Starting phenix.real_space_refine on Thu May 15 21:11:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wah_32385/05_2025/7wah_32385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wah_32385/05_2025/7wah_32385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wah_32385/05_2025/7wah_32385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wah_32385/05_2025/7wah_32385.map" model { file = "/net/cci-nas-00/data/ceres_data/7wah_32385/05_2025/7wah_32385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wah_32385/05_2025/7wah_32385.cif" } resolution = 2.45 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= -0.006 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 61 5.49 5 S 56 5.16 5 C 8130 2.51 5 N 2348 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13217 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 8, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 17} Chain: "D" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 492 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 18} Chain: "A" Number of atoms: 11895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1473, 11895 Classifications: {'peptide': 1473} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 80, 'TRANS': 1392} Chain breaks: 9 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2022 SG CYS A 86 48.068 76.770 17.624 1.00 74.00 S ATOM 2268 SG CYS A 115 48.227 74.846 14.354 1.00 96.17 S ATOM 2330 SG CYS A 123 50.567 73.956 17.218 1.00 70.51 S ATOM 2354 SG CYS A 126 46.859 73.185 17.504 1.00 60.85 S ATOM 4438 SG CYS A 463 42.328 90.654 47.896 1.00 71.44 S ATOM 4500 SG CYS A 472 42.013 91.085 44.076 1.00 57.69 S ATOM 4514 SG CYS A 474 45.077 92.311 45.949 1.00 59.04 S ATOM 4536 SG CYS A 477 44.492 88.593 45.583 1.00 60.88 S ATOM 6350 SG CYS A 706 31.561 96.931 73.123 1.00 95.71 S ATOM 6365 SG CYS A 708 34.219 98.389 75.450 1.00 77.27 S ATOM 6387 SG CYS A 711 35.034 95.356 73.340 1.00 74.09 S ATOM 8250 SG CYS A 965 30.141 81.704 108.993 1.00 40.04 S ATOM 11040 SG CYS A1312 28.017 82.679 105.973 1.00 54.59 S ATOM 11103 SG CYS A1342 29.737 85.304 108.209 1.00 31.20 S ATOM 11121 SG CYS A1345 31.771 83.230 105.905 1.00 60.12 S Time building chain proxies: 8.67, per 1000 atoms: 0.66 Number of scatterers: 13217 At special positions: 0 Unit cell: (84.66, 123.67, 172.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 56 16.00 P 61 15.00 O 2618 8.00 N 2348 7.00 C 8130 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: 3.23 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 123 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 115 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 477 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 472 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 711 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 706 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1342 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 965 " Number of angles added : 21 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 23 sheets defined 28.5% alpha, 29.7% beta 20 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 removed outlier: 3.547A pdb=" N GLY A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 57 through 76 removed outlier: 3.705A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.928A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 167' Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 300 removed outlier: 5.706A pdb=" N SER A 296 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 340 through 343 removed outlier: 3.626A pdb=" N LYS A 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 344 through 364 Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 removed outlier: 3.654A pdb=" N ARG A 598 " --> pdb=" O TRP A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.540A pdb=" N GLU A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 649 Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.951A pdb=" N ILE A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.579A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'A' and resid 1163 through 1168 Processing helix chain 'A' and resid 1179 through 1183 Processing helix chain 'A' and resid 1231 through 1247 Processing helix chain 'A' and resid 1254 through 1258 Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1306 through 1310 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 