Starting phenix.real_space_refine on Mon Jun 23 23:08:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ja1_61287/06_2025/9ja1_61287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ja1_61287/06_2025/9ja1_61287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ja1_61287/06_2025/9ja1_61287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ja1_61287/06_2025/9ja1_61287.map" model { file = "/net/cci-nas-00/data/ceres_data/9ja1_61287/06_2025/9ja1_61287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ja1_61287/06_2025/9ja1_61287_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 46 5.49 5 Mg 2 5.21 5 S 155 5.16 5 C 17449 2.51 5 N 4851 2.21 5 O 5323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27832 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10060 Classifications: {'peptide': 1286} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1226} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 8724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8724 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 1049} Chain breaks: 8 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2091 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 254} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1726 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain breaks: 1 Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "H" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1076 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 915 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 343 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 95 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "G" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "R" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'5*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 455 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "N" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 274 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 801 SG CYS A 107 79.169 69.802 134.237 1.00113.93 S ATOM 825 SG CYS A 110 81.207 66.922 134.814 1.00115.89 S ATOM 1214 SG CYS A 167 80.148 70.092 137.646 1.00138.65 S ATOM 496 SG CYS A 67 103.172 65.287 92.226 1.00 92.92 S ATOM 518 SG CYS A 70 101.495 61.730 92.325 1.00 96.22 S ATOM 571 SG CYS A 77 99.619 64.509 90.963 1.00 90.60 S ATOM 18302 SG CYS B1163 96.266 52.331 102.842 1.00 85.76 S ATOM 18320 SG CYS B1166 94.640 55.415 104.131 1.00 72.75 S ATOM 18445 SG CYS B1182 98.065 55.624 102.371 1.00 98.24 S ATOM 18464 SG CYS B1185 97.921 53.948 105.761 1.00100.34 S ATOM 19440 SG CYS C 86 85.115 68.632 24.753 1.00124.90 S ATOM 19457 SG CYS C 88 87.179 69.511 24.635 1.00145.22 S ATOM 19513 SG CYS C 95 83.575 71.585 26.271 1.00 95.43 S ATOM 24401 SG CYS J 7 56.311 81.575 37.716 1.00 67.90 S ATOM 24424 SG CYS J 10 55.804 79.686 34.831 1.00 59.59 S ATOM 24704 SG CYS J 45 52.736 80.199 37.276 1.00 78.73 S ATOM 24710 SG CYS J 46 53.792 82.608 34.597 1.00 66.44 S ATOM 25829 SG CYS L 31 89.768 107.370 50.410 1.00145.40 S ATOM 25849 SG CYS L 34 89.609 109.908 48.503 1.00156.92 S ATOM 25953 SG CYS L 48 92.098 109.607 51.066 1.00158.75 S ATOM 25976 SG CYS L 51 88.747 110.835 52.567 1.00155.15 S Time building chain proxies: 15.18, per 1000 atoms: 0.55 Number of scatterers: 27832 At special positions: 0 Unit cell: (123.521, 138.443, 154.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 155 16.00 P 46 15.00 Mg 2 11.99 O 5323 8.00 N 4851 7.00 C 17449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.18 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 21 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6360 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 42 sheets defined 37.9% alpha, 17.3% beta 15 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 8.73 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.540A pdb=" N ARG A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 removed outlier: 3.780A pdb=" N GLU A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.824A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.550A pdb=" N ARG A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.540A pdb=" N ILE A 511 " --> pdb=" O PRO A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.978A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.513A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 673 through 698 removed outlier: 3.841A pdb=" N GLU A 678 " --> pdb=" O PRO A 674 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 736 removed outlier: 3.549A pdb=" N ASN A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.908A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 845 removed outlier: 4.050A pdb=" N ILE A 837 " --> pdb=" O GLU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 903 through 907 removed outlier: 3.986A pdb=" N HIS A 906 " --> pdb=" O ASN A 903 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 907 " --> pdb=" O THR A 904 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 903 through 907' Processing helix chain 'A' and resid 922 through 947 removed outlier: 3.596A pdb=" N GLU A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 933 " --> pdb=" O LEU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 3.803A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.505A pdb=" N LEU A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 990 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.773A pdb=" N GLN A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1026 Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1080 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1091 through 1096 removed outlier: 3.625A pdb=" N THR A1095 " --> pdb=" O SER A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 Processing helix chain 'A' and resid 1128 through 1137 Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.913A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.733A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.831A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 4.513A pdb=" N SER B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.567A pdb=" N CYS B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 321 through 324 Processing helix chain 'B' and resid 325 through 326 No H-bonds generated for 'chain 'B' and resid 325 through 326' Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.137A pdb=" N LEU B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.648A pdb=" N LYS B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 436 removed outlier: 3.526A pdb=" N LEU B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.516A pdb=" N ALA B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.706A pdb=" N TRP B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 removed outlier: 3.645A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 605 removed outlier: 3.843A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.673A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.731A pdb=" N LEU B 710 " --> pdb=" O GLN B 706 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 706 through 711' Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.686A pdb=" N ILE B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.515A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.744A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.738A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.919A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1060 Processing helix chain 'B' and resid 1061 through 1063 No H-bonds generated for 'chain 'B' and resid 1061 through 1063' Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1144 through 1152 Processing helix chain 'B' and resid 1197 through 1209 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.739A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 268 removed outlier: 3.541A pdb=" N ASP C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.737A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.816A pdb=" N MET E 57 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET E 58 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 58' Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.730A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.656A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.506A pdb=" N SER E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 127' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.682A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.816A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.867A pdb=" N LEU K 9 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 51 Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.446A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 250 through 252 removed outlier: 3.548A pdb=" N ILE