2026/6h68_0147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h68_0147/10_2026/6h68_0147.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 68 5.49 5 S 172 5.16 5 C 23265 2.51 5 N 6431 2.21 5 O 7161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.24s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37103 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1473, 11637 Classifications: {'peptide': 1473} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1413} Chain breaks: 5 Chain: "B" Number of atoms: 9327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9327 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1115} Chain breaks: 3 Chain: "C" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2431 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1059 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Chain: "I" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 479 Classifications: {'peptide': 65} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 61} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3131 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 21, 'TRANS': 374} Chain: "N" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1254 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "R" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 685 Unusual residues: {'TTD': 1} Classifications: {'DNA': 32, 'undetermined': 1} Link IDs: {'rna3p': 30, None: 2} Not linked: pdbres=" DC T 17 " pdbres="TTD T 18 " Not linked: pdbres="TTD T 18 " pdbres=" DT T 19 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 496 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 111.354 105.008 97.479 1.00 90.73 S ATOM 480 SG CYS A 65 111.455 103.287 100.662 1.00 95.85 S ATOM 535 SG CYS A 72 108.110 102.878 99.094 1.00 78.98 S ATOM 781 SG CYS A 102 73.330 140.156 92.123 1.00 57.56 S ATOM 806 SG CYS A 105 74.187 141.090 95.518 1.00 62.21 S ATOM 1589 SG CYS A 233 70.425 140.838 94.176 1.00 67.20 S ATOM 1611 SG CYS A 236 71.957 144.444 93.407 1.00 70.90 S ATOM 20266 SG CYS B1104 101.967 112.672 112.405 1.00 81.61 S ATOM 20292 SG CYS B1107 98.955 112.783 109.563 1.00 78.87 S ATOM 20439 SG CYS B1128 102.414 113.644 108.623 1.00 84.25 S ATOM 20467 SG CYS B1131 101.357 116.882 110.978 1.00 80.71 S ATOM 29180 SG CYS I 13 45.598 111.619 35.542 1.00126.06 S ATOM 29321 SG CYS I 33 45.564 114.907 34.077 1.00123.28 S ATOM 29628 SG CYS J 7 82.162 37.513 87.404 1.00 45.16 S ATOM 29651 SG CYS J 10 80.773 35.145 89.907 1.00 59.67 S ATOM 29937 SG CYS J 46 81.874 33.928 85.861 1.00 51.64 S ATOM 31023 SG CYS L 34 110.478 57.375 56.483 1.00 74.17 S ATOM 31127 SG CYS L 48 112.701 60.181 56.772 1.00106.50 S ATOM 31150 SG CYS L 51 109.182 59.905 53.482 1.00105.75 S Time building chain proxies: 7.14, per 1000 atoms: 0.19 Number of scatterers: 37103 At special positions: 0 Unit cell: (168.54, 159, 159, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 172 16.00 P 68 15.00 O 7161 8.00 N 6431 7.00 C 23265 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 65 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 62 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 72 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 105 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 102 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 236 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 233 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1131 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 33 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " Number of angles added : 15 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8478 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 51 sheets defined 37.6% alpha, 16.5% beta 29 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 38 through 42 removed outlier: 3.994A pdb=" N LEU A 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 42' Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 111 through 126 Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 175 through 199 removed outlier: 3.905A pdb=" N ASP A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.612A pdb=" N LYS A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.729A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.978A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 407 removed outlier: 3.562A pdb=" N GLN A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.750A pdb=" N PHE A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.968A pdb=" N GLY A 622 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.572A pdb=" N THR A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 Processing helix chain 'A' and resid 728 through 739 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 802 through 824 Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.527A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 863 Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.599A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 Processing helix chain 'A' and resid 923 through 929 Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.926A pdb=" N VAL A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.521A pdb=" N LYS A1012 " --> pdb=" O ASP A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.976A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 3.609A pdb=" N LYS A1059 " --> pdb=" O ASP A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 removed outlier: 3.742A pdb=" N CYS A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1081 through 1089 removed outlier: 3.956A pdb=" N ALA A1084 " --> pdb=" O ASN A1081 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A1085 " --> pdb=" O PRO A1082 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A1086 " --> pdb=" O SER A1083 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLU A1087 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS A1088 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A1089 " --> pdb=" O ILE A1086 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1081 through 1089' Processing helix chain 'A' and resid 1093 through 1108 Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1151 through 1156 removed outlier: 3.986A pdb=" N LYS A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 3.653A pdb=" N PHE A1166 " --> pdb=" O ASN A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1198 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1218 through 1226 removed outlier: 3.890A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1259 removed outlier: 3.550A pdb=" N SER A1259 " --> pdb=" O CYS A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1265 No H-bonds generated for 'chain 'A' and resid 1263 through 1265' Processing helix chain 'A' and resid 1298 through 1307 removed outlier: 3.822A pdb=" N TYR A1302 " --> pdb=" O ASP A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.567A pdb=" N GLN A1320 " --> pdb=" O VAL A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1335 Processing helix chain 'A' and resid 1440 through 1452 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1526 through 1532 Processing helix chain 'A' and resid 1546 through 1553 Processing helix chain 'A' and resid 1555 through 1573 removed outlier: 3.553A pdb=" N ARG A1559 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1589 removed outlier: 3.987A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1606 removed outlier: 3.889A pdb=" N THR A1605 " --> pdb=" O GLN A1601 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A1606 " --> pdb=" O GLY A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.545A pdb=" N PHE A1621 " --> pdb=" O THR A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1644 Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.201A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.668A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.705A pdb=" N ILE B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 322 through 334 removed outlier: 4.183A pdb=" N VAL B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 404 through 433 removed outlier: 3.694A pdb=" N LEU B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.766A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.998A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 598 through 614 Processing helix chain 'B' and resid 677 through 681 removed outlier: 3.567A pdb=" N GLU B 680 " --> pdb=" O THR B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.646A pdb=" N ASN B 702 " --> pdb=" O SER B 698 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 698 through 703' Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.631A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.032A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.892A pdb=" N ASN B 764 " --> pdb=" O GLY B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 833 through 837 removed outlier: 3.638A pdb=" N LEU B 837 " --> pdb=" O LYS B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 952 through 958 removed outlier: 4.758A pdb=" N SER B 956 " --> pdb=" O HIS B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 975 removed outlier: 3.662A pdb=" N VAL B 964 " --> pdb=" O ILE B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1072 through 1083 Processing helix chain 'B' and resid 1084 through 1093 removed outlier: 3.506A pdb=" N LEU B1093 " --> pdb=" O GLN B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1190 removed outlier: 3.624A pdb=" N SER B1190 " --> pdb=" O ASP B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1193 No H-bonds generated for 'chain 'B' and resid 1191 through 1193' Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.508A pdb=" N PHE C 36 " --> pdb=" O ASN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 173 through 179 removed outlier: 3.864A pdb=" N THR C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.531A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 220' Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 32 through 49 removed outlier: 3.613A pdb=" N VAL D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 98 removed outlier: 3.939A pdb=" N GLN D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) 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 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.935A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 71 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 126 Processing helix chain 'G' and resid 9 through 18 removed outlier: 4.017A pdb=" N THR G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA G 14 " --> pdb=" O ASN G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.614A pdb=" N LYS G 31 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.508A