4.196A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1426 removed outlier: 4.172A pdb=" N THR A1423 " --> pdb=" O HIS A1419 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1549 Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1588 through 1594 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.737A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 5.027A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485 removed outlier: 5.027A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 611 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA8, first strand: chain 'A' and resid 497 through 504 removed outlier: 10.417A pdb=" N GLU A 497 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN A 518 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 11.024A pdb=" N ARG A 499 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N LEU A 516 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N ARG A 501 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N GLY A 514 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG A 503 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.009A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.009A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 641 through 642 removed outlier: 3.535A pdb=" N VAL A 656 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB4, first strand: chain 'A' and resid 739 through 744 removed outlier: 11.509A pdb=" N PHE A 739 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N LYS A 756 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N HIS A 741 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LYS A 754 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA A 743 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1558 through 1559 removed outlier: 6.676A pdb=" N VAL A 861 " --> pdb=" O TRP A1600 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB7, first strand: chain 'A' and resid 938 through 939 removed outlier: 6.884A pdb=" N ILE A 943 " --> pdb=" O LEU A1364 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A1453 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR A 901 " --> pdb=" O SER A1453 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER A1455 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 899 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU A1457 " --> pdb=" O CYS A 897 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS A 897 " --> pdb=" O GLU A1457 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA A1459 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 895 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU A1461 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY A 893 " --> pdb=" O GLU A1461 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1357 through 1359 removed outlier: 6.492A pdb=" N SER A1453 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR A 901 " --> pdb=" O SER A1453 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER A1455 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 899 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU A1457 " --> pdb=" O CYS A 897 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS A 897 " --> pdb=" O GLU A1457 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA A1459 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 895 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU A1461 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY A 893 " --> pdb=" O GLU A1461 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.105A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 932 through 933 removed outlier: 6.884A pdb=" N LYS A 932 " --> pdb=" O THR A1444 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AC3, first strand: chain 'A' and resid 991 through 994 removed outlier: 6.826A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1092 through 1098 removed outlier: 6.348A pdb=" N SER A1080 " --> pdb=" O GLN A1076 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN A1076 " --> pdb=" O SER A1080 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR A1082 " --> pdb=" O ILE A1074 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG A1122 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU A1046 " --> pdb=" O ARG A1122 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER A1124 " --> pdb=" O LYS A1044 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS A1044 " --> pdb=" O SER A1124 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR A1126 " --> pdb=" O PHE A1042 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A1042 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 19.741A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.425A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP A1221 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 11.323A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 47.243A pdb=" N ILE A1002 " --> pdb=" O CYS A1119 " (cutoff:3.500A) removed outlier: 40.819A pdb=" N VAL A1121 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 34.447A pdb=" N LYS A1004 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 27.522A pdb=" N ASP A1123 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 22.294A pdb=" N SER A1006 " --> pdb=" O ASP A1123 " (cutoff:3.500A) removed outlier: 16.384A pdb=" N ARG A1125 " --> pdb=" O SER A1006 " (cutoff:3.500A) removed outlier: 13.328A pdb=" N THR A1008 " --> pdb=" O ARG A1125 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLN A1127 " --> pdb=" O THR A1008 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1156 through 1159 removed outlier: 7.316A pdb=" N GLU A1196 " --> pdb=" O LYS A1189 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 3.79 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: 4055 1.34 - 1.46: 2665 1.46 - 1.58: 6730 1.58 - 1.70: 121 1.70 - 1.82: 80 Bond restraints: 13651 Sorted by residual: bond pdb=" N PRO A1138 " pdb=" CA PRO A1138 " ideal model delta sigma weight residual 1.468 1.479 -0.011 7.90e-03 1.60e+04 2.04e+00 bond pdb=" CA GLU A1196 " pdb=" CB GLU A1196 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.17e+00 bond pdb=" N PRO A1153 " pdb=" CA PRO A1153 " ideal model delta sigma weight residual 1.469 1.481 -0.013 1.28e-02 6.10e+03 9.94e-01 bond pdb=" N ASP A1315 " pdb=" CA ASP A1315 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.72e-01 bond pdb=" CB PRO A1368 " pdb=" CG PRO A1368 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.51e-01 ... (remaining 13646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 17768 1.02 - 2.05: 740 2.05 - 3.07: 146 3.07 - 4.09: 36 4.09 - 5.12: 6 Bond angle restraints: 18696 Sorted by residual: angle pdb=" C2' U R 1 " pdb=" C1' U R 1 " pdb=" N1 U R 1 " ideal model delta sigma weight residual 112.00 117.12 -5.12 1.50e+00 4.44e-01 1.16e+01 angle pdb=" O4' G R 19 " pdb=" C1' G R 19 " pdb=" N9 G R 19 " ideal model delta sigma weight residual 108.20 113.04 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" N ILE A1424 " pdb=" CA ILE A1424 " pdb=" C ILE A1424 " ideal model delta sigma weight residual 112.80 109.62 3.18 1.15e+00 7.56e-01 7.65e+00 angle pdb=" N GLY A 58 " pdb=" CA GLY A 58 " pdb=" C GLY A 58 " ideal model delta sigma weight residual 114.66 111.27 3.39 1.24e+00 6.50e-01 7.46e+00 angle pdb=" N GLY A 641 " pdb=" CA GLY A 641 " pdb=" C GLY A 641 " ideal model delta sigma weight residual 112.14 115.47 -3.33 1.29e+00 6.01e-01 6.66e+00 ... (remaining 18691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 7888 23.25 - 46.51: 290 46.51 - 69.76: 118 69.76 - 93.01: 19 93.01 - 116.27: 2 Dihedral angle restraints: 8317 sinusoidal: 4076 harmonic: 4241 Sorted by residual: dihedral pdb=" O4' A R 38 " pdb=" C1' A R 38 " pdb=" N9 A R 38 " pdb=" C4 A R 38 " ideal model delta sinusoidal sigma weight residual 68.00 137.16 -69.16 1 1.70e+01 3.46e-03 2.14e+01 dihedral pdb=" CA ASN A 640 " pdb=" C ASN A 640 " pdb=" N GLY A 641 " pdb=" CA GLY A 641 " ideal model delta harmonic sigma weight residual 180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" O4' A R 12 " pdb=" C1' A R 12 " pdb=" N9 A R 12 " pdb=" C4 A R 12 " ideal model delta sinusoidal sigma weight residual -106.00 -156.28 50.28 1 1.70e+01 3.46e-03 1.20e+01 ... (remaining 8314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1667 0.049 - 0.099: 278 0.099 - 0.148: 63 0.148 - 0.197: 0 0.197 - 0.247: 2 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1' G R 19 " pdb=" O4' G R 19 " pdb=" C2' G R 19 " pdb=" N9 G R 19 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1' U R 1 " pdb=" O4' U R 1 " pdb=" C2' U R 1 " pdb=" N1 U R 1 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE A 628 " pdb=" N ILE A 628 " pdb=" C ILE A 628 " pdb=" CB ILE A 628 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 