A 250 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 252 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.798A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.553A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.738A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.890A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB1, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB3, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB5, first strand: chain 'A' and resid 1441 through 1444 Processing sheet with id=AB6, first strand: chain 'B' and resid 95 through 97 removed outlier: 5.758A pdb=" N SER B 126 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG B 169 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 128 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.631A pdb=" N HIS B 110 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AB9, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.329A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.963A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 280 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC3, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC4, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.304A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.748A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.748A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AC8, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.362A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD1, first strand: chain 'B' and resid 915 through 917 Processing sheet with id=AD2, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD3, first strand: chain 'B' and resid 1158 through 1163 removed outlier: 3.667A pdb=" N ILE B1196 " --> pdb=" O PHE B1158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1172 through 1174 removed outlier: 3.656A pdb=" N GLN B1179 " --> pdb=" O LYS B1174 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.742A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.347A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.426A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AD9, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.443A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE2, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE3, first strand: chain 'H' and resid 95 through 98 removed outlier: 6.868A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.496A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 4 through 13 removed outlier: 4.067A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 4 through 13 removed outlier: 3.576A pdb=" N ARG G 60 " --> pdb=" O GLU G 69 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 2979 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 12.06 Time building geometry restraints manager: 7.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9021 1.34 - 1.46: 4467 1.46 - 1.58: 14604 1.58 - 1.69: 90 1.69 - 1.81: 250 Bond restraints: 28432 Sorted by residual: bond pdb=" C4 ATP T 101 " pdb=" C5 ATP T 101 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.63e+01 bond pdb=" C5 ATP T 101 " pdb=" C6 ATP T 101 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C8 ATP T 101 " pdb=" N7 ATP T 101 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.15e+01 bond pdb=" C5 ATP T 101 " pdb=" N7 ATP T 101 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.76e+01 bond pdb=" C4 ATP T 101 " pdb=" N9 ATP T 101 " ideal model delta sigma weight residual 1.374 1.333 0.041 1.00e-02 1.00e+04 1.71e+01 ... (remaining 28427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 38480 3.66 - 7.32: 113 7.32 - 10.98: 5 10.98 - 14.64: 0 14.64 - 18.30: 2 Bond angle restraints: 38600 Sorted by residual: angle pdb=" PB ATP T 101 " pdb=" O3B ATP T 101 " pdb=" PG ATP T 101 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP T 101 " pdb=" O3A ATP T 101 " pdb=" PB ATP T 101 " ideal model delta sigma weight residual 136.83 120.20 16.63 1.00e+00 1.00e+00 2.77e+02 angle pdb=" C5 ATP T 101 " pdb=" C4 ATP T 101 " pdb=" N3 ATP T 101 " ideal model delta sigma weight residual 126.80 118.74 8.06 1.00e+00 1.00e+00 6.50e+01 angle pdb=" N3 ATP T 101 " pdb=" C4 ATP T 101 " pdb=" N9 ATP T 101 " ideal model delta sigma weight residual 127.04 134.96 -7.92 1.15e+00 7.59e-01 4.76e+01 angle pdb=" C SER H 88 " pdb=" CA SER H 88 " pdb=" CB SER H 88 " ideal model delta sigma weight residual 116.54 110.25 6.29 1.15e+00 7.56e-01 2.99e+01 ... (remaining 38595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 16993 35.62 - 71.23: 273 71.23 - 106.85: 12 106.85 - 142.46: 2 142.46 - 178.08: 2 Dihedral angle restraints: 17282 sinusoidal: 7453 harmonic: 9829 Sorted by residual: dihedral pdb=" CA ALA C 39 " pdb=" C ALA C 39 " pdb=" N GLU C 40 " pdb=" CA GLU C 40 " ideal model delta harmonic sigma weight residual -180.00 -156.08 -23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA HIS L 53 " pdb=" C HIS L 53 " pdb=" N ARG L 54 " pdb=" CA ARG L 54 " ideal model delta harmonic sigma weight residual -180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" C4' DG N 4 " pdb=" C3' DG N 4 " pdb=" O3' DG N 4 " pdb=" P DA N 5 " ideal model delta sinusoidal sigma weight residual 220.00 41.92 178.08 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 17279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3813 0.064 - 0.128: 507 0.128 - 0.192: 23 0.192 - 0.256: 1 0.256 - 0.320: 2 Chirality restraints: 4346 Sorted by residual: chirality pdb=" CB VAL A 622 " pdb=" CA VAL A 622 " pdb=" CG1 VAL A 622 " pdb=" CG2 VAL A 622 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE J 2 " pdb=" CA ILE J 2 " pdb=" CG1 ILE J 2 " pdb=" CG2 ILE J 2 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.79 -2.59 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 4343 not shown) Planarity restraints: 4826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 954 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 955 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 955 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 955 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 245 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 444 " -0.014 2.00e-02 2.50e+03 1.28e-02 2.88e+00 pdb=" CG PHE A 444 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 444 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 444 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 444 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 444 " 0.000 2.00e-02 2.50e+03 ... (remaining 4823 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2684 2.74 - 3.28: 27043 3.28 - 3.82: 45981 3.82 - 4.36: 57567 4.36 - 4.90: 96971 Nonbonded interactions: 230246 Sorted by model distance: nonbonded pdb=" OE1 GLU A1403 " pdb=" OP1 DC T 16 " model vdw 2.205 3.040 nonbonded pdb=" O THR B 680 " pdb=" OG SER B 683 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR B 487 " pdb=" O ALA B 777 " model vdw 2.226 3.040 nonbonded pdb=" NH1 ARG C 35 " pdb=" OG1 THR K 41 " model vdw 2.237 3.120 nonbonded pdb=" NH2 ARG B 604 " pdb=" OE2 GLU B 691 " model vdw 2.237 3.120 ... (remaining 230241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 70.040 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.100 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.003 0.081 28454 Z= 0.182 Angle : 0.662 24.066 38621 Z= 0.381 Chirality : 0.043 0.320 4346 Planarity : 0.004 0.048 4826 Dihedral : 13.323 178.075 10922 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 0.07 % Allowed : 0.57 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3342 helix: 0.54 (0.16), residues: 1166 sheet: -0.77 (0.23), residues: 487 loop : -0.65 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1044 HIS 0.004 0.001 HIS A 399 PHE 0.029 0.001 PHE A 444 TYR 0.022 0.001 TYR B 797 ARG 0.004 0.000 ARG A 537 Details of bonding type rmsd hydrogen bonds : bond 0.18690 ( 1088) hydrogen bonds : angle 7.22723 ( 3051) metal coordination : bond 0.00891 ( 22) metal coordination : angle 11.28251 ( 21) covalent geometry : bond 0.00340 (28432) covalent geometry : angle 0.60719 (38600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 658 time to evaluate : 3.255 Fit side-chains REVERT: A 49 LYS cc_start: 0.7747 (mppt) cc_final: 0.7480 (mptt) REVERT: A 71 GLN cc_start: 0.8331 (mt0) cc_final: 0.7941 (mm-40) REVERT: A 116 ASP cc_start: 0.7114 (m-30) cc_final: 0.6836 (m-30) REVERT: A 120 GLU cc_start: 0.7944 (mm-30) cc_final: 0.6845 (tp30) REVERT: A 175 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7248 (mtp-110) REVERT: A 316 GLN cc_start: 0.7161 (mt0) cc_final: 0.6625 (mm-40) REVERT: A 453 MET cc_start: 0.9007 (mpp) cc_final: 0.8639 (mpt) REVERT: A 531 ILE cc_start: 0.8713 (tp) cc_final: 