pdb=" N TYR G 53 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 Processing helix chain 'G' and resid 67 through 70 removed outlier: 3.600A pdb=" N VAL G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 67 through 70' Processing helix chain 'G' and resid 159 through 162 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 129 through 133 removed outlier: 4.029A pdb=" N LEU H 132 " --> pdb=" O TYR H 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 51 removed outlier: 3.796A pdb=" N ARG J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 59 removed outlier: 3.861A pdb=" N GLU J 58 " --> pdb=" O ASP J 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 81 Processing helix chain 'K' and resid 112 through 141 removed outlier: 3.508A pdb=" N ALA K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 132 removed outlier: 3.960A pdb=" N GLU M 130 " --> pdb=" O ASN M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 147 removed outlier: 3.611A pdb=" N ALA M 137 " --> pdb=" O GLY M 133 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 168 Processing helix chain 'M' and resid 197 through 201 removed outlier: 3.860A pdb=" N ILE M 201 " --> pdb=" O VAL M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 208 Processing helix chain 'M' and resid 209 through 214 Processing helix chain 'M' and resid 218 through 224 Processing helix chain 'M' and resid 226 through 233 Processing helix chain 'M' and resid 240 through 246 removed outlier: 3.976A pdb=" N ALA M 244 " --> pdb=" O SER M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 254 No H-bonds generated for 'chain 'M' and resid 252 through 254' Processing helix chain 'M' and resid 255 through 273 Processing helix chain 'M' and resid 280 through 285 Processing helix chain 'M' and resid 291 through 302 removed outlier: 4.398A pdb=" N VAL M 295 " --> pdb=" O PRO M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 339 Processing helix chain 'M' and resid 346 through 354 removed outlier: 3.883A pdb=" N ASN M 354 " --> pdb=" O ALA M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 356 through 367 Processing helix chain 'M' and resid 375 through 382 removed outlier: 3.516A pdb=" N ALA M 379 " --> pdb=" O THR M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 389 Processing helix chain 'N' and resid 149 through 154 removed outlier: 3.642A pdb=" N VAL N 153 " --> pdb=" O ASP N 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 17 removed outlier: 5.717A pdb=" N ILE A 11 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU B1201 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 86 removed outlier: 9.607A pdb=" N LEU A 81 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N VAL A 361 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 245 removed outlier: 3.766A pdb=" N LYS A 242 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 494 through 497 removed outlier: 3.648A pdb=" N ALA A 479 " --> pdb=" O ARG B1047 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 486 removed outlier: 6.249A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 510 removed outlier: 4.256A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.964A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.886A pdb=" N ALA B 774 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 949 " --> pdb=" O ALA B 774 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 776 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N MET B 787 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TRP B 931 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE B 789 " --> pdb=" O TRP B 931 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B1026 " --> pdb=" O GLU B1011 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 826 through 827 removed outlier: 4.437A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B1026 " --> pdb=" O GLU B1011 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB4, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 3.782A pdb=" N HIS A1031 " --> pdb=" O ARG A1039 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A1039 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1504 through 1507 Processing sheet with id=AB6, first strand: chain 'A' and resid 1267 through 1275 removed outlier: 3.570A pdb=" N TYR A1290 " --> pdb=" O LEU A1474 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A1473 " --> pdb=" O LYS A1459 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 144 through 147 Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 73 removed outlier: 5.211A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP B 143 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE B 153 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 145 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN B 151 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC2, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AC3, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.386A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 262 " --> pdb=" O TYR B 269 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC5, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC6, first strand: chain 'B' and resid 571 through 572 removed outlier: 4.361A pdb=" N ALA B 571 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP B 595 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.548A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.548A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS L 58 " --> pdb=" O VAL B 885 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 752 through 753 removed outlier: 5.895A pdb=" N GLN B 979 " --> pdb=" O LYS B 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 824 through 825 removed outlier: 6.383A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE B 862 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 868 " --> pdb=" O PHE B 862 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1014 through 1015 Processing sheet with id=AD3, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD4, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD5, first strand: chain 'B' and resid 1158 through 1160 Processing sheet with id=AD6, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.941A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 302 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 168 through 169 removed outlier: 6.845A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.723A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE2, first strand: chain 'C' and resid 229 through 235 Processing sheet with id=AE3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE4, first strand: chain 'D' and resid 22 through 24 removed outlier: 7.014A pdb=" N TRP G 117 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE G 89 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS G 119 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU G 87 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR G 123 " --> pdb=" O GLY G 83 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY G 83 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.194A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE7, first strand: chain 'G' and resid 131 through 136 removed outlier: 3.617A pdb=" N TYR G 136 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU G 148 " --> pdb=" O TYR G 136 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN G 235 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP G 131 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.843A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF2, first strand: chain 'M' and resid 14 through 16 removed outlier: 4.210A pdb=" N LYS M 92 " --> pdb=" O GLN M 16 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR M 76 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY M 79 " --> pdb=" O TRP N 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN N 52 " --> pdb=" O PHE M 81 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 30 through 31 removed outlier: 3.980A pdb=" N SER M 98 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 344 through 345 Processing sheet with id=AF5, first strand: chain 'N' and resid 78 through 79 removed outlier: 3.974A pdb=" N THR N 78 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 110 through 111 1406 hydrogen bonds defined for protein. 3897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 10.04 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6094 1.31 - 1.43: 9916 1.43 - 1.56: 21537 1.56 - 1.68: 133 1.68 - 1.81: 274 Bond restraints: 37954 Sorted by residual: bond pdb=" N1 TTD T 18 " pdb=" C2 TTD T 18 " ideal model delta sigma weight residual 1.353 1.513 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" C2' TTD T 18 " pdb=" C3R TTD T 18 " ideal model delta sigma weight residual 1.520 1.395 0.125 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C2T TTD T 18 " pdb=" N1T TTD T 18 " ideal model delta sigma weight residual 1.360 1.481 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C2T TTD T 18 " pdb=" N3T TTD T 18 " ideal model delta sigma weight residual 1.386 1.488 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C2 TTD T 18 " pdb=" N3 TTD T 18 " ideal model delta sigma weight residual 1.396 1.487 -0.091 2.00e-02 2.50e+03 2.08e+01 ... (remaining 37949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 51135 3.39 - 6.78: 386 6.78 - 10.16: 46 10.16 - 13.55: 5 13.55 - 16.94: 1 Bond angle restraints: 51573 Sorted by residual: angle pdb=" O4P TTD T 18 " pdb=" PB TTD T 18 " pdb=" O5P TTD T 18 " ideal model delta sigma weight residual 122.50 105.56 16.94 3.00e+00 1.11e-01 3.19e+01 angle pdb=" C ILE B 588 " pdb=" N ASP B 589 " pdb=" CA ASP B 589 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 angle pdb=" CA ARG M 166 " pdb=" CB ARG M 166 " pdb=" CG ARG M 166 " ideal model delta sigma weight residual 114.10 123.69 -9.59 2.00e+00 2.50e-01 2.30e+01 angle pdb=" O5' DA U 47 " pdb=" C5' DA U 47 " pdb=" C4' DA U 47 " ideal model delta sigma weight residual 109.40 113.16 -3.76 8.00e-01 1.56e+00 2.20e+01 angle pdb=" N ASP B 819 " pdb=" CA ASP B 819 " pdb=" C ASP B 819 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 ... (remaining 51568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 22709 35.36 - 70.71: 335 70.71 - 106.07: 14 106.07 - 141.43: 10 141.43 - 176.78: 2 Dihedral angle restraints: 23070 sinusoidal: 9961 harmonic: 13109 Sorted by residual: dihedral pdb=" CA LYS A 408 " pdb=" C LYS A 408 " pdb=" N ASP A 409 " pdb=" CA ASP A 409 " ideal model delta harmonic sigma weight residual 180.00 143.01 36.99 0 5.00e+00 4.00e-02 5.47e+01 dihedral pdb=" CA ILE N 25 " pdb=" C ILE N 25 " pdb=" N PRO N 26 " pdb=" CA PRO N 26 " ideal