2007 not shown) Planarity restraints: 2203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U R 1 " 0.038 2.00e-02 2.50e+03 1.98e-02 8.78e+00 pdb=" N1 U R 1 " -0.043 2.00e-02 2.50e+03 pdb=" C2 U R 1 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U R 1 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U R 1 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U R 1 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U R 1 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U R 1 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U R 1 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO A 904 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G R 19 " 0.028 2.00e-02 2.50e+03 1.33e-02 5.28e+00 pdb=" N9 G R 19 " -0.035 2.00e-02 2.50e+03 pdb=" C8 G R 19 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G R 19 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G R 19 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G R 19 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G R 19 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G R 19 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G R 19 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G R 19 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G R 19 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G R 19 " -0.001 2.00e-02 2.50e+03 ... (remaining 2200 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2356 2.77 - 3.30: 12038 3.30 - 3.84: 22979 3.84 - 4.37: 28609 4.37 - 4.90: 46429 Nonbonded interactions: 112411 Sorted by model distance: nonbonded pdb=" OP1 U R 16 " pdb=" OG SER A 564 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR A1081 " pdb=" OE1 GLN A1105 " model vdw 2.262 3.040 nonbonded pdb=" NE2 HIS A 931 " pdb=" OG1 THR A1444 " model vdw 2.263 3.120 nonbonded pdb=" O ALA A 288 " pdb=" OG SER A 291 " model vdw 2.271 3.040 nonbonded pdb=" OP1 U R 25 " pdb=" OG SER A 948 " model vdw 2.278 3.040 ... (remaining 112406 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: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 40.550 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13667 Z= 0.116 Angle : 0.511 5.117 18717 Z= 0.285 Chirality : 0.039 0.247 2010 Planarity : 0.004 0.070 2203 Dihedral : 14.178 116.269 5581 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.55 % Allowed : 3.52 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1453 helix: 0.93 (0.28), residues: 353 sheet: 0.51 (0.29), residues: 290 loop : -0.20 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1600 HIS 0.003 0.001 HIS A 865 PHE 0.017 0.001 PHE A 757 TYR 0.010 0.001 TYR A1209 ARG 0.003 0.000 ARG A1356 Details of bonding type rmsd hydrogen bonds : bond 0.16084 ( 470) hydrogen bonds : angle 6.62964 ( 1316) metal coordination : bond 0.01017 ( 16) metal coordination : angle 1.57217 ( 21) covalent geometry : bond 0.00229 (13651) covalent geometry : angle 0.50862 (18696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 243 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8359 (mt-10) REVERT: A 28 LYS cc_start: 0.6838 (ttmt) cc_final: 0.6532 (ttpt) REVERT: A 100 GLN cc_start: 0.6771 (mt0) cc_final: 0.6570 (mt0) REVERT: A 158 LYS cc_start: 0.7591 (mmtt) cc_final: 0.5996 (ptpp) REVERT: A 165 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7826 (mttp) REVERT: A 179 LYS cc_start: 0.7538 (tptm) cc_final: 0.7245 (mttp) REVERT: A 209 LYS cc_start: 0.7904 (mttp) cc_final: 0.7542 (mtmp) REVERT: A 277 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7674 (mptt) REVERT: A 423 GLU cc_start: 0.6971 (pt0) cc_final: 0.6678 (pm20) REVERT: A 559 MET cc_start: 0.8379 (mmt) cc_final: 0.8158 (mmt) REVERT: A 577 TYR cc_start: 0.7593 (p90) cc_final: 0.7382 (p90) REVERT: A 611 ASN cc_start: 0.6104 (m110) cc_final: 0.5631 (p0) REVERT: A 692 MET cc_start: 0.5767 (ptm) cc_final: 0.4962 (ttm) REVERT: A 787 GLU cc_start: 0.7719 (pt0) cc_final: 0.6354 (mm-30) REVERT: A 1000 LYS cc_start: 0.7652 (mptt) cc_final: 0.7353 (tmtp) REVERT: A 1041 ARG cc_start: 0.7619 (mtm180) cc_final: 0.7020 (mtp-110) REVERT: A 1132 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6541 (pm20) REVERT: A 1194 LYS cc_start: 0.7130 (mmmt) cc_final: 0.6878 (mmmt) outliers start: 7 outliers final: 4 residues processed: 249 average time/residue: 1.5309 time to fit residues: 409.7026 Evaluate side-chains 141 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1350 