0.8490 (tp) REVERT: A 771 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7313 (pt0) REVERT: A 858 ASN cc_start: 0.8065 (t0) cc_final: 0.7852 (t160) REVERT: A 1102 LYS cc_start: 0.8358 (tttm) cc_final: 0.7940 (ttpt) REVERT: A 1277 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7486 (mt-10) REVERT: A 1300 LYS cc_start: 0.8529 (mtmt) cc_final: 0.8307 (mtpt) REVERT: A 1309 ASP cc_start: 0.7686 (m-30) cc_final: 0.7371 (t0) REVERT: A 1315 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8198 (mm-30) REVERT: A 1394 THR cc_start: 0.9024 (m) cc_final: 0.8754 (p) REVERT: B 29 ASP cc_start: 0.8052 (m-30) cc_final: 0.7848 (m-30) REVERT: B 53 GLN cc_start: 0.8549 (tp40) cc_final: 0.8189 (tp40) REVERT: B 244 LEU cc_start: 0.7952 (mt) cc_final: 0.7732 (mp) REVERT: B 313 MET cc_start: 0.6424 (mtm) cc_final: 0.6215 (mtp) REVERT: B 348 ARG cc_start: 0.4281 (mtm180) cc_final: 0.3028 (mtm180) REVERT: B 373 ARG cc_start: 0.6805 (mtt180) cc_final: 0.6471 (mtp85) REVERT: B 620 ARG cc_start: 0.7165 (ptp-170) cc_final: 0.6815 (tpp-160) REVERT: B 622 LYS cc_start: 0.7683 (mttt) cc_final: 0.7444 (mtmm) REVERT: B 868 MET cc_start: 0.5286 (mtp) cc_final: 0.4543 (mpt) REVERT: B 894 ASP cc_start: 0.7037 (m-30) cc_final: 0.6763 (m-30) REVERT: B 936 ASP cc_start: 0.7530 (t0) cc_final: 0.7094 (t0) REVERT: B 948 ILE cc_start: 0.8957 (mp) cc_final: 0.8587 (mt) REVERT: B 1053 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7856 (mp0) REVERT: C 19 ASP cc_start: 0.7762 (t0) cc_final: 0.7503 (t0) REVERT: C 40 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8306 (mt-10) REVERT: C 73 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8619 (mm-40) REVERT: E 103 LYS cc_start: 0.8608 (mttm) cc_final: 0.7873 (mtmm) REVERT: E 169 ARG cc_start: 0.8438 (mtt90) cc_final: 0.8212 (mtp85) REVERT: E 192 ARG cc_start: 0.8595 (mmt90) cc_final: 0.8002 (mtp85) REVERT: F 81 THR cc_start: 0.8989 (m) cc_final: 0.8666 (p) REVERT: F 129 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8454 (mmtp) REVERT: F 149 GLU cc_start: 0.8174 (tt0) cc_final: 0.7692 (mt-10) REVERT: H 21 ASN cc_start: 0.8943 (m-40) cc_final: 0.8722 (m110) REVERT: H 80 ARG cc_start: 0.8367 (mtt90) cc_final: 0.8105 (mtt-85) REVERT: H 106 GLU cc_start: 0.7741 (tp30) cc_final: 0.7495 (tp30) REVERT: H 108 SER cc_start: 0.8414 (t) cc_final: 0.8115 (t) REVERT: K 17 SER cc_start: 0.9120 (m) cc_final: 0.8652 (p) REVERT: K 20 LYS cc_start: 0.8006 (tttp) cc_final: 0.7751 (tttm) REVERT: K 55 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8231 (mtpm) REVERT: L 38 LEU cc_start: 0.4514 (mp) cc_final: 0.4079 (mt) REVERT: G 73 LYS cc_start: 0.7157 (mttt) cc_final: 0.6507 (tmtp) outliers start: 2 outliers final: 3 residues processed: 660 average time/residue: 1.4818 time to fit residues: 1131.3534 Evaluate side-chains 388 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 385 time to evaluate : 4.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain F residue 77 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 5.9990 chunk 256 optimal weight: 0.0670 chunk 142 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 306 optimal weight: 0.0170 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 339 ASN A 390 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN A 717 ASN A 881 GLN A 906 HIS A1124 HIS A1432 GLN B 110 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 469 GLN B 881 ASN B1076 HIS B1177 HIS B1179 GLN C 102 GLN C 123 ASN C 242 GLN H 52 GLN K 2 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.137030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103038 restraints weight = 34647.957| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.22 r_work: 0.3117 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28454 Z= 0.122 Angle : 0.549 14.683 38621 Z= 0.286 Chirality : 0.043 0.224 4346 Planarity : 0.004 0.066 4826 Dihedral : 11.729 179.093 4229 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.86 % Allowed : 11.90 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3342 helix: 0.82 (0.16), residues: 1187 sheet: -0.74 (0.22), residues: 492 loop : -0.60 (0.16), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1044 HIS 0.008 0.001 HIS B 648 PHE 0.022 0.001 PHE A 219 TYR 0.015 0.001 TYR B 431 ARG 0.009 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 1088) hydrogen bonds : angle 4.93307 ( 3051) metal coordination : bond 0.00707 ( 22) metal coordination : angle 5.21271 ( 21) covalent geometry : bond 0.00269 (28432) covalent geometry : angle 0.53601 (38600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 404 time to evaluate : 3.294 Fit side-chains revert: symmetry clash REVERT: A 71 GLN cc_start: 0.8406 (mt0) cc_final: 0.8056 (mm-40) REVERT: A 116 ASP cc_start: 0.7572 (m-30) cc_final: 0.7278 (m-30) REVERT: A 120 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7249 (tp30) REVERT: A 175 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7318 (mtp-110) REVERT: A 453 MET cc_start: 0.8927 (mpp) cc_final: 0.8606 (mpt) REVERT: A 677 ARG cc_start: 0.6979 (ptp-170) cc_final: 0.6773 (mtp180) REVERT: A 698 GLN cc_start: 0.4982 (OUTLIER) cc_final: 0.4567 (tm-30) REVERT: A 771 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7357 (pt0) REVERT: A 948 VAL cc_start: 0.9028 (t) cc_final: 0.8759 (m) REVERT: A 1093 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6818 (ttpt) REVERT: A 1128 GLN cc_start: 0.6854 (pt0) cc_final: 0.6643 (pt0) REVERT: A 1277 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 1285 MET cc_start: 0.7439 (mtm) cc_final: 0.6835 (mtm) REVERT: A 1300 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8343 (mtpt) REVERT: A 1309 ASP cc_start: 0.7787 (m-30) cc_final: 0.7351 (t0) REVERT: A 1315 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8238 (mm-30) REVERT: A 1336 MET cc_start: 0.9025 (ttp) cc_final: 0.8794 (ttt) REVERT: B 65 GLU cc_start: 0.7531 (tt0) cc_final: 0.7255 (tp30) REVERT: B 348 ARG cc_start: 0.4139 (mtm180) cc_final: 0.2754 (mpp-170) REVERT: B 427 ASP cc_start: 0.7660 (t0) cc_final: 0.7266 (m-30) REVERT: B 552 MET cc_start: 0.8061 (mmm) cc_final: 0.7787 (mmm) REVERT: B 620 ARG cc_start: 0.7285 (ptp-170) cc_final: 0.6610 (tpp-160) REVERT: B 622 LYS cc_start: 0.7693 (mttt) cc_final: 0.7437 (mtmm) REVERT: B 708 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: B 709 ASP cc_start: 0.8243 (t0) cc_final: 0.8020 (t0) REVERT: B 860 MET cc_start: 0.8452 (tmm) cc_final: 0.8092 (tmm) REVERT: B 868 MET cc_start: 0.5332 (mtp) cc_final: 0.4507 (mpt) REVERT: B 894 ASP cc_start: 0.7080 (m-30) cc_final: 0.6775 (m-30) REVERT: B 936 ASP cc_start: 0.7799 (t0) cc_final: 0.7323 (t0) REVERT: B 948 ILE cc_start: 0.8898 (mp) cc_final: 0.8484 (mt) REVERT: B 1050 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8747 (mp) REVERT: B 1053 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7847 (mm-30) REVERT: B 1218 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8666 (p) REVERT: C 11 ARG cc_start: 0.8617 (ptp90) cc_final: 0.8323 (ptp90) REVERT: C 19 ASP cc_start: 0.7722 (t0) cc_final: 0.7407 (t0) REVERT: C 40 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8600 (mt-10) REVERT: C 75 MET cc_start: 0.8663 (tpp) cc_final: 0.8314 (tpt) REVERT: C 187 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8765 (mttp) REVERT: C 217 ASP cc_start: 0.8254 (m-30) cc_final: 0.7985 (m-30) REVERT: C 230 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8423 (mtm) REVERT: C 265 MET cc_start: 0.8117 (ttm) cc_final: 0.7903 (ptm) REVERT: E 103 LYS cc_start: 0.8613 (mttm) cc_final: 0.7870 (mtmm) REVERT: E 104 ASN cc_start: 0.7840 (m-40) cc_final: 0.7577 (t160) REVERT: E 121 MET cc_start: 0.8073 (mmm) cc_final: 0.7860 (mmm) REVERT: E 169 ARG cc_start: 0.8492 (mtt90) cc_final: 0.8220 (mtp85) REVERT: E 192 ARG cc_start: 0.8797 (mmt90) cc_final: 0.8054 (mmm160) REVERT: F 129 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8429 (mmtp) REVERT: F 149 GLU cc_start: 0.8455 (tt0) cc_final: 0.7821 (mt-10) REVERT: H 80 ARG cc_start: 0.8486 (mtt90) cc_final: 0.8160 (mtt-85) REVERT: H 106 GLU cc_start: 0.7983 (tp30) cc_final: 0.7678 (tp30) REVERT: H 108 SER cc_start: 0.8416 (t) cc_final: 0.8089 (t) REVERT: J 42 LYS cc_start: 0.8768 (tttp) cc_final: 0.8530 (pttp) REVERT: K 17 SER cc_start: 0.9097 (m) cc_final: 0.8658 (p) REVERT: K 20 LYS cc_start: 0.7998 (tttp) cc_final: 0.7747 (tttm) REVERT: G 73 LYS cc_start: 0.7453 (mttt) cc_final: 0.6675 (tmtp) outliers start: 55 outliers final: 19 residues processed: 437 average time/residue: 1.5412 time to fit residues: 776.3907 Evaluate side-chains 377 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 351 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 1093 LYS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 762 