model delta harmonic sigma weight residual -180.00 -143.73 -36.27 0 5.00e+00 4.00e-02 5.26e+01 dihedral pdb=" CA ASP B 819 " pdb=" C ASP B 819 " pdb=" N PRO B 820 " pdb=" CA PRO B 820 " ideal model delta harmonic sigma weight residual -180.00 -144.96 -35.04 0 5.00e+00 4.00e-02 4.91e+01 ... (remaining 23067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5321 0.094 - 0.188: 444 0.188 - 0.281: 21 0.281 - 0.375: 2 0.375 - 0.469: 3 Chirality restraints: 5791 Sorted by residual: chirality pdb=" C5 TTD T 18 " pdb=" C4 TTD T 18 " pdb=" C6 TTD T 18 " pdb=" C5T TTD T 18 " both_signs ideal model delta sigma weight residual False -3.16 -2.69 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C1R TTD T 18 " pdb=" C2R TTD T 18 " pdb=" N1T TTD T 18 " pdb=" O4R TTD T 18 " both_signs ideal model delta sigma weight residual False 2.39 1.93 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" C5T TTD T 18 " pdb=" C5 TTD T 18 " pdb=" C4T TTD T 18 " pdb=" C6T TTD T 18 " both_signs ideal model delta sigma weight residual False 2.95 2.52 0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 5788 not shown) Planarity restraints: 6422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1R TTD T 18 " -0.039 2.00e-02 2.50e+03 3.39e-02 2.59e+01 pdb=" C2T TTD T 18 " 0.002 2.00e-02 2.50e+03 pdb=" C4T TTD T 18 " 0.023 2.00e-02 2.50e+03 pdb=" C5T TTD T 18 " -0.061 2.00e-02 2.50e+03 pdb=" C6T TTD T 18 " 0.064 2.00e-02 2.50e+03 pdb=" N1T TTD T 18 " 0.019 2.00e-02 2.50e+03 pdb=" N3T TTD T 18 " 0.001 2.00e-02 2.50e+03 pdb=" O2T TTD T 18 " 0.001 2.00e-02 2.50e+03 pdb=" O4T TTD T 18 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 67 " -0.045 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO G 68 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO G 68 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 68 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U R 2 " 0.035 2.00e-02 2.50e+03 1.79e-02 7.21e+00 pdb=" N1 U R 2 " -0.037 2.00e-02 2.50e+03 pdb=" C2 U R 2 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U R 2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U R 2 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U R 2 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U R 2 " 0.011 2.00e-02 2.50e+03 pdb=" C5 U R 2 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U R 2 " -0.006 2.00e-02 2.50e+03 ... (remaining 6419 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7134 2.77 - 3.31: 33284 3.31 - 3.84: 61625 3.84 - 4.37: 70532 4.37 - 4.90: 117691 Nonbonded interactions: 290266 Sorted by model distance: nonbonded pdb=" OD1 ASP B 946 " pdb=" OG SER J 9 " model vdw 2.243 3.040 nonbonded pdb=" O VAL A 418 " pdb=" OG SER A 421 " model vdw 2.268 3.040 nonbonded pdb=" O LEU M 178 " pdb=" OG1 THR M 182 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 791 " pdb=" O SER A1061 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR N 78 " pdb=" O ILE N 89 " model vdw 2.281 3.040 ... (remaining 290261 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 41.270 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.600 37976 Z= 0.346 Angle : 0.904 24.337 51588 Z= 0.493 Chirality : 0.054 0.469 5791 Planarity : 0.007 0.068 6422 Dihedral : 12.243 176.784 14592 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.05 % Allowed : 1.18 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.10), residues: 4447 helix: -2.30 (0.10), residues: 1500 sheet: -2.14 (0.18), residues: 670 loop : -2.70 (0.11), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 19 TYR 0.037 0.002 TYR A1595 PHE 0.033 0.003 PHE C 315 TRP 0.021 0.002 TRP A 530 HIS 0.012 0.002 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.27 (37954) covalent geometry : angle 0.86342 / 0.49 (51573) hydrogen bonds : bond 0.16062 / 10.81 ( 1459) hydrogen bonds : angle 7.38380 / 5.18 ( 4047) metal coordination : bond 0.26287 / 18.53 ( 20) metal coordination : angle 15.65493 / 9.23 ( 15) Misc. bond : bond 0.06076 / 3.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1367 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.8959 (mt) cc_final: 0.8549 (tp) REVERT: A 382 GLN cc_start: 0.8330 (mt0) cc_final: 0.8128 (mt0) REVERT: A 433 ASP cc_start: 0.8416 (m-30) cc_final: 0.8205 (m-30) REVERT: A 603 HIS cc_start: 0.6877 (m-70) cc_final: 0.6605 (m90) REVERT: A 620 ASN cc_start: 0.7096 (m-40) cc_final: 0.6702 (m-40) REVERT: A 656 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8767 (mm-40) REVERT: A 750 ILE cc_start: 0.6912 (mt) cc_final: 0.6595 (tt) REVERT: A 769 VAL cc_start: 0.8172 (t) cc_final: 0.7536 (t) REVERT: A 771 PHE cc_start: 0.7845 (m-80) cc_final: 0.7544 (m-10) REVERT: A 780 ILE cc_start: 0.8968 (pt) cc_final: 0.8752 (mm) REVERT: A 796 SER cc_start: 0.8696 (m) cc_final: 0.8412 (p) REVERT: A 852 ASP cc_start: 0.8418 (m-30) cc_final: 0.7755 (p0) REVERT: A 882 ILE cc_start: 0.7679 (mt) cc_final: 0.7392 (tt) REVERT: A 888 LYS cc_start: 0.9034 (mttt) cc_final: 0.8815 (mmmt) REVERT: A 900 VAL cc_start: 0.8658 (m) cc_final: 0.7826 (m) REVERT: A 944 MET cc_start: 0.8003 (mtt) cc_final: 0.7758 (mtp) REVERT: A 960 MET cc_start: 0.8373 (mtm) cc_final: 0.7654 (mmm) REVERT: A 1012 LYS cc_start: 0.7747 (pttt) cc_final: 0.7516 (pttp) REVERT: A 1036 ASN cc_start: 0.8318 (m-40) cc_final: 0.8069 (m-40) REVERT: A 1085 LEU cc_start: 0.7059 (pp) cc_final: 0.6622 (mm) REVERT: A 1120 TYR cc_start: 0.6895 (p90) cc_final: 0.6276 (p90) REVERT: A 1139 ASN cc_start: 0.7955 (t0) cc_final: 0.7721 (m110) REVERT: A 1154 LEU cc_start: 0.7562 (tp) cc_final: 0.6787 (mt) REVERT: A 1238 MET cc_start: 0.7535 (ttp) cc_final: 0.7205 (ttm) REVERT: A 1476 LEU cc_start: 0.8759 (mt) cc_final: 0.8088 (mp) REVERT: A 1479 ASP cc_start: 0.6393 (t70) cc_final: 0.6169 (m-30) REVERT: A 1533 GLU cc_start: 0.7301 (tt0) cc_final: 0.7034 (tp30) REVERT: A 1613 MET cc_start: 0.8296 (mtt) cc_final: 0.7762 (mtm) REVERT: A 1629 ASN cc_start: 0.8898 (m-40) cc_final: 0.8468 (t0) REVERT: A 1646 LEU cc_start: 0.5891 (tp) cc_final: 0.5646 (pt) REVERT: B 155 VAL cc_start: 0.8442 (t) cc_final: 0.8230 (p) REVERT: B 172 LEU cc_start: 0.9156 (mt) cc_final: 0.8794 (mp) REVERT: B 243 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8014 (mm-40) REVERT: B 315 LYS cc_start: 0.8010 (ttmm) cc_final: 0.7727 (tptm) REVERT: B 381 LEU cc_start: 0.8888 (tp) cc_final: 0.8580 (tp) REVERT: B 393 ASN cc_start: 0.8583 (t0) cc_final: 0.8252 (t0) REVERT: B 415 GLU cc_start: 0.8713 (tp30) cc_final: 0.8094 (tp30) REVERT: B 449 VAL cc_start: 0.8927 (t) cc_final: 0.8560 (p) REVERT: B 528 LEU cc_start: 0.8739 (mt) cc_final: 0.8312 (mt) REVERT: B 614 GLU cc_start: 0.8003 (tp30) cc_final: 0.7747 (tp30) REVERT: B 764 ASN cc_start: 0.7869 (m-40) cc_final: 0.7391 (t0) REVERT: B 765 PHE cc_start: 0.8008 (m-80) cc_final: 0.7144 (m-80) REVERT: B 1014 TYR cc_start: 0.7210 (m-80) cc_final: 0.6116 (m-80) REVERT: B 1033 TYR cc_start: 0.8379 (m-80) cc_final: 0.7808 (m-80) REVERT: B 1180 PHE cc_start: 0.8717 (t80) cc_final: 0.8396 (t80) REVERT: C 179 PHE cc_start: 0.8324 (m-10) cc_final: 0.8078 (m-10) REVERT: E 31 THR cc_start: 0.8621 (p) cc_final: 0.7831 (p) REVERT: E 96 PHE cc_start: 0.7162 (t80) cc_final: 0.6894 (t80) REVERT: E 111 VAL cc_start: 0.8466 (t) cc_final: 0.8207 (t) REVERT: E 136 ASN cc_start: 0.8437 (t0) cc_final: 0.8158 (t0) REVERT: E 208 TYR cc_start: 0.6948 (t80) cc_final: 0.6074 (t80) REVERT: E 211 TYR cc_start: 0.7992 (m-80) cc_final: 0.7779 (m-80) REVERT: F 60 GLN cc_start: 0.8839 (tt0) cc_final: 0.8441 (tp-100) REVERT: F 69 LEU cc_start: 0.7524 (tp) cc_final: 0.7231 (tp) REVERT: F 87 LYS cc_start: 0.8187 (pttt) cc_final: 0.7357 (mmmt) REVERT: F 110 ASP cc_start: 0.6832 (t70) cc_final: 0.6452 (t70) REVERT: F 125 LEU cc_start: 0.8505 (tp) cc_final: 0.8110 (tp) REVERT: F 150 GLU cc_start: 0.7465 (pt0) cc_final: 0.6864 (mp0) REVERT: G 42 PRO cc_start: 0.5328 (Cg_endo) cc_final: 0.4763 (Cg_exo) REVERT: G 76 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7787 (mmmt) REVERT: G 80 VAL cc_start: 0.6679 (t) cc_final: 0.6314 (p) REVERT: G 133 LEU cc_start: 0.9105 (mt) cc_final: 0.8899 (mt) REVERT: H 54 SER cc_start: 0.8470 (t) cc_final: 0.8261 (p) REVERT: H 142 LEU cc_start: 0.7099 (tp) cc_final: 0.6849 (tp) REVERT: J 16 ASP cc_start: 0.8320 (p0) cc_final: 0.7455 (p0) REVERT: J 30 LEU cc_start: 0.6372 (tp) cc_final: 0.5869 (tp) REVERT: J 52 THR cc_start: 0.7729 (p) cc_final: 0.7473 (p) REVERT: K 59 THR cc_start: 0.6958 (p) cc_final: 0.6584 (p) REVERT: K 65 ILE cc_start: 0.8518 (mt) cc_final: 0.8284 (mm) REVERT: K 66 VAL cc_start: 0.7494 (m) cc_final: 0.7117 (p) REVERT: K 69 ASP cc_start: 0.8356 (p0) cc_final: 0.8127 (p0) REVERT: K 70 HIS cc_start: 0.8374 (m-70) cc_final: 0.7812 (m170) REVERT: K 132 GLU cc_start: 0.8418 (tt0) cc_final: 0.7831 (tm-30) REVERT: K 133 SER cc_start: 0.9448 (m) cc_final: 0.9167 (p) REVERT: L 56 LEU cc_start: 0.8858 (mt) cc_final: 0.8536 (mp) REVERT: M 132 PHE cc_start: 0.7654 (m-10) cc_final: 0.7146 (m-80) REVERT: M 153 LYS cc_start: 0.6215 (tttt) cc_final: 0.5540 (tmtt) REVERT: M 236 TYR cc_start: 0.6883 (t80) cc_final: 0.6633 (t80) REVERT: M 246 LYS cc_start: 0.7075 (mmtp) cc_final: 0.6787 (pttt) REVERT: M 256 MET cc_start: 0.7123 (ttm) cc_final: 0.6844 (ttt) REVERT: N 91 ASP cc_start: 0.7358 (t0) cc_final: 0.6312 (m-30) outliers start: 2 outliers final: 0 residues processed: 1368 average time/residue: 0.2567 time to fit residues: 548.6519 Evaluate side-chains 725 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 725 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 106 HIS A 213 ASN A 224 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 HIS ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1453 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 209 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN B 587 GLN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS F 100 GLN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN H 137 GLN I 21 ASN I 44 ASN K 70 HIS M 18 GLN M 71 GLN ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS N 52 GLN N 128 ASN N 132 GLN N 170 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.117035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.100062 restraints weight = 136337.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.102037 restraints weight = 87617.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.103500 restraints weight = 62462.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104427 restraints weight = 48199.