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0060 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 0.0170 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.0270 chunk 119 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.2292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 30 ASN A 170 GLN A 306 HIS A 626 HIS A1018 GLN A1084 ASN A1246 ASN A1476 GLN ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.183236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158123 restraints weight = 15828.155| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.64 r_work: 0.3774 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13667 Z= 0.107 Angle : 0.517 6.177 18717 Z= 0.277 Chirality : 0.040 0.306 2010 Planarity : 0.004 0.066 2203 Dihedral : 16.128 114.037 2553 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.95 % Allowed : 10.78 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1453 helix: 1.33 (0.28), residues: 362 sheet: 0.41 (0.28), residues: 302 loop : 0.00 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1600 HIS 0.005 0.001 HIS A1483 PHE 0.011 0.001 PHE A 757 TYR 0.011 0.001 TYR A 591 ARG 0.006 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 470) hydrogen bonds : angle 5.15019 ( 1316) metal coordination : bond 0.01123 ( 16) metal coordination : angle 1.97069 ( 21) covalent geometry : bond 0.00220 (13651) covalent geometry : angle 0.51329 (18696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8254 (mt-10) REVERT: A 28 LYS cc_start: 0.6839 (ttmt) cc_final: 0.6562 (ttpt) REVERT: A 47 LYS cc_start: 0.6296 (tmtt) cc_final: 0.5896 (tptp) REVERT: A 100 GLN cc_start: 0.6823 (mt0) cc_final: 0.6592 (mt0) REVERT: A 158 LYS cc_start: 0.7664 (mmtt) cc_final: 0.5977 (ptpp) REVERT: A 165 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7879 (mttp) REVERT: A 179 LYS cc_start: 0.7800 (tptm) cc_final: 0.7154 (mttp) REVERT: A 209 LYS cc_start: 0.8007 (mttp) cc_final: 0.7618 (mtmp) REVERT: A 213 GLU cc_start: 0.7819 (mp0) cc_final: 0.7398 (mp0) REVERT: A 215 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7603 (mtt90) REVERT: A 423 GLU cc_start: 0.7363 (pt0) cc_final: 0.6860 (pm20) REVERT: A 584 ASP cc_start: 0.7827 (t0) cc_final: 0.7573 (t0) REVERT: A 692 MET cc_start: 0.5824 (ptm) cc_final: 0.4815 (ttm) REVERT: A 787 GLU cc_start: 0.7737 (pt0) cc_final: 0.6361 (mm-30) REVERT: A 798 ASP cc_start: 0.7669 (m-30) cc_final: 0.7375 (m-30) REVERT: A 849 LYS cc_start: 0.6927 (tptp) cc_final: 0.6593 (tmtt) REVERT: A 894 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6930 (mmtt) REVERT: A 1000 LYS cc_start: 0.7581 (mptt) cc_final: 0.6976 (tmmm) REVERT: A 1041 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7001 (mtp-110) REVERT: A 1076 GLN cc_start: 0.6811 (tt0) cc_final: 0.6120 (tm130) REVERT: A 1115 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5875 (pp20) REVERT: A 1132 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6579 (pm20) REVERT: A 1194 LYS cc_start: 0.7333 (mmmt) cc_final: 0.7052 (mmmt) REVERT: A 1300 MET cc_start: 0.7466 (mmt) cc_final: 0.7258 (mmt) REVERT: A 1522 TRP cc_start: 0.6400 (m-10) cc_final: 0.6117 (m-10) outliers start: 25 outliers final: 7 residues processed: 167 average time/residue: 1.5559 time to fit residues: 279.9582 Evaluate side-chains 142 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.176705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150754 restraints weight = 16027.625| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.67 r_work: 0.3692 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13667 Z= 0.223 Angle : 0.628 6.936 18717 Z= 0.333 Chirality : 0.046 0.337 2010 Planarity : 0.005 0.063 2203 Dihedral : 16.151 112.431 2551 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.81 % Allowed : 12.27 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1453 helix: 1.05 (0.28), residues: 348 sheet: 0.28 (0.28), residues: 311 loop : -0.17 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1600 HIS 0.006 0.001 HIS A1429 PHE 0.024 0.002 PHE A 757 TYR 0.013 0.002 TYR A 458 ARG 0.005 0.001 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 470) hydrogen bonds : angle 5.30517 ( 1316) metal coordination : bond 0.00773 ( 16) metal coordination : angle 2.20246 ( 21) covalent geometry : bond 0.00504 (13651) covalent geometry : angle 0.62420 (18696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.467 Fit side-chains REVERT: A 13 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8351 (mt-10) REVERT: A 28 LYS cc_start: 0.6970 (ttmt) cc_final: 0.6563 (ttpt) REVERT: A 108 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.5631 (mtt-85) REVERT: A 158 LYS cc_start: 0.7703 (mmtt) cc_final: 0.6009 (ptpp) REVERT: A 165 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7940 (mttp) REVERT: A 179 LYS cc_start: 0.7879 (tptm) cc_final: 0.7322 (mttp) REVERT: A 209 LYS cc_start: 0.7956 (mttp) cc_final: 0.7530 (mtmp) REVERT: A 213 GLU cc_start: 0.7992 (mp0) cc_final: 0.7557 (mp0) REVERT: A 277 LYS cc_start: 0.7973 (mtpm) cc_final: 0.7472 (mptt) REVERT: A 423 GLU cc_start: 0.7391 (pt0) cc_final: 0.6613 (pm20) REVERT: A 572 MET cc_start: 0.7947 (ttp) cc_final: 0.7580 (tmm) REVERT: A 584 ASP cc_start: 0.7924 (t0) cc_final: 0.7597 (t70) REVERT: A 651 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7190 (ptt180) REVERT: A 692 MET cc_start: 0.5843 (ptm) cc_final: 0.4884 (ttp) REVERT: A 849 LYS cc_start: 0.7090 (tptp) cc_final: 0.6733 (tmtt) REVERT: A 1000 LYS cc_start: 0.7626 (mptt) cc_final: 0.6928 (tmmm) REVERT: A 1041 ARG cc_start: 0.7878 (mtm180) cc_final: 0.7047 (mtp-110) REVERT: A 1115 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5807 (pp20) REVERT: A 1132 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6632 (pm20) REVERT: A 1261 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8070 (p) REVERT: A 1305 MET cc_start: 0.6896 (ttm) cc_final: 0.6680 (ttm) REVERT: A 1367 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.6242 (p0) outliers start: 36 outliers final: 15 residues processed: 155 average time/residue: 1.4398 time to fit residues: 241.8306 Evaluate side-chains 146 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1313 HIS Chi-restraints excluded: chain A residue 1345 CYS Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1444 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0181 > 50: distance: 38 - 92: 28.957 distance: 41 - 89: 10.067 distance: 68 - 72: 16.963 distance: 72 - 73: 12.866 distance: 73 - 74: 6.735 distance: 73 - 76: 17.359 distance: 74 - 75: 23.345 distance: 74 - 81: 34.116 distance: 76 - 77: 8.869 distance: 77 - 78: 9.387 distance: 78 - 79: 12.074 distance: 78 - 80: 19.725 distance: 81 - 82: 14.121 distance: 82 - 83: 3.681 distance: 82 - 85: 21.852 distance: 83 - 84: 15.343 distance: 83 - 89: 6.962 distance: 85 - 86: 24.332 distance: 86 - 87: 21.387 distance: 86 - 88: 19.101 distance: 89 - 90: 8.738 distance: 90 - 91: 15.454 distance: 90 - 93: 14.861 distance: 91 - 92: 12.988 distance: 91 - 97: 6.249 distance: 93 - 94: 7.076 distance: 94 - 95: 17.750 distance: 94 - 96: 12.275 distance: 97 - 98: 11.797 distance: 97 - 196: 21.069 distance: 98 - 99: 13.151 distance: 98 - 101: 10.893 distance: 99 - 100: 17.095 distance: 99 - 104: 10.395 distance: 100 - 193: 17.451 distance: 101 - 102: 23.338 distance: 101 - 103: 16.605 distance: 104 - 105: 10.609 distance: 105 - 106: 10.507 distance: 105 - 108: 8.497 distance: 106 - 107: 18.833 distance: 106 - 115: 7.415 distance: 108 - 109: 13.929 distance: 109 - 110: 3.293 distance: 109 - 111: 7.920 distance: 110 - 112: 10.765 distance: 111 - 113: 6.292 distance: 112 - 114: 15.243 distance: 113 - 114: 11.034 distance: 115 - 116: 15.887 distance: 116 - 117: 7.337 distance: 116 - 119: 9.436 distance: 117 - 118: 12.551 distance: 117 - 124: 4.455 distance: 119 - 120: 36.294 distance: 120 - 121: 24.499 distance: 121 - 122: 25.507 distance: 121 - 123: 23.177 distance: 124 - 125: 18.314 distance: 125 - 126: 4.120 distance: 125 - 128: 8.409 distance: 126 - 127: 16.350 distance: 126 - 130: 18.941 distance: 128 - 129: 20.255 distance: 130 - 131: 14.276 distance: 131 - 132: 13.540 distance: 131 - 134: 21.460 distance: 132 - 133: 21.463 distance: 132 - 138: 38.325 distance: 134 - 135: 22.751 distance: 135 - 136: 7.783 distance: 135 - 137: 17.187 distance: 138 - 144: 33.932 distance: 139 - 140: 17.359 distance: 139 - 142: 12.100 distance: 140 - 141: 21.931 distance: 140 - 145: 27.046 distance: 142 - 143: 23.860 distance: 143 - 144: 23.718 distance: 145 - 146: 22.530 distance: 146 - 147: 12.308 distance: 146 - 149: 30.047 distance: 147 - 148: 25.393 distance: 147 - 154: 5.113 distance: 149 - 150: 31.154 distance: 150 - 151: 13.077 distance: 151 - 152: 18.245 distance: 151 - 153: 20.675