ASN Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain K residue 29 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 107 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 308 optimal weight: 4.9990 chunk 315 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 134 optimal weight: 0.0070 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 282 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 ASN A 877 HIS A 959 ASN A1432 GLN B 115 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS C 224 GLN F 78 GLN H 52 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098686 restraints weight = 34728.121| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.21 r_work: 0.3054 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28454 Z= 0.166 Angle : 0.558 12.084 38621 Z= 0.288 Chirality : 0.044 0.176 4346 Planarity : 0.004 0.051 4826 Dihedral : 11.811 179.392 4225 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.01 % Allowed : 13.02 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3342 helix: 0.85 (0.16), residues: 1180 sheet: -0.70 (0.22), residues: 483 loop : -0.66 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 31 HIS 0.026 0.001 HIS A1124 PHE 0.024 0.001 PHE A 219 TYR 0.013 0.001 TYR J 44 ARG 0.006 0.000 ARG B 730 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 1088) hydrogen bonds : angle 4.65666 ( 3051) metal coordination : bond 0.00652 ( 22) metal coordination : angle 4.86781 ( 21) covalent geometry : bond 0.00399 (28432) covalent geometry : angle 0.54656 (38600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 364 time to evaluate : 2.925 Fit side-chains REVERT: A 112 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7874 (ttpp) REVERT: A 116 ASP cc_start: 0.7642 (m-30) cc_final: 0.7389 (m-30) REVERT: A 123 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7654 (mtm110) REVERT: A 175 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7313 (mtp-110) REVERT: A 453 MET cc_start: 0.8950 (mpp) cc_final: 0.8662 (mpt) REVERT: A 771 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7385 (pt0) REVERT: A 847 ASP cc_start: 0.8293 (p0) cc_final: 0.7994 (p0) REVERT: A 858 ASN cc_start: 0.8245 (t0) cc_final: 0.8010 (t160) REVERT: A 948 VAL cc_start: 0.9080 (t) cc_final: 0.8803 (m) REVERT: A 1093 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6932 (ttpt) REVERT: A 1124 HIS cc_start: 0.6926 (OUTLIER) cc_final: 0.6717 (p90) REVERT: A 1128 GLN cc_start: 0.6917 (pt0) cc_final: 0.6708 (pt0) REVERT: A 1141 THR cc_start: 0.8882 (m) cc_final: 0.8461 (p) REVERT: A 1277 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 1285 MET cc_start: 0.7504 (mtm) cc_final: 0.7026 (mtm) REVERT: A 1300 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8388 (mtpt) REVERT: A 1309 ASP cc_start: 0.7872 (m-30) cc_final: 0.6795 (p0) REVERT: A 1315 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8309 (mm-30) REVERT: B 65 GLU cc_start: 0.7585 (tt0) cc_final: 0.7302 (tp30) REVERT: B 348 ARG cc_start: 0.4328 (mtm180) cc_final: 0.2833 (mpp80) REVERT: B 552 MET cc_start: 0.8172 (mmm) cc_final: 0.7878 (mmm) REVERT: B 620 ARG cc_start: 0.7346 (ptp-170) cc_final: 0.6645 (tpp-160) REVERT: B 622 LYS cc_start: 0.7656 (mttt) cc_final: 0.7290 (mtmm) REVERT: B 687 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: B 709 ASP cc_start: 0.8300 (t0) cc_final: 0.8005 (t0) REVERT: B 868 MET cc_start: 0.5422 (mtp) cc_final: 0.4524 (mpt) REVERT: B 894 ASP cc_start: 0.7127 (m-30) cc_final: 0.6808 (m-30) REVERT: B 936 ASP cc_start: 0.7921 (t0) cc_final: 0.7593 (t0) REVERT: B 948 ILE cc_start: 0.8799 (mp) cc_final: 0.8474 (mt) REVERT: B 1053 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7839 (mp0) REVERT: C 11 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8311 (ptp90) REVERT: C 40 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8599 (mt-10) REVERT: C 75 MET cc_start: 0.8718 (tpp) cc_final: 0.8378 (tpt) REVERT: C 187 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8868 (mttp) REVERT: C 217 ASP cc_start: 0.8328 (m-30) cc_final: 0.8115 (m-30) REVERT: E 103 LYS cc_start: 0.8605 (mttm) cc_final: 0.7899 (mtmm) REVERT: E 169 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8235 (mtp85) REVERT: E 192 ARG cc_start: 0.8839 (mmt90) cc_final: 0.8089 (mtp85) REVERT: F 114 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7010 (mm-30) REVERT: F 129 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8450 (mmtp) REVERT: F 149 GLU cc_start: 0.8465 (tt0) cc_final: 0.7765 (mt-10) REVERT: H 106 GLU cc_start: 0.7867 (tp30) cc_final: 0.7553 (tp30) REVERT: H 108 SER cc_start: 0.8377 (t) cc_final: 0.8025 (t) REVERT: K 20 LYS cc_start: 0.8076 (tttp) cc_final: 0.7822 (tttm) REVERT: G 73 LYS cc_start: 0.7553 (mttt) cc_final: 0.6734 (tmtp) outliers start: 89 outliers final: 31 residues processed: 424 average time/residue: 1.5393 time to fit residues: 753.0416 Evaluate side-chains 367 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 331 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 1093 LYS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain K residue 29 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 18 GLN A 282 ASN A 316 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN A1124 HIS A1432 GLN F 78 GLN H 52 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.098066 restraints weight = 35140.858| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.23 r_work: 0.3046 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28454 Z= 0.153 Angle : 0.540 10.983 38621 Z= 0.279 Chirality : 0.043 0.223 4346 Planarity : 0.004 0.046 4826 Dihedral : 11.793 179.795 4223 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.48 % Allowed : 14.10 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3342 helix: 0.93 (0.16), residues: 1183 sheet: -0.69 (0.22), residues: 491 loop : -0.61 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.005 0.001 HIS A 451 PHE 0.023 0.001 PHE A 219 TYR 0.016 0.001 TYR B 431 ARG 0.009 0.000 ARG F 119 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 1088) hydrogen bonds : angle 4.48690 ( 3051) metal coordination : bond 0.00607 ( 22) metal coordination : angle 4.61003 ( 21) covalent geometry : bond 0.00369 (28432) covalent geometry : angle 0.52947 (38600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 348 time to evaluate : 2.918 Fit side-chains REVERT: A 41 MET cc_start: 0.7374 (mmt) cc_final: 0.7157 (mmt) REVERT: A 112 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7940 (ttpp) REVERT: A 175 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7315 (mtp-110) REVERT: A 453 MET cc_start: 0.8980 (mpp) cc_final: 0.8734 (mpt) REVERT: A 716 ASP cc_start: 0.7379 (t0) cc_final: 0.6597 (m-30) REVERT: A 724 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7356 (pt0) REVERT: A 771 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7395 (pt0) REVERT: A 948 VAL cc_start: 0.9100 (t) cc_final: 0.8825 (m) REVERT: A 1141 THR cc_start: 0.8919 (m) cc_final: 0.8504 (p) REVERT: A 1277 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 1280 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7601 (mm-30) REVERT: A 1285 MET cc_start: 0.7479 (mtm) cc_final: 0.6999 (mtm) REVERT: A 1309 ASP cc_start: 0.8032 (m-30) cc_final: 0.6984 (p0) REVERT: A 1315 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8335 (mm-30) REVERT: A 1438 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8778 (t) REVERT: B 65 GLU cc_start: 0.7602 (tt0) cc_final: 0.7314 (tp30) REVERT: B 348 ARG cc_start: 0.4373 (mtm180) cc_final: 0.2814 (mpp80) REVERT: B 373 ARG cc_start: 0.6794 (mtp85) cc_final: 0.6548 (mtp85) REVERT: B 473 MET cc_start: 0.3514 (OUTLIER) cc_final: 0.3143 (tpt) REVERT: B 502 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6785 (mt) REVERT: B 552 MET cc_start: 0.8153 (mmm) cc_final: 0.7848 (mmm) REVERT: B 620 ARG cc_start: 0.7362 (ptp-170) cc_final: 0.6723 (tpp-160) REVERT: B 622 LYS cc_start: 0.7638 (mttt) cc_final: 0.7302 (mtmm) REVERT: B 687 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: B 708 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: B 894 ASP cc_start: 0.7123 (m-30) cc_final: 0.6864 (m-30) REVERT: B 936 ASP cc_start: 0.7783 (t0) cc_final: 0.7447 (t0) REVERT: B 948 ILE cc_start: 0.8803 (mp) cc_final: 0.8490 (mt) REVERT: B 1053 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7812 (mp0) REVERT: C 11 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8492 (ptp90) REVERT: C 40 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8560 (mt-10) REVERT: C 75 MET cc_start: 0.8740 (tpp) cc_final: 0.8417 (tpt) REVERT: C 187 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8917 (mttp) REVERT: C 217 ASP cc_start: 0.8295 (m-30) cc_final: 0.8092 (m-30) REVERT: E 94 LYS cc_start: 