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.105151 restraints weight = 40016.083| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 37976 Z= 0.271 Angle : 0.827 11.669 51588 Z= 0.431 Chirality : 0.049 0.369 5791 Planarity : 0.006 0.073 6422 Dihedral : 14.441 176.065 5662 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.12), residues: 4447 helix: -0.94 (0.12), residues: 1521 sheet: -1.90 (0.18), residues: 670 loop : -2.42 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 957 TYR 0.027 0.002 TYR A1595 PHE 0.033 0.003 PHE C 67 TRP 0.034 0.003 TRP A1530 HIS 0.012 0.002 HIS B 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.27 (37954) covalent geometry : angle 0.82049 / 0.43 (51573) hydrogen bonds : bond 0.05510 / 3.77 ( 1459) hydrogen bonds : angle 6.14061 / 4.32 ( 4047) metal coordination : bond 0.01243 / 0.72 ( 20) metal coordination : angle 6.16775 / 3.07 ( 15) Misc. bond : bond 0.00374 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 815 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8561 (mt-10) REVERT: A 519 LEU cc_start: 0.8877 (mt) cc_final: 0.8561 (mt) REVERT: A 521 GLN cc_start: 0.8107 (tp40) cc_final: 0.7711 (tp-100) REVERT: A 589 MET cc_start: 0.7488 (mmm) cc_final: 0.7229 (mmp) REVERT: A 601 MET cc_start: 0.9292 (mmp) cc_final: 0.8837 (mmm) REVERT: A 780 ILE cc_start: 0.9304 (pt) cc_final: 0.8928 (mm) REVERT: A 852 ASP cc_start: 0.8263 (m-30) cc_final: 0.7870 (p0) REVERT: A 900 VAL cc_start: 0.8664 (m) cc_final: 0.8329 (m) REVERT: A 960 MET cc_start: 0.8234 (mtm) cc_final: 0.6894 (mmm) REVERT: A 964 LYS cc_start: 0.8272 (tttt) cc_final: 0.7744 (tttp) REVERT: A 981 TYR cc_start: 0.8074 (t80) cc_final: 0.7458 (t80) REVERT: A 994 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8132 (mt-10) REVERT: A 1000 MET cc_start: 0.9029 (mtt) cc_final: 0.8368 (mmt) REVERT: A 1057 ILE cc_start: 0.9159 (mm) cc_final: 0.8793 (tp) REVERT: A 1059 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7780 (mptt) REVERT: A 1063 MET cc_start: 0.4660 (mtm) cc_final: 0.3176 (mmt) REVERT: A 1120 TYR cc_start: 0.6972 (p90) cc_final: 0.6518 (p90) REVERT: A 1121 ASP cc_start: 0.8262 (p0) cc_final: 0.7830 (p0) REVERT: A 1139 ASN cc_start: 0.8423 (t0) cc_final: 0.7908 (m110) REVERT: A 1226 VAL cc_start: 0.8729 (t) cc_final: 0.8328 (t) REVERT: A 1262 LEU cc_start: 0.8753 (mt) cc_final: 0.8468 (mt) REVERT: A 1493 CYS cc_start: 0.6544 (m) cc_final: 0.6205 (m) REVERT: A 1588 MET cc_start: 0.6692 (tpp) cc_final: 0.5496 (tpp) REVERT: A 1629 ASN cc_start: 0.9061 (m-40) cc_final: 0.8683 (t0) REVERT: B 40 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7129 (tt0) REVERT: B 243 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8737 (mm-40) REVERT: B 275 MET cc_start: 0.7145 (tpp) cc_final: 0.6877 (tpp) REVERT: B 314 LYS cc_start: 0.8677 (tppt) cc_final: 0.8466 (mtmt) REVERT: B 315 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7726 (tptm) REVERT: B 397 THR cc_start: 0.8942 (m) cc_final: 0.8590 (m) REVERT: B 502 MET cc_start: 0.7888 (ttp) cc_final: 0.7349 (ttt) REVERT: B 523 GLU cc_start: 0.8120 (mp0) cc_final: 0.7255 (tp30) REVERT: B 595 TRP cc_start: 0.8134 (m100) cc_final: 0.7490 (m-10) REVERT: B 757 TYR cc_start: 0.7422 (t80) cc_final: 0.6959 (t80) REVERT: B 764 ASN cc_start: 0.8024 (m-40) cc_final: 0.7497 (t0) REVERT: B 936 MET cc_start: 0.8513 (ttm) cc_final: 0.8142 (ttm) REVERT: B 958 MET cc_start: 0.8475 (mtp) cc_final: 0.8220 (ttp) REVERT: B 1015 SER cc_start: 0.9127 (t) cc_final: 0.8927 (p) REVERT: B 1033 TYR cc_start: 0.8390 (m-80) cc_final: 0.7741 (m-80) REVERT: B 1038 HIS cc_start: 0.7584 (m90) cc_final: 0.7093 (m90) REVERT: B 1066 HIS cc_start: 0.8136 (m-70) cc_final: 0.7745 (m-70) REVERT: B 1188 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6675 (tp30) REVERT: C 71 MET cc_start: 0.7524 (mmm) cc_final: 0.7006 (mmt) REVERT: C 157 TYR cc_start: 0.8034 (m-80) cc_final: 0.7274 (m-80) REVERT: F 60 GLN cc_start: 0.8761 (tt0) cc_final: 0.8499 (tp-100) REVERT: F 87 LYS cc_start: 0.8448 (pttt) cc_final: 0.7514 (mmmt) REVERT: F 111 LEU cc_start: 0.8119 (pt) cc_final: 0.7599 (pt) REVERT: F 150 GLU cc_start: 0.8195 (pt0) cc_final: 0.6607 (mp0) REVERT: G 42 PRO cc_start: 0.6251 (Cg_endo) cc_final: 0.5812 (Cg_exo) REVERT: G 46 TYR cc_start: 0.5602 (t80) cc_final: 0.5372 (t80) REVERT: G 69 LEU cc_start: 0.7731 (mt) cc_final: 0.7216 (mt) REVERT: G 80 VAL cc_start: 0.6422 (t) cc_final: 0.6177 (p) REVERT: G 235 ASN cc_start: 0.7173 (t0) cc_final: 0.6904 (m-40) REVERT: H 125 LEU cc_start: 0.8749 (mt) cc_final: 0.8315 (mt) REVERT: I 39 LYS cc_start: 0.7951 (mppt) cc_final: 0.7589 (mmtt) REVERT: J 16 ASP cc_start: 0.8245 (p0) cc_final: 0.7411 (p0) REVERT: J 21 TYR cc_start: 0.8202 (t80) cc_final: 0.7828 (t80) REVERT: J 25 LEU cc_start: 0.7463 (mt) cc_final: 0.7142 (mt) REVERT: K 50 LEU cc_start: 0.6609 (mt) cc_final: 0.5674 (tt) REVERT: L 40 LEU cc_start: 0.7671 (tp) cc_final: 0.7445 (tp) REVERT: L 68 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7516 (tm-30) REVERT: M 30 PHE cc_start: 0.7987 (t80) cc_final: 0.7253 (t80) REVERT: M 90 LEU cc_start: 0.6900 (mt) cc_final: 0.6665 (mt) REVERT: M 132 PHE cc_start: 0.7477 (m-10) cc_final: 0.6990 (m-80) REVERT: M 153 LYS cc_start: 0.6556 (tttt) cc_final: 0.5758 (tmtt) REVERT: M 236 TYR cc_start: 0.7139 (t80) cc_final: 0.6758 (t80) REVERT: M 256 MET cc_start: 0.7128 (ttm) cc_final: 0.6684 (ttt) REVERT: M 349 LEU cc_start: 0.8859 (tp) cc_final: 0.8562 (mt) outliers start: 1 outliers final: 1 residues processed: 816 average time/residue: 0.2274 time to fit residues: 301.9570 Evaluate side-chains 566 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 565 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: [441, 57, 373, 400, 1, 247, 30, 255, 203, 294, 279] chunk 441 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 373 optimal weight: 0.9990 chunk 400 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 247 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 203 optimal weight: 20.0000 chunk 294 optimal weight: 20.0000 chunk 279 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 260 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 617 HIS ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1062 HIS ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 212 ASN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN B 710 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1157 GLN B1165 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN E 114 ASN E 153 HIS G 8 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 GLN ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.117086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099827 restraints weight = 137258.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.101819 restraints weight = 88228.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.103246 restraints weight = 62877.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.104139 restraints weight = 48812.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104919 restraints weight = 40630.330| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 37976 Z= 0.196 Angle : 0.715 11.271 51588 Z= 0.371 Chirality : 0.046 0.392 5791 Planarity : 0.005 0.075 6422 Dihedral : 14.279 174.252 5662 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.03 % Allowed : 2.88 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.12), residues: 4447 helix: -0.44 (0.12), residues: 1517 sheet: -1.73 (0.19), residues: 663 loop : -2.22 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 24 TYR 0.017 0.002 TYR A1553 PHE 0.030 0.002 PHE B 35 TRP 0.018 0.002 TRP A 530 HIS 0.012 0.002 HIS B1082 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (37954) covalent geometry : angle 0.70878 / 0.37 (51573) hydrogen bonds : bond 0.04737 / 3.21 ( 1459) hydrogen bonds : angle 5.78532 / 4.10 ( 4047) metal coordination : bond 0.00605 / 0.36 ( 20) metal coordination : angle 5.71679 / 3.11 ( 15) Misc. bond : bond 0.00076 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 742 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8534 (mt-10) REVERT: A 519 LEU cc_start: 0.8855 (mt) cc_final: 0.8536 (mt) REVERT: A 521 GLN cc_start: 0.8057 (tp40) cc_final: 0.7719 (tp-100) REVERT: A 590 ASN cc_start: 0.6935 (t0) cc_final: 0.6630 (m-40) REVERT: A 601 MET cc_start: 0.9275 (mmp) cc_final: 0.8802 (mmm) REVERT: A 852 ASP cc_start: 0.8228 (m-30) cc_final: 0.7874 (p0) REVERT: A 900 VAL cc_start: 0.8615 (m) cc_final: 0.8380 (m) REVERT: A 960 MET cc_start: 0.8145 (mtm) cc_final: 0.7429 (mmm) REVERT: A 964 LYS cc_start: 0.8253 (tttt) cc_final: 0.7918 (tttp) REVERT: A 981 TYR cc_start: 0.7950 (t80) cc_final: 0.7339 (t80) REVERT: A 994 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 1000 MET cc_start: 0.9043 (mtt) cc_final: 0.8251 (mmt) REVERT: A 1026 GLN cc_start: 0.8155 (mm110) cc_final: 0.7930 (mm-40) REVERT: A 1049 MET cc_start: 0.8050 (mtp) cc_final: 0.7713 (mtp) REVERT: A 1057 ILE cc_start: 0.9010 (mm) cc_final: 0.8709 (tp) REVERT: A 1120 TYR cc_start: 0.6846 (p90) cc_final: 0.6489 (p90) REVERT: A 1121 ASP cc_start: 0.8421 (p0) cc_final: 0.8095 (p0) REVERT: A 1139 ASN cc_start: 0.8398 (t0) cc_final: 0.7952 (m110) REVERT: A 1175 MET cc_start: 0.8199 (tpp) cc_final: 0.7975 (tpp) REVERT: A 1221 ARG cc_start: 0.8159 (tpt170) cc_final: 0.7667 (tpp80) REVERT: A 1226 VAL cc_start: 0.8487 (t) cc_final: 0.8105 (t) REVERT: A 1479 ASP cc_start: 0.5804 (t70) cc_final: 0.5375 (m-30) REVERT: A 1485 MET cc_start: 0.6217 (mtm) cc_final: 0.5691 (mtm) REVERT: A 1493 CYS cc_start: 0.6776 (m) cc_final: 0.6364 (m) REVERT: A 1588 MET cc_start: 0.6571 (tpp) cc_final: 0.5311 (tpp) REVERT: A 1629 ASN cc_start: 0.8825 (m-40) cc_final: 0.8226 (t0) REVERT: A 1654 PHE cc_start: 0.7890 (p90) cc_final: 0.7057 (p90) REVERT: B 243 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8811 (mm-40) REVERT: B 265 ARG cc_start: 0.7685 (mtp85) cc_final: 0.6937 (mtp85) REVERT: B 275 MET cc_start: 0.7096 (tpp) cc_final: 0.6771 (tpp) REVERT: B 315 LYS cc_start: 0.7879 (ttmm) cc_final: 0.7601 (tptm) REVERT: B 393 ASN cc_start: 0.8523 (t0) cc_final: 0.8002 (t0) REVERT: B 502 MET cc_start: 0.7773 (ttp) cc_final: 0.7304 (ttt) REVERT: B 595 TRP cc_start: 0.8279 (m100) cc_final: 0.7999 (m-10) REVERT: B 764 ASN cc_start: 0.7768 (m-40) cc_final: 0.7540 (t0) REVERT: B 896 GLN cc_start: 0.7641 (pm20) cc_final: 0.7316 (mm-40) REVERT: B 936 MET cc_start: 0.8519 (ttt) cc_final: 0.8262 (ttt) REVERT: B 1015 SER cc_start: 0.9188 (t) cc_final: 0.8727 (p) REVERT: B 1033 TYR cc_start: 0.8410 (m-80) cc_final: 0.7774 (m-80) REVERT: B 1066 HIS cc_start: 0.7898 (m-70) cc_final: 0.7598 (m-70) REVERT: B 1188 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6429 (tp30) REVERT: F 87 LYS cc_start: 0.8321 (pttt) cc_final: 0.7922 (mtmt) REVERT: F 150 GLU cc_start: 0.8156 (pt0) cc_final: 0.6570 (mp0) REVERT: G 42 PRO cc_start: 0.5887 (Cg_endo) cc_final: 0.5529 (Cg_exo) REVERT: G 229 LEU cc_start: 0.5650 (pp) cc_final: 0.5386 (pp) REVERT: H 125 LEU cc_start: 0.8808 (mt) cc_final: 0.8474 (mt) REVERT: J 16 ASP cc_start: 0.8292 (p0) cc_final: 0.7359 (p0) REVERT: K 59 THR cc_start: 0.7056 (p) cc_final: 0.6822 (p) REVERT: K 63 PHE cc_start: 0.6408 (m-10) cc_final: 0.6126 (m-10) REVERT: L 40 LEU cc_start: 0.7719 (tp) cc_final: 0.7420 (tp) REVERT: L 56 LEU cc_start: 0.8586 (mm) cc_final: 0.8185 (mp) REVERT: L 68 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8209 (tm-30) REVERT: M 30 PHE cc_start: 0.7872 (t80) cc_final: 0.7306 (t80) REVERT: M 90 LEU cc_start: 0.6810 (mt) cc_final: 0.6601 (mt) REVERT: M 153 LYS cc_start: 0.6650 (tttt) cc_final: 0.5817 (tmtt) REVERT: M 236 TYR cc_start: 0.7159 (t80) cc_final: 0.6806 (t80) REVERT: M 256 MET cc_start: 0.7069 (ttm) cc_final: 0.6645 (ttt) REVERT: M 349 LEU cc_start: 0.8843 (tp) cc_final: 0.8432 (mp) REVERT: N 150 TYR cc_start: 0.7070 (m-10) cc_final: 0.6755 (m-10) outliers start: 1 outliers final: 0 residues processed: 743 average time/residue: 0.2234 time to fit residues: 271.5872 Evaluate side-chains 542 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: [234, 110, 77, 432, 193, 215, 319, 184, 120, 446, 46] chunk 234 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 432 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 319 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 446 optimal weight: 40.0000 chunk 46 optimal weight: 9.