0.7722 (mttt) cc_final: 0.7221 (ptmt) REVERT: E 103 LYS cc_start: 0.8606 (mttm) cc_final: 0.7903 (mtmm) REVERT: E 169 ARG cc_start: 0.8498 (mtt90) cc_final: 0.8194 (mtp85) REVERT: E 192 ARG cc_start: 0.8828 (mmt90) cc_final: 0.8129 (mmm160) REVERT: F 81 THR cc_start: 0.9090 (m) cc_final: 0.8841 (p) REVERT: F 129 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8456 (mmtp) REVERT: F 149 GLU cc_start: 0.8454 (tt0) cc_final: 0.7776 (mt-10) REVERT: H 78 SER cc_start: 0.9242 (OUTLIER) cc_final: 0.8896 (t) REVERT: H 106 GLU cc_start: 0.7875 (tp30) cc_final: 0.7601 (tp30) REVERT: H 108 SER cc_start: 0.8384 (t) cc_final: 0.8038 (t) REVERT: J 26 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7190 (mt0) REVERT: K 17 SER cc_start: 0.9022 (m) cc_final: 0.8283 (p) REVERT: K 20 LYS cc_start: 0.8052 (tttp) cc_final: 0.7794 (tttm) REVERT: G 73 LYS cc_start: 0.7556 (mttt) cc_final: 0.6791 (tmtp) outliers start: 103 outliers final: 44 residues processed: 420 average time/residue: 1.5557 time to fit residues: 757.2291 Evaluate side-chains 371 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 318 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain G residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 100 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 316 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 282 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1432 GLN B 469 GLN F 78 GLN H 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096316 restraints weight = 34517.708| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.19 r_work: 0.3019 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28454 Z= 0.188 Angle : 0.575 16.373 38621 Z= 0.289 Chirality : 0.044 0.237 4346 Planarity : 0.004 0.046 4826 Dihedral : 11.833 179.953 4223 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.42 % Allowed : 15.18 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3342 helix: 0.91 (0.16), residues: 1183 sheet: -0.67 (0.22), residues: 490 loop : -0.67 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 31 HIS 0.007 0.001 HIS A 399 PHE 0.023 0.002 PHE A 219 TYR 0.012 0.001 TYR J 44 ARG 0.008 0.000 ARG F 119 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 1088) hydrogen bonds : angle 4.49431 ( 3051) metal coordination : bond 0.01020 ( 22) metal coordination : angle 7.46354 ( 21) covalent geometry : bond 0.00461 (28432) covalent geometry : angle 0.54867 (38600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 336 time to evaluate : 2.845 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.7437 (mmt) cc_final: 0.7190 (mmt) REVERT: A 112 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7987 (ttpp) REVERT: A 175 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7294 (mtp-110) REVERT: A 453 MET cc_start: 0.9003 (mpp) cc_final: 0.8740 (mpt) REVERT: A 716 ASP cc_start: 0.7348 (t0) cc_final: 0.6528 (m-30) REVERT: A 724 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7369 (pt0) REVERT: A 771 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7451 (pt0) REVERT: A 948 VAL cc_start: 0.9095 (t) cc_final: 0.8817 (m) REVERT: A 1093 LYS cc_start: 0.7324 (ttpp) cc_final: 0.6733 (mtpt) REVERT: A 1141 THR cc_start: 0.8937 (m) cc_final: 0.8498 (p) REVERT: A 1277 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 1280 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7621 (mm-30) REVERT: A 1285 MET cc_start: 0.7530 (mtm) cc_final: 0.7060 (mtm) REVERT: A 1309 ASP cc_start: 0.8035 (m-30) cc_final: 0.6984 (p0) REVERT: A 1315 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8343 (mm-30) REVERT: B 65 GLU cc_start: 0.7583 (tt0) cc_final: 0.7304 (tp30) REVERT: B 348 ARG cc_start: 0.4421 (mtm180) cc_final: 0.2803 (mpp80) REVERT: B 473 MET cc_start: 0.3595 (OUTLIER) cc_final: 0.3231 (tpt) REVERT: B 620 ARG cc_start: 0.7425 (ptp-170) cc_final: 0.6815 (tpp-160) REVERT: B 622 LYS cc_start: 0.7624 (mttt) cc_final: 0.7294 (mtmm) REVERT: B 687 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: B 894 ASP cc_start: 0.7231 (m-30) cc_final: 0.6934 (m-30) REVERT: B 936 ASP cc_start: 0.7909 (t0) cc_final: 0.7519 (t0) REVERT: B 948 ILE cc_start: 0.8821 (mp) cc_final: 0.8492 (mt) REVERT: B 1053 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7993 (mp0) REVERT: C 11 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8496 (ptp90) REVERT: C 40 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8521 (mt-10) REVERT: C 75 MET cc_start: 0.8753 (tpp) cc_final: 0.8432 (tpt) REVERT: C 187 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8922 (mttp) REVERT: E 85 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7197 (mp0) REVERT: E 94 LYS cc_start: 0.7733 (mttt) cc_final: 0.7218 (ptmt) REVERT: E 103 LYS cc_start: 0.8644 (mttm) cc_final: 0.7908 (mtmm) REVERT: E 169 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8207 (mtp85) REVERT: E 192 ARG cc_start: 0.8827 (mmt90) cc_final: 0.8122 (mmm160) REVERT: F 81 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8889 (p) REVERT: F 129 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8425 (mmtp) REVERT: F 149 GLU cc_start: 0.8487 (tt0) cc_final: 0.7811 (mt-10) REVERT: H 27 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: H 78 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.8846 (t) REVERT: H 106 GLU cc_start: 0.7895 (tp30) cc_final: 0.7616 (tp30) REVERT: H 108 SER cc_start: 0.8390 (t) cc_final: 0.8033 (t) REVERT: J 26 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7220 (mt0) REVERT: K 17 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8281 (p) REVERT: K 20 LYS cc_start: 0.8066 (tttp) cc_final: 0.7816 (tttm) REVERT: K 39 ASP cc_start: 0.8242 (m-30) cc_final: 0.7810 (p0) REVERT: G 73 LYS cc_start: 0.7724 (mttt) cc_final: 0.6821 (tmtp) outliers start: 101 outliers final: 51 residues processed: 407 average time/residue: 1.5206 time to fit residues: 715.7248 Evaluate side-chains 385 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain G residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 62 optimal weight: 3.9990 chunk 315 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 277 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 193 optimal weight: 0.7980 chunk 233 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 252 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 282 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN B 60 GLN H 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.098031 restraints weight = 35017.272| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.21 r_work: 0.3045 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28454 Z= 0.127 Angle : 0.520 12.284 38621 Z= 0.267 Chirality : 0.043 0.240 4346 Planarity : 0.004 0.046 4826 Dihedral : 11.809 179.690 4223 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.08 % Allowed : 16.44 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.15), residues: 3342 helix: 1.09 (0.16), residues: 1175 sheet: -0.43 (0.22), residues: 476 loop : -0.60 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 192 HIS 0.004 0.001 HIS A 451 PHE 0.025 0.001 PHE A 714 TYR 0.017 0.001 TYR B 431 ARG 0.009 0.000 ARG F 119 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 1088) hydrogen bonds : angle 4.32997 ( 3051) metal coordination : bond 0.00864 ( 22) metal coordination : angle 4.46250 ( 21) covalent geometry : bond 0.00303 (28432) covalent geometry : angle 0.50916 (38600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 344 time to evaluate : 3.179 Fit side-chains REVERT: A 112 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7993 (ttpp) REVERT: A 123 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7621 (mtp-110) REVERT: A 175 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7285 (mtp-110) REVERT: A 453 MET cc_start: 0.8994 (mpp) cc_final: 0.8735 (mpt) REVERT: A 716 ASP cc_start: 0.7283 (t0) cc_final: 0.6467 (m-30) REVERT: A 724 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7376 (pt0) REVERT: A 771 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7517 (pt0) REVERT: A 948 VAL cc_start: 0.9081 (t) cc_final: 0.8815 (m) REVERT: A 1093 LYS cc_start: 0.7388 (ttpp) cc_final: 0.6800 (mtpt) REVERT: A 1141 THR cc_start: 0.8935 (m) cc_final: 0.8516 (p) REVERT: A 1277 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7624 (mt-10) REVERT: A 1280 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7587 (mm-30) REVERT: A 1285 MET cc_start: 0.7483 (mtm) cc_final: 0.7068 (mtm) REVERT: A 1309 ASP cc_start: 0.8112 (m-30) cc_final: 0.6968 (p0) REVERT: A 1315 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8347 (mm-30) REVERT: A 1334 ASP cc_start: 0.8681 (m-30) cc_final: 0.8464 (t0) REVERT: A 1345 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8057 (ttp80) REVERT: A 1438 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8758 (t) REVERT: B 65 GLU cc_start: 0.7572 (tt0) cc_final: 0.7284 (tp30) REVERT: B 244 LEU cc_start: 0.7985 (mm) cc_final: 0.7690 (mp) REVERT: B 310 MET cc_start: 0.6477 (mmt) cc_final: 0.6247 (tpt) REVERT: B 348 ARG cc_start: 0.4414 (mtm180) cc_final: 0.2743 (mpp80) REVERT: B 392 ARG cc_start: 0.7064 (mmm-85) cc_final: 0.6851 (mmm-85) REVERT: B 473 MET cc_start: 0.3567 (OUTLIER) cc_final: 0.3143 (tpt) REVERT: B 502 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6909 (mt) REVERT: B 513 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8437 (mm110) REVERT: B 552 MET cc_start: 0.8163 (mmm) cc_final: 0.7880 (mmm) REVERT: B 620 ARG cc_start: 0.7422 (ptp-170) cc_final: 0.6821 (tpm170) REVERT: B 622 LYS cc_start: 0.7626 (mttt) cc_final: 0.7313 (mtmm) REVERT: B 687 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: B 708 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: B 894 ASP cc_start: 0.7198 (m-30) cc_final: 0.6892 (m-30) REVERT: B 936 ASP cc_start: 0.7971 (t0) cc_final: 0.7584 (t0) REVERT: B 948 ILE cc_start: 0.8826 (mp) cc_final: 0.8494 (mt) REVERT: B 953 LEU cc_start: 0.8539 (tt) cc_final: 0.8226 (tm) REVERT: B 1053 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7964 (mp0) REVERT: C 11 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8508 (ptp90) REVERT: C 40 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8504 (mt-10) REVERT: C 75 MET cc_start: 0.8754 (tpp) cc_final: 0.8440 (tpt) REVERT: C 123 ASN cc_start: 0.8444 (t0) cc_final: 0.8118 (t0) REVERT: C 187 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8933 (mttp) REVERT: E 85 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7290 (mm-30) REVERT: E 94 LYS cc_start: 0.7744 (mttt) cc_final: 0.7240 (ptmt) REVERT: E 103 LYS cc_start: 0.8632 (mttm) cc_final: 0.7910 (mtmm) REVERT: E 169 ARG cc_start: 0.8517 (mtt90) cc_final: 0.8185 (mtp85) REVERT: E 192 ARG cc_start: 0.8814 (mmt90) cc_final: 0.8112 (mmm160) REVERT: F 81 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8843 (p) REVERT: F 129 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8437 (mmtp) REVERT: F 149 GLU cc_start: 0.8450 (tt0) cc_final: 0.7808 (mt-10) REVERT: H 27 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: H 78 SER cc_start: 0.9241 (p) cc_final: 0.8870 (t) REVERT: H 106 GLU cc_start: 0.7879 (tp30) cc_final: 0.7594 (tp30) REVERT: H 108 SER cc_start: 0.8372 (t) cc_final: 0.8028 (t) REVERT: J 26 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: K 17 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8272 (p) REVERT: K 20 LYS cc_start: 0.8041 (tttp) cc_final: 0.7794 (tttm) REVERT: K 39 ASP cc_start: 0.8138 (m-30) cc_final: 0.7720 (p0) REVERT: G 73 LYS cc_start: 0.7708 (mttt) cc_final: 0.6810 (tmtp) outliers start: 91 outliers final: 47 residues processed: 407 average time/residue: 1.8678 time to fit residues: 888.1366 Evaluate side-chains 388 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 328 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 7 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 305 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 282 ASN A 311 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1432 GLN B 60 GLN H 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.097341 restraints weight = 34674.686| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.20 r_work: 0.3041 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28454 Z= 0.133 Angle : 0.538 17.429 38621 Z= 0.270 Chirality : 0.043 0.305 4346 Planarity : 0.004 0.055 4826 Dihedral : 11.805 179.888 4223 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.91 % Allowed : 16.77 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3342 helix: 1.12 (0.16), residues: 1178 sheet: -0.42 (0.22), residues: 487 loop : -0.55 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.004 0.001 HIS A 451 PHE 0.026 0.001 PHE A 714 TYR 0.011 0.001 TYR J 44 ARG 0.009 0.000 ARG F 119 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 1088) hydrogen bonds : angle 4.29365 ( 3051) metal coordination : bond 0.00978 ( 22) metal coordination : angle 7.08635 ( 21) covalent geometry : bond 0.00317 (28432) covalent geometry : angle 0.51249 (38600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 342 time to evaluate : 3.275 Fit side-chains REVERT: A 112 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8013 (ttpp) REVERT: A 123 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7709 (mtp-110) REVERT: A 175 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7317 (mtp-110) REVERT: A 453 MET cc_start: 0.8982 (mpp) cc_final: 0.8725 (mpt) REVERT: A 716 ASP cc_start: 0.7292 (t0) cc_final: 0.6487 (m-30) REVERT: A 724 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7370 (pt0) REVERT: A 771 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7381 (pt0) REVERT: A 948 VAL cc_start: 0.9086 (t) cc_final: 0.8822 (m) REVERT: A 1093 LYS cc_start: 0.7426 (ttpp) cc_final: 0.6932 (mtmt) REVERT: A 1141 THR cc_start: 0.8945 (m) cc_final: 0.8529 (p) REVERT: A 1277 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 1280 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7564 (mm-30) REVERT: A 1285 MET cc_start: 0.7482 (mtm) cc_final: 0.7071 (mtm) REVERT: A 1309 ASP cc_start: 0.8095 (m-30) cc_final: 0.6963 (p0) REVERT: A 1315 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8359 (mm-30) REVERT: A 1334 ASP cc_start: 0.8643 (m-30) cc_final: 0.8438 (t0) REVERT: A 1345 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8062 (ttp80) REVERT: A 1398 MET cc_start: 0.9231 (ttp) cc_final: 0.8940 (ttm) REVERT: A 1438 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8722 (t) REVERT: B 65 GLU cc_start: 0.7587 (tt0) cc_final: 0.7291 (tp30) REVERT: B 244 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7756 (mp) REVERT: B 348 ARG cc_start: 0.4447 (mtm180) cc_final: 0.2820 (mpp80) REVERT: B 473 MET cc_start: 0.3496 (OUTLIER) cc_final: 0.3071 (tpt) REVERT: B 502 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6893 (mt) REVERT: B 552 MET cc_start: 0.8177 (mmm) cc_final: 0.7896 (mmm) REVERT: B 620 ARG cc_start: 0.7425 (ptp-170) cc_final: 0.6875 (tpm170) REVERT: B 622 LYS cc_start: 0.7659 (mttt) cc_final: 0.7333 (mtmm) REVERT: B 667 GLN cc_start: 0.6813 (tt0) cc_final: 0.5997 (tm-30) REVERT: B 687 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: B 868 MET cc_start: 0.5505 (mtp) cc_final: 0.4477 (mpt) REVERT: B 894 ASP cc_start: 0.7197 (m-30) cc_final: 0.6853 (m-30) REVERT: B 936 ASP cc_start: 0.8039 (t0) cc_final: 0.7665 (t0) REVERT: B 948 ILE cc_start: 0.8833 (mp) cc_final: 0.8501 (mt) REVERT: B 1053 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7965 (mp0) REVERT: C 11 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8498 (ptp90) REVERT: C 40 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8522 (mt-10) REVERT: C 75 MET cc_start: 0.8747 (tpp) cc_final: 0.8434 (tpt) REVERT: C 187 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8916 (mttp) REVERT: E 85 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7244 (mp0) REVERT: E 94 LYS cc_start: 0.7774 (mttt) cc_final: 0.7267 (ptmt) REVERT: E 103 LYS cc_start: 0.8649 (mttm) cc_final: 0.7916 (mtmm) REVERT: E 169 ARG cc_start: 0.8510 (mtt90) cc_final: 0.8187 (mtp85) REVERT: E 192 ARG cc_start: 0.8814 (mmt90) cc_final: 0.8113 (mmm160) REVERT: F 81 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8886 (p) REVERT: F 129 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8440 (mmtp) REVERT: F 149 GLU cc_start: 0.8458 (tt0) cc_final: 0.7776 (mt-10) REVERT: H 27 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: H 78 SER cc_start: 0.9232 (p) cc_final: 0.8874 (t) REVERT: H 106 GLU cc_start: 0.7881 (tp30) cc_final: 0.7594 (tp30) REVERT: H 108 SER cc_start: 0.8369 (t) cc_final: 0.8025 (t) REVERT: J 26 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7191 (mt0) REVERT: K 17 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8263 (p) REVERT: K 20 LYS cc_start: 0.8026 (tttp) cc_final: 0.7779 (tttm) REVERT: K 39 ASP cc_start: 0.8183 (m-30) cc_final: 0.7777 (p0) REVERT: G 73 LYS cc_start: 0.7738 (mttt) cc_final: 0.6884 (tmtp) outliers start: 86 outliers final: 50 residues processed: 402 average time/residue: 1.5162 time to fit residues: 706.4351 Evaluate side-chains 392 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 330 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain G residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 276 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1432 GLN B 60 GLN H 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095511 restraints weight = 35240.505| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.18 r_work: 