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 224 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 246 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN B 710 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS B 975 HIS ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN G 8 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.114892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097268 restraints weight = 140418.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.099325 restraints weight = 89055.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.100731 restraints weight = 62673.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.101822 restraints weight = 48242.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 75)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.102519 restraints weight = 39697.647| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 37976 Z= 0.229 Angle : 0.751 11.197 51588 Z= 0.388 Chirality : 0.047 0.393 5791 Planarity : 0.005 0.058 6422 Dihedral : 14.235 172.618 5662 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.12), residues: 4447 helix: -0.43 (0.12), residues: 1537 sheet: -1.71 (0.19), residues: 659 loop : -2.21 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 90 TYR 0.034 0.002 TYR A1595 PHE 0.030 0.002 PHE A 223 TRP 0.028 0.002 TRP A 530 HIS 0.012 0.002 HIS B1082 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (37954) covalent geometry : angle 0.74438 / 0.39 (51573) hydrogen bonds : bond 0.04790 / 3.26 ( 1459) hydrogen bonds : angle 5.77396 / 4.08 ( 4047) metal coordination : bond 0.01394 / 0.71 ( 20) metal coordination : angle 5.76612 / 2.95 ( 15) Misc. bond : bond 0.00051 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 696 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8551 (mt-10) REVERT: A 369 LEU cc_start: 0.8143 (mt) cc_final: 0.7941 (mt) REVERT: A 519 LEU cc_start: 0.8891 (mt) cc_final: 0.8608 (mt) REVERT: A 590 ASN cc_start: 0.7490 (t0) cc_final: 0.7065 (t0) REVERT: A 601 MET cc_start: 0.9210 (mmp) cc_final: 0.8781 (mmm) REVERT: A 670 ILE cc_start: 0.9278 (tp) cc_final: 0.8964 (tp) REVERT: A 852 ASP cc_start: 0.8288 (m-30) cc_final: 0.7855 (p0) REVERT: A 960 MET cc_start: 0.8196 (mtm) cc_final: 0.7543 (mmm) REVERT: A 981 TYR cc_start: 0.8147 (t80) cc_final: 0.7563 (t80) REVERT: A 994 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 1000 MET cc_start: 0.9032 (mtt) cc_final: 0.8177 (mmt) REVERT: A 1012 LYS cc_start: 0.8534 (ptpt) cc_final: 0.8308 (pttt) REVERT: A 1055 ILE cc_start: 0.7770 (mm) cc_final: 0.7170 (mt) REVERT: A 1057 ILE cc_start: 0.9153 (mm) cc_final: 0.8826 (tp) REVERT: A 1121 ASP cc_start: 0.8557 (p0) cc_final: 0.8307 (p0) REVERT: A 1139 ASN cc_start: 0.8445 (t0) cc_final: 0.7911 (m110) REVERT: A 1175 MET cc_start: 0.8282 (tpp) cc_final: 0.7883 (tpp) REVERT: A 1176 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.5929 (tpp80) REVERT: A 1200 MET cc_start: 0.8644 (mtt) cc_final: 0.8251 (mtp) REVERT: A 1485 MET cc_start: 0.5928 (mtm) cc_final: 0.5393 (mtm) REVERT: A 1493 CYS cc_start: 0.6927 (m) cc_final: 0.6528 (m) REVERT: A 1588 MET cc_start: 0.6678 (tpp) cc_final: 0.5590 (tpp) REVERT: A 1613 MET cc_start: 0.8336 (mtp) cc_final: 0.8043 (mtp) REVERT: A 1615 TYR cc_start: 0.7241 (t80) cc_final: 0.6852 (t80) REVERT: A 1629 ASN cc_start: 0.8866 (m-40) cc_final: 0.8206 (t0) REVERT: A 1654 PHE cc_start: 0.7690 (p90) cc_final: 0.6827 (p90) REVERT: B 108 MET cc_start: 0.6723 (mtp) cc_final: 0.6490 (mtt) REVERT: B 243 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8928 (mm-40) REVERT: B 265 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7004 (mtm110) REVERT: B 275 MET cc_start: 0.7143 (tpp) cc_final: 0.6871 (tpp) REVERT: B 393 ASN cc_start: 0.8547 (t0) cc_final: 0.8009 (t0) REVERT: B 502 MET cc_start: 0.7823 (ttp) cc_final: 0.7349 (ttp) REVERT: B 528 LEU cc_start: 0.8549 (mt) cc_final: 0.8309 (mt) REVERT: B 683 ASN cc_start: 0.7612 (m110) cc_final: 0.7183 (m-40) REVERT: B 759 ASP cc_start: 0.8920 (m-30) cc_final: 0.8658 (m-30) REVERT: B 764 ASN cc_start: 0.8075 (m-40) cc_final: 0.7437 (t0) REVERT: B 874 TYR cc_start: 0.6258 (t80) cc_final: 0.5405 (t80) REVERT: B 936 MET cc_start: 0.8641 (ttt) cc_final: 0.8434 (ttm) REVERT: B 1033 TYR cc_start: 0.8277 (m-80) cc_final: 0.7681 (m-80) REVERT: B 1066 HIS cc_start: 0.8188 (m-70) cc_final: 0.7854 (m-70) REVERT: B 1075 GLU cc_start: 0.6861 (mp0) cc_final: 0.6579 (mp0) REVERT: B 1188 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6579 (tp30) REVERT: D 29 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6961 (pt0) REVERT: E 58 MET cc_start: 0.6247 (mpp) cc_final: 0.5495 (mpp) REVERT: F 87 LYS cc_start: 0.8521 (pttt) cc_final: 0.7972 (mtmt) REVERT: F 103 MET cc_start: 0.7460 (mtp) cc_final: 0.7229 (mtp) REVERT: F 150 GLU cc_start: 0.8070 (pt0) cc_final: 0.7049 (mp0) REVERT: G 42 PRO cc_start: 0.6074 (Cg_endo) cc_final: 0.5653 (Cg_exo) REVERT: G 229 LEU cc_start: 0.5609 (pp) cc_final: 0.5311 (pp) REVERT: H 11 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7964 (tp40) REVERT: H 79 TRP cc_start: 0.7314 (t60) cc_final: 0.6662 (t60) REVERT: J 16 ASP cc_start: 0.8225 (p0) cc_final: 0.7253 (p0) REVERT: K 50 LEU cc_start: 0.6837 (mt) cc_final: 0.5664 (tt) REVERT: K 63 PHE cc_start: 0.6711 (m-10) cc_final: 0.6491 (m-10) REVERT: L 40 LEU cc_start: 0.7681 (tp) cc_final: 0.7433 (tp) REVERT: L 56 LEU cc_start: 0.8649 (mm) cc_final: 0.8246 (mp) REVERT: L 68 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8347 (tm-30) REVERT: M 30 PHE cc_start: 0.8039 (t80) cc_final: 0.7577 (t80) REVERT: M 90 LEU cc_start: 0.6868 (mt) cc_final: 0.6647 (mt) REVERT: M 153 LYS cc_start: 0.6648 (tttt) cc_final: 0.5869 (tmtt) REVERT: M 236 TYR cc_start: 0.7218 (t80) cc_final: 0.6797 (t80) REVERT: M 256 MET cc_start: 0.7030 (ttm) cc_final: 0.6714 (ttp) outliers start: 4 outliers final: 0 residues processed: 699 average time/residue: 0.2244 time to fit residues: 257.6494 Evaluate side-chains 503 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 502 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: [156, 366, 25, 131, 265, 392, 436, 134, 348, 192, 103] chunk 156 optimal weight: 6.9990 chunk 366 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 392 optimal weight: 30.0000 chunk 436 optimal weight: 30.0000 chunk 134 optimal weight: 3.9990 chunk 348 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 HIS ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 212 ASN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN C 99 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN E 153 HIS F 60 GLN G 8 ASN G 65 HIS ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.116722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.099797 restraints weight = 138308.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102056 restraints weight = 91573.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.103776 restraints weight = 62386.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104320 restraints weight = 47880.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.104494 restraints weight = 38198.954| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37976 Z= 0.152 Angle : 0.677 10.725 51588 Z= 0.348 Chirality : 0.045 0.390 5791 Planarity : 0.005 0.058 6422 Dihedral : 14.092 169.810 5662 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.12), residues: 4447 helix: -0.12 (0.13), residues: 1528 sheet: -1.56 (0.19), residues: 654 loop : -2.06 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 201 TYR 0.027 0.002 TYR A1595 PHE 0.025 0.002 PHE B 963 TRP 0.027 0.001 TRP A 530 HIS 0.009 0.001 HIS B1082 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (37954) covalent geometry : angle 0.67290 / 0.35 (51573) hydrogen bonds : bond 0.04295 / 2.92 ( 1459) hydrogen bonds : angle 5.45414 / 3.87 ( 4047) metal coordination : bond 0.00616 / 0.34 ( 20) metal coordination : angle 4.42006 / 2.43 ( 15) Misc. bond : bond 0.00062 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 708 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8524 (mt-10) REVERT: A 226 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8118 (mmmm) REVERT: A 369 LEU cc_start: 0.8128 (mt) cc_final: 0.7924 (mt) REVERT: A 519 LEU cc_start: 0.8827 (mt) cc_final: 0.8519 (mt) REVERT: A 590 ASN cc_start: 0.7303 (t0) cc_final: 0.6820 (t0) REVERT: A 601 MET cc_start: 0.9141 (mmp) cc_final: 0.8769 (mmm) REVERT: A 852 ASP cc_start: 0.8319 (m-30) cc_final: 0.7589 (p0) REVERT: A 900 VAL cc_start: 0.8585 (m) cc_final: 0.8353 (m) REVERT: A 928 MET cc_start: 0.8915 (ttt) cc_final: 0.8427 (tpp) REVERT: A 981 TYR cc_start: 0.7984 (t80) cc_final: 0.7585 (t80) REVERT: A 1000 MET cc_start: 0.8954 (mtt) cc_final: 0.8120 (mmt) REVERT: A 1012 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8158 (mtmt) REVERT: A 1057 ILE cc_start: 0.8949 (mm) cc_final: 0.8668 (tp) REVERT: A 1120 TYR cc_start: 0.7210 (p90) cc_final: 0.6901 (p90) REVERT: A 1121 ASP cc_start: 0.8542 (p0) cc_final: 0.8217 (p0) REVERT: A 1132 TYR cc_start: 0.6870 (m-80) cc_final: 0.6584 (m-80) REVERT: A 1139 ASN cc_start: 0.8369 (t0) cc_final: 0.7951 (m110) REVERT: A 1175 MET cc_start: 0.8415 (tpp) cc_final: 0.7978 (tpp) REVERT: A 1176 ARG cc_start: 0.7434 (mmm-85) cc_final: 0.5608 (tpp80) REVERT: A 1485 MET cc_start: 0.5896 (mtm) cc_final: 0.5374 (mtm) REVERT: A 1493 CYS cc_start: 0.6853 (m) cc_final: 0.6466 (m) REVERT: A 1588 MET cc_start: 0.6414 (tpp) cc_final: 0.5354 (tpp) REVERT: A 1629 ASN cc_start: 0.8674 (m-40) cc_final: 0.8212 (t0) REVERT: A 1654 PHE cc_start: 0.7785 (p90) cc_final: 0.6755 (p90) REVERT: B 265 ARG cc_start: 0.7755 (mtp85) cc_final: 0.6962 (mtm110) REVERT: B 393 ASN cc_start: 0.8450 (t0) cc_final: 0.7995 (t0) REVERT: B 430 MET cc_start: 0.8234 (tmm) cc_final: 0.7990 (tmm) REVERT: B 502 MET cc_start: 0.7731 (ttp) cc_final: 0.7363 (ttp) REVERT: B 523 GLU cc_start: 0.8561 (mp0) cc_final: 0.7951 (mp0) REVERT: B 726 MET cc_start: 0.8069 (tmm) cc_final: 0.7453 (tmm) REVERT: B 764 ASN cc_start: 0.7864 (m-40) cc_final: 0.7125 (t0) REVERT: B 962 MET cc_start: 0.6897 (ppp) cc_final: 0.6387 (tmm) REVERT: B 1027 TYR cc_start: 0.7752 (t80) cc_final: 0.7406 (t80) REVERT: B 1033 TYR cc_start: 0.8329 (m-80) cc_final: 0.7688 (m-80) REVERT: B 1066 HIS cc_start: 0.8222 (m-70) cc_final: 0.7785 (m-70) REVERT: B 1075 GLU cc_start: 0.6907 (mp0) cc_final: 0.6693 (mp0) REVERT: D 29 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6992 (pt0) REVERT: F 87 LYS cc_start: 0.8436 (pttt) cc_final: 0.8002 (mtmt) REVERT: F 150 GLU cc_start: 0.7863 (pt0) cc_final: 0.6920 (mp0) REVERT: G 42 PRO cc_start: 0.6086 (Cg_endo) cc_final: 0.5693 (Cg_exo) REVERT: G 229 LEU cc_start: 0.5644 (pp) cc_final: 0.5367 (pp) REVERT: H 79 TRP cc_start: 0.7328 (t60) cc_final: 0.6648 (t60) REVERT: J 16 ASP cc_start: 0.8126 (p0) cc_final: 0.6890 (p0) REVERT: K 50 LEU cc_start: 0.6841 (mt) cc_final: 0.5825 (tt) REVERT: K 63 PHE cc_start: 0.6844 (m-10) cc_final: 0.6529 (m-10) REVERT: K 69 ASP cc_start: 0.8725 (p0) cc_final: 0.8467 (p0) REVERT: L 56 LEU cc_start: 0.8548 (mm) cc_final: 0.8129 (mp) REVERT: L 68 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8293 (tm-30) REVERT: M 30 PHE cc_start: 0.8033 (t80) cc_final: 0.7339 (t80) REVERT: M 90 LEU cc_start: 0.7005 (mt) cc_final: 0.6753 (mp) REVERT: M 153 LYS cc_start: 0.6551 (tttt) cc_final: 0.5892 (tmtt) REVERT: M 236 TYR cc_start: 0.7268 (t80) cc_final: 0.6751 (t80) REVERT: M 256 MET cc_start: 0.7026 (ttm) cc_final: 0.6685 (ttp) outliers start: 2 outliers final: 2 residues processed: 710 average time/residue: 0.2155 time to fit residues: 253.0395 Evaluate side-chains 516 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 514 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: [19, 338, 137, 183, 357, 228, 15, 173, 386, 163, 154] chunk 19 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 357 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 386 optimal weight: 30.0000 chunk 163 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN F 60 GLN G 8 ASN H 11 GLN J 53 HIS M 16 GLN ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.115280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097644 restraints weight = 140508.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099763 restraints weight = 88667.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.101256 restraints weight = 61968.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.102261 restraints weight = 47858.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.102939 restraints weight = 39481.117| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37976 Z= 0.194 Angle : 0.711 14.232 51588 Z= 0.365 Chirality : 0.046 0.392 5791 Planarity : 0.005 0.053 6422 Dihedral : 14.073 169.136 5662 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.03 % Allowed : 1.78 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.12), residues: 4447 helix: -0.10 (0.13), residues: 1529 sheet: -1.55 (0.19), residues: 664 loop : -2.06 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 634 TYR 0.023 0.002 TYR A1104 PHE 0.031 0.002 PHE B 938 TRP 0.067 0.002 TRP A 530 HIS 0.008 0.001 HIS B1082 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (37954) covalent geometry : angle 0.70691 / 0.36 (51573) hydrogen bonds : bond 0.04400 / 2.98 ( 1459) hydrogen bonds : angle 5.50123 / 3.90 ( 4047) metal coordination : bond 0.00582 / 0.34 ( 20) metal coordination : angle 4.46391 / 2.31 ( 15) Misc. bond : bond 0.00071 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 671 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8566 (mt-10) REVERT: A 222 GLU cc_start: 0.7769 (tp30) cc_final: 0.7563 (tp30) REVERT: A 226 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8154 (mmmm) REVERT: A 519 LEU cc_start: 0.9000 (mt) cc_final: 0.8710 (mt) REVERT: A 590 ASN cc_start: 0.7395 (t0) cc_final: 0.6943 (t0) REVERT: A 601 MET cc_start: 0.9217 (mmp) cc_final: 0.8764 (mmm) REVERT: A 831 ASP cc_start: 0.7710 (p0) cc_final: 0.6908 (p0) REVERT: A 917 MET cc_start: 0.8626 (tmm) cc_final: 0.8392 (tmm) REVERT: A 960 MET cc_start: 0.8261 (mtm) cc_final: 0.7681 (mmm) REVERT: A 981 TYR cc_start: 0.8131 (t80) cc_final: 0.7790 (t80) REVERT: A 1000 MET cc_start: 0.8932 (mtt) cc_final: 0.8646 (tpp) REVERT: A 1057 ILE cc_start: 0.9013 (mm) cc_final: 0.8754 (tp) REVERT: A 1063 MET cc_start: 0.3554 (mpp) cc_final: 0.2777 (mmt) REVERT: A 1121 ASP cc_start: 0.8628 (p0) cc_final: 0.8349 (p0) REVERT: A 1139 ASN cc_start: 0.8416 (t0) cc_final: 0.7860 (m110) REVERT: A 1175 MET cc_start: 0.8449 (tpp) cc_final: 0.8160 (tpp) REVERT: A 1176 ARG cc_start: 0.7500 (mmm-85) cc_final: 0.5633 (tpp80) REVERT: A 1485 MET cc_start: 0.5741 (mtm) cc_final: 0.5328 (mtm) REVERT: A 1493 CYS cc_start: 0.6911 (m) cc_final: 0.6559 (m) REVERT: A 1588 MET cc_start: 0.6594 (tpp) cc_final: 0.5582 (tpp) REVERT: A 1613 MET cc_start: 0.8320 (mtp) cc_final: 0.8072 (mtp) REVERT: A 1615 TYR cc_start: 0.7226 (t80) cc_final: 0.6846 (t80) REVERT: A 1629 ASN cc_start: 0.8734 (m-40) cc_final: 0.8271 (t0) REVERT: A 1654 PHE cc_start: 0.7620 (p90) cc_final: 0.6788 (p90) REVERT: B 265 ARG cc_start: 0.7744 (mtp85) cc_final: 0.6969 (mtm110) REVERT: B 275 MET cc_start: 0.7080 (tpp) cc_final: 0.6807 (tpp) REVERT: B 393 ASN cc_start: 0.8423 (t0) cc_final: 0.7891 (t0) REVERT: B 502 MET cc_start: 0.7759 (ttp) cc_final: 0.7319 (ttp) REVERT: B 528 LEU cc_start: 0.8510 (mt) cc_final: 0.8295 (mt) REVERT: B 742 TYR cc_start: 0.7157 (m-80) cc_final: 0.6951 (m-80) REVERT: B 764 ASN cc_start: 0.7897 (m-40) cc_final: 0.7160 (t0) REVERT: B 936 MET cc_start: 0.8578 (ttt) cc_final: 0.8275 (ttt) REVERT: B 1027 TYR cc_start: 0.7948 (t80) cc_final: 0.7282 (t80) REVERT: B 1033 TYR cc_start: 0.8262 (m-80) cc_final: 0.7545 (m-80) REVERT: B 1097 ASP cc_start: 0.6843 (m-30) cc_final: 0.6601 (m-30) REVERT: D 29 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6954 (pt0) REVERT: F 87 LYS cc_start: 0.8524 (pttt) cc_final: 0.8028 (mtmt) REVERT: F 150 GLU cc_start: 0.7915 (pt0) cc_final: 0.7045 (mp0) REVERT: G 42 PRO cc_start: 0.6322 (Cg_endo) cc_final: 0.5887 (Cg_exo) REVERT: G 229 LEU cc_start: 0.5390 (pp) cc_final: 0.5144 (pp) REVERT: H 79 TRP cc_start: 0.7373 (t60) cc_final: 0.6383 (t60) REVERT: J 13 VAL cc_start: 0.8891 (p) cc_final: 0.8610 (p) REVERT: J 16 ASP cc_start: 0.8315 (p0) cc_final: 0.7166 (p0) REVERT: K 50 LEU cc_start: 0.7111 (mt) cc_final: 0.6137 (tt) REVERT: K 63 PHE cc_start: 0.6888 (m-10) cc_final: 0.6643 (m-10) REVERT: K 69 ASP cc_start: 0.8934 (p0) cc_final: 0.8604 (p0) REVERT: L 56 LEU cc_start: 0.8632 (mm) cc_final: 0.8228 (mp) REVERT: L 68 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8295 (tm-30) REVERT: M 30 PHE cc_start: 0.7976 (t80) cc_final: 0.7436 (t80) REVERT: M 90 LEU cc_start: 0.6878 (mt) cc_final: 0.6634 (mp) REVERT: M 153 LYS cc_start: 0.6707 (tttt) cc_final: 0.6036 (tmtt) REVERT: M 217 ARG cc_start: 0.5856 (mtm180) cc_final: 0.5537 (mtm-85) REVERT: M 236 TYR cc_start: 0.7183 (t80) cc_final: 0.6614 (t80) REVERT: M 256 MET cc_start: 0.7092 (ttm) cc_final: 0.6693 (ttp) outliers start: 1 outliers final: 0 residues processed: 672 average time/residue: 0.2193 time to fit residues: 243.0083 Evaluate side-chains 495 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: [366, 323, 230, 429, 274, 256, 437, 364, 344, 298, 103] chunk 366 optimal weight: 5.9990 chunk 323 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 429 optimal weight: 0.9990 chunk 274 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 437 optimal weight: 4.9990 chunk 364 optimal weight: 7.9990 chunk 344 optimal weight: 30.0000 chunk 298 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 ASN ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 GLN C 65 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 20 HIS G 36 ASN H 11 GLN H 52 GLN M 16 GLN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.113855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096528 restraints weight = 142088.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.098538 restraints weight = 89876.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099887 restraints weight = 63527.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.100902 restraints weight = 49101.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.101511 restraints weight = 40815.198| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 37976 Z= 0.212 Angle : 0.738 14.502 51588 Z= 0.379 Chirality : 0.047 0.390 5791 Planarity : 0.005 0.085 6422 Dihedral : 14.087 168.580 5662 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.10 % Allowed : 1.48 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.12), residues: 4447 helix: -0.12 (0.13), residues: 1516 sheet: -1.54 (0.20), residues: 646 loop : -2.06 (0.13), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 68 TYR 0.033 0.002 TYR A1595 PHE 0.044 0.002 PHE A 986 TRP 0.068 0.002 TRP A 530 HIS 0.008 0.001 HIS B1082 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (37954) covalent geometry : angle 0.73348 / 0.38 (51573) hydrogen bonds : bond 0.04560 / 3.09 ( 1459) hydrogen bonds : angle 5.53102 / 3.92 ( 4047) metal coordination : bond 0.00739 / 0.43 ( 20) metal coordination : angle 4.93498 / 2.51 ( 15) Misc. bond : bond 0.00069 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 648 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8630 (mt-10) REVERT: A 423 LEU cc_start: 0.8295 (tp) cc_final: 0.8073 (mp) REVERT: A 519 LEU cc_start: 0.9030 (mt) cc_final: 0.8764 (mt) REVERT: A 601 MET cc_start: 0.9200 (mmp) cc_final: 0.8725 (mmm) REVERT: A 816 LEU cc_start: 0.9027 (tp) cc_final: 0.8803 (tp) REVERT: A 928 MET cc_start: 0.8990 (ttt) cc_final: 0.8537 (tpp) REVERT: A 960 MET cc_start: 0.8257 (mtm) cc_final: 0.6898 (mmp) REVERT: A 981 TYR cc_start: 0.8253 (t80) cc_final: 0.8032 (t80) REVERT: A 1000 MET cc_start: 0.8973 (mtt) cc_final: 0.8714 (tpp) REVERT: A 1049 MET cc_start: 0.8617 (ppp) cc_final: 0.8327 (ppp) REVERT: A 1057 ILE cc_start: 0.8966 (mm) cc_final: 0.8709 (tp) REVERT: A 1063 MET cc_start: 0.3689 (mpp) cc_final: 0.3000 (mmt) REVERT: A 1104 TYR cc_start: 0.7802 (t80) cc_final: 0.7333 (t80) REVERT: A 1121 ASP cc_start: 0.8668 (p0) cc_final: 0.8393 (p0) REVERT: A 1132 TYR cc_start: 0.7141 (m-80) cc_final: 0.6743 (m-80) REVERT: A 1139 ASN cc_start: 0.8542 (t0) cc_final: 0.7855 (m110) REVERT: A 1175 MET cc_start: 0.8503 (tpp) cc_final: 0.8112 (tpp) REVERT: A 1176 ARG cc_start: 0.7557 (mmm-85) cc_final: 0.5644 (tpp80) REVERT: A 1485 MET cc_start: 0.5941 (mtm) cc_final: 0.5465 (mtm) REVERT: A 1588 MET cc_start: 0.6324 (tpp) cc_final: 0.5219 (tpp) REVERT: A 1629 ASN cc_start: 0.8793 (m-40) cc_final: 0.8285 (t0) REVERT: A 1654 PHE cc_start: 0.7667 (p90) cc_final: 0.6853 (p90) REVERT: B 265 ARG cc_start: 0.7768 (mtp85) cc_final: 0.6944 (mtm110) REVERT: B 275 MET cc_start: 0.7148 (tpp) cc_final: 0.6870 (tpp) REVERT: B 393 ASN cc_start: 0.8413 (t0) cc_final: 0.7889 (t0) REVERT: B 502 MET cc_start: 0.7705 (ttp) cc_final: 0.7299 (ttp) REVERT: B 649 MET cc_start: 0.8562 (mtm) cc_final: 0.8322 (mpp) REVERT: B 726 MET cc_start: 0.8091 (tmm) cc_final: 0.7675 (tmm) REVERT: B 764 ASN cc_start: 0.7959 (m-40) cc_final: 0.7359 (t0) REVERT: B 787 MET cc_start: 0.7183 (ttp) cc_final: 0.6847 (ttt) REVERT: B 936 MET cc_start: 0.8730 (ttt) cc_final: 0.8468 (ttt) REVERT: B 1033 TYR cc_start: 0.8295 (m-80) cc_final: 0.7577 (m-80) REVERT: B 1061 LYS cc_start: 0.7992 (tttt) cc_final: 0.7686 (ttmt) REVERT: B 1097 ASP cc_start: 0.6756 (m-30) cc_final: 0.6523 (m-30) REVERT: D 29 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6891 (pt0) REVERT: E 93 MET cc_start: 0.8807 (tpp) cc_final: 0.8551 (tpp) REVERT: F 87 LYS cc_start: 0.8531 (pttt) cc_final: 0.8093 (mtmt) REVERT: F 122 MET cc_start: 0.7872 (mmp) cc_final: 0.7627 (mmm) REVERT: F 150 GLU cc_start: 0.8000 (pt0) cc_final: 0.7096 (mp0) REVERT: G 42 PRO cc_start: 0.6349 (Cg_endo) cc_final: 0.5934 (Cg_exo) REVERT: H 79 TRP cc_start: 0.7497 (t60) cc_final: 0.6123 (t60) REVERT: K 69 ASP cc_start: 0.8744 (p0) cc_final: 0.8390 (p0) REVERT: K 142 MET cc_start: 0.8229 (tmm) cc_final: 0.7937 (tmm) REVERT: L 30 ILE cc_start: 0.9560 (tt) cc_final: 0.9359 (tp) REVERT: L 56 LEU cc_start: 0.8696 (mm) cc_final: 0.8296 (mp) REVERT: L 68 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8318 (tm-30) REVERT: M 90 LEU cc_start: 0.6893 (mt) cc_final: 0.6675 (mp) REVERT: M 153 LYS cc_start: 0.6688 (tttt) cc_final: 0.5997 (tmtt) REVERT: M 236 TYR cc_start: 0.7212 (t80) cc_final: 0.6518 (t80) REVERT: M 256 MET cc_start: 0.7019 (ttm) cc_final: 0.6682 (ttp) REVERT: M 397 MET cc_start: 0.0008 (ppp) cc_final: -0.0226 (ppp) outliers start: 4 outliers final: 1 residues processed: 651 average time/residue: 0.2236 time to fit residues: 240.7936 Evaluate side-chains 488 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 487 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: [298, 103, 404, 315, 239, 331, 280, 77, 291, 314, 380] chunk 298 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 404 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 280 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 291 optimal weight: 6.9990 chunk 314 optimal weight: 0.9980 chunk 380 optimal weight: 0.0870 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 840 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1250 GLN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN C 65 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN G 8 ASN H 52 GLN M 16 GLN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.116751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.100071 restraints weight = 137644.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.102287 restraints weight = 92082.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.103706 restraints weight = 63180.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104286 restraints weight = 49813.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104713 restraints weight = 39935.939| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 37976 Z= 0.132 Angle : 0.677 11.843 51588 Z= 0.347 Chirality : 0.046 0.388 5791 Planarity : 0.004 0.053 6422 Dihedral : 13.947 167.701 5662 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.08 % Allowed : 0.75 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.12), residues: 4447 helix: 0.07 (0.13), residues: 1529 sheet: -1.33 (0.20), residues: 639 loop : -1.89 (0.13), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 201 TYR 0.021 0.001 TYR A1595 PHE 0.055 0.002 PHE A 986 TRP 0.059 0.002 TRP A 530 HIS 0.006 0.001 HIS M 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (37954) covalent geometry : angle 0.67354 / 0.35 (51573) hydrogen bonds : bond 0.04066 / 2.73 ( 1459) hydrogen bonds : angle 5.27193 / 3.73 ( 4047) metal coordination : bond 0.00423 / 0.26 ( 20) metal coordination : angle 3.94554 / 2.22 ( 15) Misc. bond : bond 0.00057 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 687 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.9007 (mt) cc_final: 0.8715 (tt) REVERT: A 114 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8598 (mt-10) REVERT: A 226 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8095 (mmmm) REVERT: A 519 LEU cc_start: 0.8996 (mt) cc_final: 0.8707 (mt) REVERT: A 601 MET cc_start: 0.9154 (mmp) cc_final: 0.8698 (mmm) REVERT: A 928 MET cc_start: 0.9005 (ttt) cc_final: 0.8634 (tpp) REVERT: A 960 MET cc_start: 0.8265 (mtm) cc_final: 0.7006 (mmp) REVERT: A 1049 MET cc_start: 0.8548 (ppp) cc_final: 0.8257 (ppp) REVERT: A 1057 ILE cc_start: 0.8932 (mm) cc_final: 0.8652 (tp) REVERT: A 1063 MET cc_start: 0.3657 (mpp) cc_final: 0.2835 (mmt) REVERT: A 1104 TYR cc_start: 0.7948 (t80) cc_final: 0.7354 (t80) REVERT: A 1121 ASP cc_start: 0.8582 (p0) cc_final: 0.8303 (p0) REVERT: A 1139 ASN cc_start: 0.8441 (t0) cc_final: 0.7833 (m110) REVERT: A 1167 ARG cc_start: 0.8757 (ptt-90) cc_final: 0.8442 (ptt-90) REVERT: A 1175 MET cc_start: 0.8536 (tpp) cc_final: 0.8191 (tpp) REVERT: A 1176 ARG cc_start: 0.7489 (mmm-85) cc_final: 0.5674 (tpp80) REVERT: A 1238 MET cc_start: 0.8669 (tpt) cc_final: 0.8409 (tpp) REVERT: A 1485 MET cc_start: 0.5702 (mtm) cc_final: 0.5327 (mtm) REVERT: A 1493 CYS cc_start: 0.6750 (m) cc_final: 0.6469 (m) REVERT: A 1588 MET cc_start: 0.6169 (tpp) cc_final: 0.5121 (tpp) REVERT: A 1629 ASN cc_start: 0.8669 (m-40) cc_final: 0.8256 (t0) REVERT: A 1654 PHE cc_start: 0.7559 (p90) cc_final: 0.6828 (p90) REVERT: B 265 ARG cc_start: 0.7752 (mtp85) cc_final: 0.6927 (mtm110) REVERT: B 275 MET cc_start: 0.7160 (tpp) cc_final: 0.6827 (tpp) REVERT: B 393 ASN cc_start: 0.8307 (t0) cc_final: 0.7821 (t0) REVERT: B 502 MET cc_start: 0.7617 (ttp) cc_final: 0.7195 (ttp) REVERT: B 649 MET cc_start: 0.8547 (mtm) cc_final: 0.8333 (mpp) REVERT: B 726 MET cc_start: 0.8124 (tmm) cc_final: 0.7616 (tmm) REVERT: B 764 ASN cc_start: 0.7762 (m-40) cc_final: 0.7219 (t0) REVERT: B 936 MET cc_start: 0.8484 (ttt) cc_final: 0.8140 (ttm) REVERT: B 1013 MET cc_start: 0.7418 (tpp) cc_final: 0.7118 (tpp) REVERT: B 1033 TYR cc_start: 0.8250 (m-80) cc_final: 0.7640 (m-80) REVERT: B 1097 ASP cc_start: 0.6948 (m-30) cc_final: 0.6745 (m-30) REVERT: F 87 LYS cc_start: 0.8524 (pttt) cc_final: 0.8201 (mtmt) REVERT: F 103 MET cc_start: 0.7540 (mtp) cc_final: 0.7101 (ttp) REVERT: F 150 GLU cc_start: 0.7925 (pt0) cc_final: 0.7183 (mp0) REVERT: G 42 PRO cc_start: 0.6121 (Cg_endo) cc_final: 0.5754 (Cg_exo) REVERT: G 229 LEU cc_start: 0.5626 (pp) cc_final: 0.5361 (pp) REVERT: H 79 TRP cc_start: 0.7405 (t60) cc_final: 0.5996 (t60) REVERT: J 13 VAL cc_start: 0.8905 (p) cc_final: 0.8645 (p) REVERT: J 16 ASP cc_start: 0.8290 (p0) cc_final: 0.7101 (p0) REVERT: K 69 ASP cc_start: 0.8712 (p0) cc_final: 0.8404 (p0) REVERT: L 56 LEU cc_start: 0.8612 (mm) cc_final: 0.7742 (tp) REVERT: L 68 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8353 (tm-30) REVERT: M 90 LEU cc_start: 0.6981 (mt) cc_final: 0.6744 (mp) REVERT: M 153 LYS cc_start: 0.6551 (tttt) cc_final: 0.5974 (tmtt) REVERT: M 217 ARG cc_start: 0.5845 (mtm180) cc_final: 0.5491 (mtm-85) REVERT: M 236 TYR cc_start: 0.7116 (t80) cc_final: 0.6456 (t80) REVERT: M 256 MET cc_start: 0.6994 (ttm) cc_final: 0.6655 (ttp) REVERT: M 294 LEU cc_start: 0.7609 (mt) cc_final: 0.7221 (tp) outliers start: 3 outliers final: 2 residues processed: 690 average time/residue: 0.2178 time to fit residues: 247.9396 Evaluate side-chains 507 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 505 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: [400, 397, 19, 386, 192, 173, 112, 382, 66, 38, 323] chunk 400 optimal weight: 9.9990 chunk 397 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 386 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 112 optimal weight: 0.4980 chunk 382 optimal weight: 6.9990 chunk 66 optimal weight: 0.0170 chunk 38 optimal weight: 0.2980 chunk 323 optimal weight: 3.9990 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN M 16 GLN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.116557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099738 restraints weight = 137710.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.101713 restraints weight = 88387.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.103098 restraints weight = 62664.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.103965 restraints weight = 48357.