0.3015 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28454 Z= 0.186 Angle : 0.578 14.911 38621 Z= 0.289 Chirality : 0.044 0.297 4346 Planarity : 0.004 0.049 4826 Dihedral : 11.852 179.677 4223 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.01 % Allowed : 17.01 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3342 helix: 1.01 (0.16), residues: 1177 sheet: -0.44 (0.22), residues: 492 loop : -0.62 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 31 HIS 0.008 0.001 HIS A 399 PHE 0.029 0.002 PHE A 714 TYR 0.018 0.001 TYR B 431 ARG 0.009 0.000 ARG F 119 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 1088) hydrogen bonds : angle 4.40616 ( 3051) metal coordination : bond 0.00809 ( 22) metal coordination : angle 7.36247 ( 21) covalent geometry : bond 0.00458 (28432) covalent geometry : angle 0.55185 (38600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 327 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8067 (ttpp) REVERT: A 123 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7810 (mtp-110) REVERT: A 175 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7369 (mtp-110) REVERT: A 453 MET cc_start: 0.9028 (mpp) cc_final: 0.8762 (mpt) REVERT: A 716 ASP cc_start: 0.7329 (t0) cc_final: 0.6520 (m-30) REVERT: A 724 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7395 (pt0) REVERT: A 771 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7465 (pt0) REVERT: A 948 VAL cc_start: 0.9156 (t) cc_final: 0.8887 (m) REVERT: A 1039 LYS cc_start: 0.7640 (tptp) cc_final: 0.7376 (tttm) REVERT: A 1141 THR cc_start: 0.8964 (m) cc_final: 0.8520 (p) REVERT: A 1277 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7666 (mt-10) REVERT: A 1280 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7586 (mm-30) REVERT: A 1285 MET cc_start: 0.7577 (mtm) cc_final: 0.7163 (mtm) REVERT: A 1309 ASP cc_start: 0.8094 (m-30) cc_final: 0.7038 (p0) REVERT: A 1315 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8397 (mm-30) REVERT: A 1345 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8175 (ttp80) REVERT: B 60 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7741 (tp40) REVERT: B 65 GLU cc_start: 0.7623 (tt0) cc_final: 0.7333 (tp30) REVERT: B 244 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7800 (mp) REVERT: B 310 MET cc_start: 0.6576 (mmt) cc_final: 0.6317 (tpt) REVERT: B 473 MET cc_start: 0.3509 (OUTLIER) cc_final: 0.3108 (tpt) REVERT: B 502 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6993 (mt) REVERT: B 552 MET cc_start: 0.8213 (mmm) cc_final: 0.7940 (mmm) REVERT: B 620 ARG cc_start: 0.7473 (ptp-170) cc_final: 0.6966 (tpm170) REVERT: B 622 LYS cc_start: 0.7708 (mttt) cc_final: 0.7395 (mtmm) REVERT: B 667 GLN cc_start: 0.6880 (tt0) cc_final: 0.6052 (tm-30) REVERT: B 687 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 894 ASP cc_start: 0.7291 (m-30) cc_final: 0.7047 (m-30) REVERT: B 936 ASP cc_start: 0.8057 (t0) cc_final: 0.7671 (t0) REVERT: B 948 ILE cc_start: 0.8891 (mp) cc_final: 0.8559 (mt) REVERT: B 1053 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8080 (mp0) REVERT: C 11 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8584 (ptp90) REVERT: C 40 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8542 (mt-10) REVERT: C 75 MET cc_start: 0.8781 (tpp) cc_final: 0.8477 (tpt) REVERT: C 187 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8973 (mttp) REVERT: E 85 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7223 (mp0) REVERT: E 94 LYS cc_start: 0.7809 (mttt) cc_final: 0.7316 (ptmt) REVERT: E 103 LYS cc_start: 0.8639 (mttm) cc_final: 0.7905 (mtmm) REVERT: E 169 ARG cc_start: 0.8590 (mtt90) cc_final: 0.8274 (mtp85) REVERT: E 192 ARG cc_start: 0.8824 (mmt90) cc_final: 0.8153 (mmm160) REVERT: F 81 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8857 (p) REVERT: F 129 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8449 (mmtp) REVERT: H 27 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: H 78 SER cc_start: 0.9270 (p) cc_final: 0.8915 (t) REVERT: H 80 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8157 (mtt-85) REVERT: H 106 GLU cc_start: 0.7899 (tp30) cc_final: 0.7617 (tp30) REVERT: H 108 SER cc_start: 0.8379 (t) cc_final: 0.8015 (t) REVERT: J 26 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7197 (mt0) REVERT: K 17 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8301 (p) REVERT: K 20 LYS cc_start: 0.8087 (tttp) cc_final: 0.7851 (tttm) REVERT: K 39 ASP cc_start: 0.8200 (m-30) cc_final: 0.7822 (p0) REVERT: G 73 LYS cc_start: 0.7786 (mttt) cc_final: 0.6904 (tmtp) outliers start: 89 outliers final: 54 residues processed: 390 average time/residue: 1.6102 time to fit residues: 737.9240 Evaluate side-chains 383 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 316 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain G residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 224 optimal weight: 0.5980 chunk 269 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 chunk 307 optimal weight: 0.9980 chunk 333 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 245 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1432 GLN B 60 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN H 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097913 restraints weight = 34411.865| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.19 r_work: 0.3039 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28454 Z= 0.118 Angle : 0.540 13.663 38621 Z= 0.271 Chirality : 0.043 0.319 4346 Planarity : 0.004 0.048 4826 Dihedral : 11.828 179.956 4223 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.71 % Allowed : 17.48 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3342 helix: 1.15 (0.16), residues: 1171 sheet: -0.37 (0.23), residues: 472 loop : -0.52 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 192 HIS 0.004 0.001 HIS A 451 PHE 0.030 0.001 PHE A 714 TYR 0.010 0.001 TYR B 275 ARG 0.009 0.000 ARG F 119 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 1088) hydrogen bonds : angle 4.28936 ( 3051) metal coordination : bond 0.00637 ( 22) metal coordination : angle 6.76923 ( 21) covalent geometry : bond 0.00275 (28432) covalent geometry : angle 0.51605 (38600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 333 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7987 (ttpp) REVERT: A 123 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7693 (mtp-110) REVERT: A 175 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7355 (mtp-110) REVERT: A 453 MET cc_start: 0.9001 (mpp) cc_final: 0.8701 (mpt) REVERT: A 716 ASP cc_start: 0.7197 (t0) cc_final: 0.6401 (m-30) REVERT: A 724 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7335 (pt0) REVERT: A 771 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7361 (pt0) REVERT: A 948 VAL cc_start: 0.9119 (t) cc_final: 0.8863 (m) REVERT: A 1039 LYS cc_start: 0.7509 (tptp) cc_final: 0.7256 (tttm) REVERT: A 1093 LYS cc_start: 0.7407 (ttpp) cc_final: 0.6821 (mtmm) REVERT: A 1141 THR cc_start: 0.8976 (m) cc_final: 0.8545 (p) REVERT: A 1277 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 1280 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7541 (mm-30) REVERT: A 1285 MET cc_start: 0.7528 (mtm) cc_final: 0.7089 (mtm) REVERT: A 1309 ASP cc_start: 0.8074 (m-30) cc_final: 0.6993 (p0) REVERT: A 1315 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8364 (mm-30) REVERT: A 1334 ASP cc_start: 0.8660 (m-30) cc_final: 0.8445 (t0) REVERT: A 1345 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8087 (ttp80) REVERT: A 1438 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8712 (t) REVERT: B 65 GLU cc_start: 0.7595 (tt0) cc_final: 0.7349 (tp30) REVERT: B 244 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7824 (mp) REVERT: B 310 MET cc_start: 0.6540 (mmt) cc_final: 0.6293 (tpt) REVERT: B 396 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6856 (t0) REVERT: B 473 MET cc_start: 0.3437 (OUTLIER) cc_final: 0.3034 (tpt) REVERT: B 502 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6942 (mt) REVERT: B 552 MET cc_start: 0.8166 (mmm) cc_final: 0.7897 (mmm) REVERT: B 620 ARG cc_start: 0.7447 (ptp-170) cc_final: 0.6931 (tpm170) REVERT: B 622 LYS cc_start: 0.7625 (mttt) cc_final: 0.7316 (mtmm) REVERT: B 667 GLN cc_start: 0.6814 (tt0) cc_final: 0.6012 (tm-30) REVERT: B 708 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: B 894 ASP cc_start: 0.7198 (m-30) cc_final: 0.6877 (m-30) REVERT: B 936 ASP cc_start: 0.8004 (t0) cc_final: 0.7625 (t0) REVERT: B 948 ILE cc_start: 0.8830 (mp) cc_final: 0.8503 (mt) REVERT: B 1053 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7977 (mp0) REVERT: C 11 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8535 (ptp90) REVERT: C 40 