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104684 restraints weight = 40204.598| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37976 Z= 0.141 Angle : 0.682 12.660 51588 Z= 0.348 Chirality : 0.045 0.393 5791 Planarity : 0.005 0.053 6422 Dihedral : 13.905 168.324 5662 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.12), residues: 4447 helix: 0.12 (0.13), residues: 1517 sheet: -1.27 (0.20), residues: 633 loop : -1.88 (0.13), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1105 TYR 0.031 0.001 TYR A1595 PHE 0.043 0.002 PHE B 895 TRP 0.028 0.002 TRP A 530 HIS 0.020 0.001 HIS B 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (37954) covalent geometry : angle 0.67935 / 0.35 (51573) hydrogen bonds : bond 0.04085 / 2.73 ( 1459) hydrogen bonds : angle 5.26452 / 3.71 ( 4047) metal coordination : bond 0.00443 / 0.26 ( 20) metal coordination : angle 3.67563 / 1.95 ( 15) Misc. bond : bond 0.00030 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 660 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7135 (mm-30) REVERT: A 96 ILE cc_start: 0.9120 (mt) cc_final: 0.8843 (tt) REVERT: A 114 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8641 (mt-10) REVERT: A 222 GLU cc_start: 0.8071 (tp30) cc_final: 0.7701 (tp30) REVERT: A 226 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8134 (mmmm) REVERT: A 519 LEU cc_start: 0.8977 (mt) cc_final: 0.8698 (mt) REVERT: A 601 MET cc_start: 0.9223 (mmp) cc_final: 0.8717 (mmm) REVERT: A 928 MET cc_start: 0.9040 (ttt) cc_final: 0.8468 (tpp) REVERT: A 960 MET cc_start: 0.8178 (mtm) cc_final: 0.6964 (mmp) REVERT: A 964 LYS cc_start: 0.7604 (tttp) cc_final: 0.7364 (tttp) REVERT: A 1049 MET cc_start: 0.8582 (ppp) cc_final: 0.8256 (ppp) REVERT: A 1063 MET cc_start: 0.3695 (mpp) cc_final: 0.2974 (mmt) REVERT: A 1104 TYR cc_start: 0.7977 (t80) cc_final: 0.7249 (t80) REVERT: A 1121 ASP cc_start: 0.8577 (p0) cc_final: 0.8289 (p0) REVERT: A 1139 ASN cc_start: 0.8447 (t0) cc_final: 0.7803 (m110) REVERT: A 1150 LYS cc_start: 0.7507 (mttt) cc_final: 0.7203 (mmtp) REVERT: A 1175 MET cc_start: 0.8601 (tpp) cc_final: 0.8282 (tpp) REVERT: A 1176 ARG cc_start: 0.7457 (mmm-85) cc_final: 0.5632 (tpp80) REVERT: A 1485 MET cc_start: 0.5903 (mtm) cc_final: 0.5480 (mtm) REVERT: A 1588 MET cc_start: 0.6289 (tpp) cc_final: 0.5102 (tpp) REVERT: A 1613 MET cc_start: 0.7825 (ptp) cc_final: 0.7543 (ptp) REVERT: A 1629 ASN cc_start: 0.8698 (m-40) cc_final: 0.8302 (t0) REVERT: B 31 ASP cc_start: 0.7686 (p0) cc_final: 0.7364 (t70) REVERT: B 200 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8429 (mt-10) REVERT: B 265 ARG cc_start: 0.7737 (mtp85) cc_final: 0.6923 (mtm110) REVERT: B 275 MET cc_start: 0.7337 (tpp) cc_final: 0.6953 (tpp) REVERT: B 393 ASN cc_start: 0.8301 (t0) cc_final: 0.7789 (t0) REVERT: B 502 MET cc_start: 0.7611 (ttp) cc_final: 0.7176 (ttp) REVERT: B 726 MET cc_start: 0.8273 (tmm) cc_final: 0.7618 (tmm) REVERT: B 764 ASN cc_start: 0.7876 (m-40) cc_final: 0.7307 (t0) REVERT: B 874 TYR cc_start: 0.5944 (t80) cc_final: 0.5171 (t80) REVERT: B 936 MET cc_start: 0.8576 (ttt) cc_final: 0.8159 (ttm) REVERT: B 1033 TYR cc_start: 0.8153 (m-80) cc_final: 0.7490 (m-80) REVERT: B 1097 ASP cc_start: 0.6952 (m-30) cc_final: 0.6722 (m-30) REVERT: F 87 LYS cc_start: 0.8417 (pttt) cc_final: 0.8175 (mtmt) REVERT: F 103 MET cc_start: 0.7678 (mtp) cc_final: 0.7282 (ttp) REVERT: F 150 GLU cc_start: 0.8132 (pt0) cc_final: 0.7268 (mp0) REVERT: G 42 PRO cc_start: 0.6486 (Cg_endo) cc_final: 0.6099 (Cg_exo) REVERT: G 229 LEU cc_start: 0.5755 (pp) cc_final: 0.5488 (pp) REVERT: H 20 TYR cc_start: 0.7074 (m-10) cc_final: 0.6857 (m-80) REVERT: H 79 TRP cc_start: 0.7513 (t60) cc_final: 0.6057 (t60) REVERT: K 69 ASP cc_start: 0.8648 (p0) cc_final: 0.8297 (p0) REVERT: L 56 LEU cc_start: 0.8609 (mm) cc_final: 0.7801 (tp) REVERT: L 68 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8329 (tm-30) REVERT: M 30 PHE cc_start: 0.7805 (t80) cc_final: 0.7117 (t80) REVERT: M 90 LEU cc_start: 0.7205 (mt) cc_final: 0.6907 (mp) REVERT: M 153 LYS cc_start: 0.6694 (tttt) cc_final: 0.6044 (tmtt) REVERT: M 217 ARG cc_start: 0.5940 (mtm180) cc_final: 0.5597 (mtm-85) REVERT: M 236 TYR cc_start: 0.6996 (t80) cc_final: 0.6269 (t80) REVERT: M 256 MET cc_start: 0.7055 (ttm) cc_final: 0.6705 (ttp) REVERT: M 401 PHE cc_start: 0.8005 (t80) cc_final: 0.7674 (t80) outliers start: 1 outliers final: 0 residues processed: 661 average time/residue: 0.2153 time to fit residues: 235.3460 Evaluate side-chains 501 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: [15, 91, 342, 145, 179, 173, 174, 176, 18, 200, 393] chunk 15 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 342 optimal weight: 0.0370 chunk 145 optimal weight: 8.9990 chunk 179 optimal weight: 0.2980 chunk 173 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 overall best weight: 2.6664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 ASN ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN C 65 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN M 16 GLN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.116498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.099008 restraints weight = 138723.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.101120 restraints weight = 87964.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.102624 restraints weight = 61733.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103659 restraints weight = 47387.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104261 restraints weight = 39011.759| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37976 Z= 0.148 Angle : 0.695 15.190 51588 Z= 0.352 Chirality : 0.046 0.394 5791 Planarity : 0.005 0.052 6422 Dihedral : 13.869 168.967 5662 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.08 % Allowed : 0.30 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 4447 helix: 0.17 (0.13), residues: 1521 sheet: -1.23 (0.20), residues: 630 loop : -1.87 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 651 TYR 0.025 0.001 TYR A1595 PHE 0.031 0.002 PHE M 382 TRP 0.041 0.002 TRP B 525 HIS 0.011 0.001 HIS B 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (37954) covalent geometry : angle 0.69165 / 0.35 (51573) hydrogen bonds : bond 0.04044 / 2.71 ( 1459) hydrogen bonds : angle 5.27971 / 3.73 ( 4047) metal coordination : bond 0.00517 / 0.31 ( 20) metal coordination : angle 3.88571 / 2.20 ( 15) Misc. bond : bond 0.00030 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8894 Ramachandran restraints generated. 4447 Oldfield, 0 Emsley, 4447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 658 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7217 (mm-30) REVERT: A 96 ILE cc_start: 0.8992 (mt) cc_final: 0.8709 (tt) REVERT: A 114 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8611 (mt-10) REVERT: A 519 LEU cc_start: 0.8982 (mt) cc_final: 0.8718 (mt) REVERT: A 589 MET cc_start: 0.6127 (mmp) cc_final: 0.5875 (mmp) REVERT: A 590 ASN cc_start: 0.7131 (t0) cc_final: 0.6737 (t0) REVERT: A 601 MET cc_start: 0.9173 (mmp) cc_final: 0.8670 (mmm) REVERT: A 960 MET cc_start: 0.8137 (mtm) cc_final: 0.7618 (mtt) REVERT: A 1049 MET cc_start: 0.8602 (ppp) cc_final: 0.8294 (ppp) REVERT: A 1057 ILE cc_start: 0.8889 (mm) cc_final: 0.8654 (tp) REVERT: A 1063 MET cc_start: 0.3779 (mpp) cc_final: 0.3043 (mmt) REVERT: A 1104 TYR cc_start: 0.7960 (t80) cc_final: 0.7378 (t80) REVERT: A 1121 ASP cc_start: 0.8575 (p0) cc_final: 0.8304 (p0) REVERT: A 1139 ASN cc_start: 0.8453 (t0) cc_final: 0.7790 (m110) REVERT: A 1150 LYS cc_start: 0.7494 (mttt) cc_final: 0.7166 (mmtp) REVERT: A 1175 MET cc_start: 0.8632 (tpp) cc_final: 0.8285 (tpp) REVERT: A 1176 ARG cc_start: 0.7444 (mmm-85) cc_final: 0.5644 (tpp80) REVERT: A 1238 MET cc_start: 0.8752 (tpt) cc_final: 0.8328 (tpt) REVERT: A 1485 MET cc_start: 0.6015 (mtm) cc_final: 0.5596 (mtm) REVERT: A 1588 MET cc_start: 0.6238 (tpp) cc_final: 0.5124 (tpp) REVERT: A 1629 ASN cc_start: 0.8748 (m-40) cc_final: 0.8370 (t0) REVERT: B 31 ASP cc_start: 0.7603 (p0) cc_final: 0.7259 (t70) REVERT: B 200 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8410 (mt-10) REVERT: B 265 ARG cc_start: 0.7753 (mtp85) cc_final: 0.6941 (mtm110) REVERT: B 275 MET cc_start: 0.7232 (tpp) cc_final: 0.6902 (tpp) REVERT: B 373 MET cc_start: 0.7260 (ppp) cc_final: 0.7044 (ppp) REVERT: B 393 ASN cc_start: 0.8251 (t0) cc_final: 0.7718 (t0) REVERT: B 502 MET cc_start: 0.7592 (ttp) cc_final: 0.7203 (ttp) REVERT: B 726 MET cc_start: 0.8192 (tmm) cc_final: 0.7700 (tmm) REVERT: B 764 ASN cc_start: 0.7903 (m-40) cc_final: 0.7267 (t0) REVERT: B 874 TYR cc_start: 0.5819 (t80) cc_final: 0.5209 (t80) REVERT: B 936 MET cc_start: 0.8679 (ttt) cc_final: 0.8323 (ttm) REVERT: B 1013 MET cc_start: 0.7334 (tpp) cc_final: 0.7009 (tpp) REVERT: B 1033 TYR cc_start: 0.8084 (m-80) cc_final: 0.7457 (m-80) REVERT: B 1075 GLU cc_start: 0.6825 (mp0) cc_final: 0.6620 (mp0) REVERT: F 87 LYS cc_start: 0.8511 (pttt) cc_final: 0.8177 (mtmt) REVERT: F 150 GLU cc_start: 0.8111 (pt0) cc_final: 0.7364 (mp0) REVERT: G 42 PRO cc_start: 0.6441 (Cg_endo) cc_final: 0.6027 (Cg_exo) REVERT: G 229 LEU cc_start: 0.5586 (pp) cc_final: 0.5323 (pp) REVERT: H 79 TRP cc_start: 0.7460 (t60) cc_final: 0.5960 (t60) REVERT: K 50 LEU cc_start: 0.6843 (mt) cc_final: 0.6111 (tt) REVERT: K 69 ASP cc_start: 0.8651 (p0) cc_final: 0.8335 (p0) REVERT: L 56 LEU cc_start: 0.8597 (mm) cc_final: 0.8288 (mp) REVERT: L 68 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8356 (tm-30) REVERT: M 30 PHE cc_start: 0.7843 (t80) cc_final: 0.7200 (t80) REVERT: M 90 LEU cc_start: 0.7221 (mt) cc_final: 0.6939 (mp) REVERT: M 153 LYS cc_start: 0.6687 (tttt) cc_final: 0.6051 (tmtt) REVERT: M 217 ARG cc_start: 0.5988 (mtm180) cc_final: 0.5637 (mtm-85) REVERT: M 236 TYR cc_start: 0.7092 (t80) cc_final: 0.6365 (t80) REVERT: M 256 MET cc_start: 0.7046 (ttm) cc_final: 0.6692 (ttp) outliers start: 3 outliers final: 1 residues processed: 661 average time/residue: 0.2171 time to fit residues: 238.2572 Evaluate side-chains 493 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 492 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: [285, 103, 60, 323, 428, 443, 235, 255, 221, 262, 439] chunk 285 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 428 optimal weight: 9.9990 chunk 443 optimal weight: 9.9990 chunk 235 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 439 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN M 16 GLN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS M 378 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.115635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.098359 restraints weight = 138101.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100429 restraints weight = 87167.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.101827 restraints weight = 61191.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.102865 restraints weight = 47164.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103537 restraints weight = 38731.233| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37976 Z= 0.167 Angle : 0.695 13.465 51588 Z= 0.356 Chirality : 0.046 0.399 5791 Planarity : 0.005 0.052 6422 Dihedral : 13.880 168.895 5662 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 4447 helix: 0.16 (0.13), residues: 1530 sheet: -1.16 (0.21), residues: 621 loop : -1.89 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 956 TYR 0.020 0.002 TYR A 314 PHE 0.025 0.002 PHE B 895 TRP 0.022 0.002 TRP A 530 HIS 0.010 0.001 HIS B 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (37954) covalent geometry : angle 0.69183 / 0.36 (51573) hydrogen bonds : bond 0.04152 / 2.79 ( 1459) hydrogen bonds : angle 5.29271 / 3.74 ( 4047) metal coordination : bond 0.00599 / 0.35 ( 20) metal coordination : angle 4.19036 / 2.44 ( 15) Misc. bond : bond 0.00035 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7066.18 seconds wall clock time: 122 minutes 54.94 seconds (7374.94 seconds total)