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8506 (mt-10) REVERT: C 75 MET cc_start: 0.8759 (tpp) cc_final: 0.8453 (tpt) REVERT: C 187 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8920 (mttp) REVERT: E 85 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7197 (mp0) REVERT: E 94 LYS cc_start: 0.7764 (mttt) cc_final: 0.7257 (ptmt) REVERT: E 103 LYS cc_start: 0.8650 (mttm) cc_final: 0.7933 (mtmm) REVERT: E 169 ARG cc_start: 0.8505 (mtt90) cc_final: 0.8176 (mtp85) REVERT: E 192 ARG cc_start: 0.8806 (mmt90) cc_final: 0.8112 (mmm160) REVERT: F 81 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8837 (p) REVERT: F 129 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8417 (mmtp) REVERT: F 149 GLU cc_start: 0.8467 (tt0) cc_final: 0.7780 (mt-10) REVERT: H 27 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: H 78 SER cc_start: 0.9123 (p) cc_final: 0.8786 (t) REVERT: H 106 GLU cc_start: 0.7873 (tp30) cc_final: 0.7580 (tp30) REVERT: H 108 SER cc_start: 0.8364 (t) cc_final: 0.8017 (t) REVERT: J 26 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7167 (mt0) REVERT: K 17 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8261 (p) REVERT: K 20 LYS cc_start: 0.8021 (tttp) cc_final: 0.7778 (tttm) REVERT: K 39 ASP cc_start: 0.8175 (m-30) cc_final: 0.7796 (p0) REVERT: G 73 LYS cc_start: 0.7730 (mttt) cc_final: 0.6865 (tmtp) outliers start: 80 outliers final: 49 residues processed: 393 average time/residue: 1.6013 time to fit residues: 730.6384 Evaluate side-chains 385 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 323 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain G residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 17 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 302 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 288 optimal weight: 0.6980 chunk 233 optimal weight: 2.9990 chunk 337 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1432 GLN B1013 ASN F 78 GLN H 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.096518 restraints weight = 34546.037| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.19 r_work: 0.3018 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28454 Z= 0.166 Angle : 0.559 13.791 38621 Z= 0.281 Chirality : 0.044 0.317 4346 Planarity : 0.004 0.049 4826 Dihedral : 11.828 179.910 4223 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.57 % Allowed : 17.92 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3342 helix: 1.07 (0.16), residues: 1177 sheet: -0.33 (0.22), residues: 477 loop : -0.57 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.005 0.001 HIS A 399 PHE 0.031 0.001 PHE A 714 TYR 0.014 0.001 TYR H 93 ARG 0.009 0.000 ARG F 119 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 1088) hydrogen bonds : angle 4.32997 ( 3051) metal coordination : bond 0.00655 ( 22) metal coordination : angle 6.81309 ( 21) covalent geometry : bond 0.00406 (28432) covalent geometry : angle 0.53604 (38600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 316 time to evaluate : 3.240 Fit side-chains revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8002 (ttpp) REVERT: A 123 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7688 (mtp-110) REVERT: A 175 ARG cc_start: 0.8001 (mtm-85) cc_final: 0.7357 (mtp-110) REVERT: A 453 MET cc_start: 0.9010 (mpp) cc_final: 0.8751 (mpt) REVERT: A 716 ASP cc_start: 0.7159 (t0) cc_final: 0.6389 (m-30) REVERT: A 724 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7332 (pt0) REVERT: A 771 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7434 (pt0) REVERT: A 924 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7675 (mmtm) REVERT: A 948 VAL cc_start: 0.9131 (t) cc_final: 0.8874 (m) REVERT: A 1039 LYS cc_start: 0.7605 (tptp) cc_final: 0.7336 (tttm) REVERT: A 1093 LYS cc_start: 0.7463 (ttpp) cc_final: 0.6871 (mtmm) REVERT: A 1141 THR cc_start: 0.8985 (m) cc_final: 0.8550 (p) REVERT: A 1277 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 1280 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7524 (mm-30) REVERT: A 1285 MET cc_start: 0.7533 (mtm) cc_final: 0.7113 (mtm) REVERT: A 1309 ASP cc_start: 0.8082 (m-30) cc_final: 0.6991 (p0) REVERT: A 1315 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8363 (mm-30) REVERT: A 1334 ASP cc_start: 0.8676 (m-30) cc_final: 0.8463 (t0) REVERT: A 1345 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8097 (ttp80) REVERT: A 1398 MET cc_start: 0.9124 (ttt) cc_final: 0.8906 (ttm) REVERT: B 65 GLU cc_start: 0.7593 (tt0) cc_final: 0.7342 (tp30) REVERT: B 244 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7891 (mp) REVERT: B 434 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6804 (ppp80) REVERT: B 473 MET cc_start: 0.3553 (OUTLIER) cc_final: 0.3166 (tpt) REVERT: B 552 MET cc_start: 0.8170 (mmm) cc_final: 0.7905 (mmm) REVERT: B 595 ARG cc_start: 0.7240 (ttp-170) cc_final: 0.7032 (tmm160) REVERT: B 620 ARG cc_start: 0.7450 (ptp-170) cc_final: 0.6937 (tpm170) REVERT: B 622 LYS cc_start: 0.7617 (mttt) cc_final: 0.7302 (mtmm) REVERT: B 667 GLN cc_start: 0.6846 (tt0) cc_final: 0.6035 (tm-30) REVERT: B 687 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 708 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: B 729 ILE cc_start: 0.8801 (mm) cc_final: 0.8550 (mp) REVERT: B 894 ASP cc_start: 0.7265 (m-30) cc_final: 0.7000 (m-30) REVERT: B 936 ASP cc_start: 0.7958 (t0) cc_final: 0.7567 (t0) REVERT: B 948 ILE cc_start: 0.8831 (mp) cc_final: 0.8511 (mt) REVERT: B 1053 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8023 (mp0) REVERT: C 11 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8544 (ptp90) REVERT: C 40 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8549 (mt-10) REVERT: C 75 MET cc_start: 0.8766 (tpp) cc_final: 0.8454 (tpt) REVERT: C 187 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8936 (mttp) REVERT: E 85 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7217 (mp0) REVERT: E 94 LYS cc_start: 0.7778 (mttt) cc_final: 0.7275 (ptmt) REVERT: E 103 LYS cc_start: 0.8661 (mttm) cc_final: 0.7934 (mtmm) REVERT: E 169 ARG cc_start: 0.8515 (mtt90) cc_final: 0.8187 (mtp85) REVERT: E 192 ARG cc_start: 0.8797 (mmt90) cc_final: 0.8106 (mmm160) REVERT: F 81 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8840 (p) REVERT: F 129 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8408 (mmtp) REVERT: H 27 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: H 78 SER cc_start: 0.9180 (p) cc_final: 0.8833 (t) REVERT: H 80 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8095 (mtt-85) REVERT: H 106 GLU cc_start: 0.7844 (tp30) cc_final: 0.7557 (tp30) REVERT: H 108 SER cc_start: 0.8374 (t) cc_final: 0.8017 (t) REVERT: J 26 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7181 (mt0) REVERT: K 17 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8257 (p) REVERT: K 20 LYS cc_start: 0.8030 (tttp) cc_final: 0.7783 (tttm) REVERT: K 39 ASP cc_start: 0.8206 (m-30) cc_final: 0.7853 (p0) REVERT: G 73 LYS cc_start: 0.7742 (mttt) cc_final: 0.6888 (tmtp) outliers start: 76 outliers final: 53 residues processed: 374 average time/residue: 1.5586 time to fit residues: 673.3716 Evaluate side-chains 380 residues out of total 2966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 313 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain G residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 243 optimal weight: 0.9980 chunk 228 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 327 optimal weight: 6.9990 chunk 250 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN A1432 GLN B1013 ASN H 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.132095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.097506 restraints weight = 34657.642| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.20 r_work: 0.3033 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28454 Z= 0.132 Angle : 0.545 13.535 38621 Z= 0.273 Chirality : 0.043 0.301 4346 Planarity : 0.004 0.047 4826 Dihedral : 11.822 179.986 4223 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.54 % Allowed : 17.99 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3342 helix: 1.14 (0.16), residues: 1177 sheet: -0.36 (0.22), residues: 482 loop : -0.54 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 192 HIS 0.004 0.001 HIS A 451 PHE 0.031 0.001 PHE A 714 TYR 0.013 0.001 TYR H 93 ARG 0.009 0.000 ARG F 119 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 1088) hydrogen bonds : angle 4.27295 ( 3051) metal coordination : bond 0.00620 ( 22) metal coordination : angle 6.66656 ( 21) covalent geometry : bond 0.00317 (28432) covalent geometry : angle 0.52203 (38600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21771.39 seconds wall clock time: 373 minutes 18.56 seconds (22398.56 seconds total)