Starting phenix.real_space_refine on Mon Dec 30 14:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wml_37655/12_2024/8wml_37655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wml_37655/12_2024/8wml_37655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wml_37655/12_2024/8wml_37655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wml_37655/12_2024/8wml_37655.map" model { file = "/net/cci-nas-00/data/ceres_data/8wml_37655/12_2024/8wml_37655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wml_37655/12_2024/8wml_37655.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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 37 5.49 5 S 59 5.16 5 C 8257 2.51 5 N 2352 2.21 5 O 2574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13283 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 801 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Chain: "A" Number of atoms: 11970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1480, 11970 Classifications: {'peptide': 1480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 80, 'TRANS': 1399} Chain breaks: 10 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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 1751 SG CYS A 115 44.200 70.724 13.004 1.00131.49 S ATOM 1837 SG CYS A 126 42.456 70.766 16.086 1.00112.45 S ATOM 3980 SG CYS A 463 50.942 47.998 41.997 1.00 81.09 S ATOM 4042 SG CYS A 472 51.301 48.738 37.726 1.00 74.56 S ATOM 4078 SG CYS A 477 47.887 49.681 39.900 1.00 60.45 S ATOM 5793 SG CYS A 706 61.570 37.416 67.738 1.00 58.75 S ATOM 5808 SG CYS A 708 59.314 35.586 68.966 1.00 45.92 S ATOM 5830 SG CYS A 711 58.183 38.707 67.815 1.00 63.61 S ATOM 7691 SG CYS A 965 55.254 41.191 107.546 1.00 39.84 S ATOM 10434 SG CYS A1312 58.008 41.928 105.065 1.00 34.04 S ATOM 10673 SG CYS A1342 56.999 38.321 105.946 1.00 35.83 S ATOM 10691 SG CYS A1345 54.778 40.368 103.752 1.00 28.51 S Time building chain proxies: 8.70, per 1000 atoms: 0.65 Number of scatterers: 13283 At special positions: 0 Unit cell: (90.95, 102, 188.7, 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 59 16.00 P 37 15.00 O 2574 8.00 N 2352 7.00 C 8257 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: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " 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 472 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 477 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 706 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 711 " pdb=" ZN A1704 " 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 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1345 " Number of angles added : 6 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 21 sheets defined 30.4% alpha, 21.6% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 removed outlier: 3.746A pdb=" N VAL A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 76 removed outlier: 4.012A 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: 4.290A 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 281 through 292 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.125A pdb=" N ALA A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.589A pdb=" N LYS A 309 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 344 through 365 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 555 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 689 removed outlier: 3.526A pdb=" N ARG A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.558A pdb=" N ILE A 812 " --> pdb=" O LYS A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.878A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1031 Processing helix chain 'A' and resid 1165 through 1169 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 1304 Processing helix chain 'A' and resid 1328 through 1336 removed outlier: 3.758A pdb=" N LYS A1331 " --> pdb=" O TYR A1328 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG A1336 " --> pdb=" O LEU A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 4.345A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1427 removed outlier: 3.687A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1476 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1532 Processing helix chain 'A' and resid 1538 through 1548 removed outlier: 3.593A pdb=" N GLU A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 3.885A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1595 Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 19 through 39 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 52 through 64 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: 4.350A 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 42 removed outlier: 3.509A pdb=" N TYR A 55 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.785A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 557 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.785A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 removed outlier: 3.832A pdb=" N ALA A 488 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 497 through 504 removed outlier: 11.554A pdb=" N GLU A 497 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N ASN A 518 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 11.675A pdb=" N ARG A 499 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 10.232A pdb=" N LEU A 516 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N ARG A 501 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N GLY A 514 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG A 503 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 723 through 724 removed outlier: 6.614A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 661 Processing sheet with id=AB1, first strand: chain 'A' and resid 739 through 744 removed outlier: 11.513A pdb=" N PHE A 739 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N LYS A 756 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N HIS A 741 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 9.728A pdb=" N LYS A 754 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ALA A 743 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 865 through 868 removed outlier: 3.519A pdb=" N ARG A1412 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AB4, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.590A pdb=" N PHE A1456 " --> pdb=" O CYS A 897 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A1460 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 893 " --> pdb=" O PHE A1460 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.392A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 932 through 933 removed outlier: 6.698A pdb=" N LYS A 932 " --> pdb=" O THR A1444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB8, first strand: chain 'A' and resid 993 through 994 removed outlier: 7.266A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 993 through 994 removed outlier: 3.687A pdb=" N TYR A1228 " --> pdb=" O ILE A1002 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1092 through 1097 removed outlier: 5.789A pdb=" N ASN A1084 " --> pdb=" O PHE A1073 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A1073 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL A1086 " --> pdb=" O ALA A1071 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA A1071 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG A1122 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A1046 " --> pdb=" O ARG A1122 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER A1124 " --> pdb=" O LYS A1044 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS A1044 " --> pdb=" O SER A1124 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR A1126 " --> pdb=" O PHE A1042 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A1042 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A1128 " --> pdb=" O LYS A1040 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1187 through 1190 removed outlier: 7.563A pdb=" N GLU A1196 " --> pdb=" O LYS A1189 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS A1201 " --> pdb=" O TYR A1209 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A1209 " --> pdb=" O CYS A1201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1276 through 1279 removed outlier: 6.826A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 6.52 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2214 1.32 - 1.45: 3810 1.45 - 1.57: 7474 1.57 - 1.69: 76 1.69 - 1.82: 85 Bond restraints: 13659 Sorted by residual: bond pdb=" C LYS B 32 " pdb=" O LYS B 32 " ideal model delta sigma weight residual 1.237 1.196 0.040 1.17e-02 7.31e+03 1.18e+01 bond pdb=" N MET A1211 " pdb=" CA MET A1211 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.23e-02 6.61e+03 1.09e+01 bond pdb=" N PHE A1158 " pdb=" CA PHE A1158 " ideal model delta sigma weight residual 1.454 1.496 -0.041 1.31e-02 5.83e+03 9.94e+00 bond pdb=" N LEU A 580 " pdb=" CA LEU A 580 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.23e-02 6.61e+03 9.20e+00 bond pdb=" O3' A R 3 " pdb=" P U R 4 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 9.14e+00 ... (remaining 13654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 17790 1.94 - 3.87: 618 3.87 - 5.81: 148 5.81 - 7.74: 16 7.74 - 9.68: 5 Bond angle restraints: 18577 Sorted by residual: angle pdb=" N TRP A1533 " pdb=" CA TRP A1533 " pdb=" C TRP A1533 " ideal model delta sigma weight residual 113.55 104.65 8.90 1.26e+00 6.30e-01 4.99e+01 angle pdb=" CA LYS A1099 " pdb=" CB LYS A1099 " pdb=" CG LYS A1099 " ideal model delta sigma weight residual 114.10 123.78 -9.68 2.00e+00 2.50e-01 2.34e+01 angle pdb=" CA PHE A1158 " pdb=" C PHE A1158 " pdb=" O PHE A1158 " ideal model delta sigma weight residual 121.47 116.20 5.27 1.15e+00 7.56e-01 2.10e+01 angle pdb=" CA ASP A1581 " pdb=" CB ASP A1581 " pdb=" CG ASP A1581 " ideal model delta sigma weight residual 112.60 117.10 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" CA ARG A1504 " pdb=" C ARG A1504 " pdb=" O ARG A1504 " ideal model delta sigma weight residual 121.81 116.68 5.13 1.18e+00 7.18e-01 1.89e+01 ... (remaining 18572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 7313 17.35 - 34.70: 734 34.70 - 52.05: 205 52.05 - 69.40: 73 69.40 - 86.75: 21 Dihedral angle restraints: 8346 sinusoidal: 3898 harmonic: 4448 Sorted by residual: 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 -163.09 57.09 1 1.70e+01 3.46e-03 1.52e+01 dihedral pdb=" CA ASP A 77 " pdb=" C ASP A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " 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 3 " pdb=" C1' A R 3 " pdb=" N9 A R 3 " pdb=" C4 A R 3 " ideal model delta sinusoidal sigma weight residual -106.00 -159.99 53.99 1 1.70e+01 3.46e-03 1.37e+01 ... (remaining 8343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1627 0.064 - 0.128: 270 0.128 - 0.192: 59 0.192 - 0.256: 10 0.256 - 0.320: 6 Chirality restraints: 1972 Sorted by residual: chirality pdb=" P G R 2 " pdb=" OP1 G R 2 " pdb=" OP2 G R 2 " pdb=" O5' G R 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.73 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" P G R 5 " pdb=" OP1 G R 5 " pdb=" OP2 G R 5 " pdb=" O5' G R 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.70 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" P G R 11 " pdb=" OP1 G R 11 " pdb=" OP2 G R 11 " pdb=" O5' G R 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.69 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1969 not shown) Planarity restraints: 2284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1211 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C MET A1211 " -0.056 2.00e-02 2.50e+03 pdb=" O MET A1211 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA A1212 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 780 " 0.265 9.50e-02 1.11e+02 1.19e-01 9.77e+00 pdb=" NE ARG A 780 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 780 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 780 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 780 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 63 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C PHE B 63 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE B 63 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG B 64 " -0.016 2.00e-02 2.50e+03 ... (remaining 2281 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 125 2.64 - 3.20: 10969 3.20 - 3.77: 18725 3.77 - 4.33: 26531 4.33 - 4.90: 44930 Nonbonded interactions: 101280 Sorted by model distance: nonbonded pdb=" O GLU A 707 " pdb=" OE1 GLU A 707 " model vdw 2.070 3.040 nonbonded pdb=" O GLU A 707 " pdb=" CD GLU A 707 " model vdw 2.125 3.270 nonbonded pdb=" O THR A1008 " pdb=" NE2 GLN A1127 " model vdw 2.228 3.120 nonbonded pdb=" N GLU A1318 " pdb=" OE1 GLU A1318 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR A1072 " pdb=" O ASN A1084 " model vdw 2.270 3.040 ... (remaining 101275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 39.300 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:15.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 0.005 0.071 13659 Z= 0.334 Angle : 0.859 9.679 18577 Z= 0.499 Chirality : 0.056 0.320 1972 Planarity : 0.006 0.119 2284 Dihedral : 16.120 86.753 5474 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % 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: -1.13 (0.21), residues: 1519 helix: 1.15 (0.27), residues: 412 sheet: -1.15 (0.31), residues: 268 loop : -1.64 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1120 HIS 0.011 0.001 HIS A1001 PHE 0.040 0.002 PHE A1220 TYR 0.017 0.002 TYR A1228 ARG 0.020 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.556 Fit side-chains REVERT: A 226 ASP cc_start: 0.8110 (p0) cc_final: 0.7566 (t0) REVERT: A 487 ASP cc_start: 0.7524 (t70) cc_final: 0.7307 (t70) REVERT: A 1099 LYS cc_start: 0.7075 (mmpt) cc_final: 0.6593 (ttpt) REVERT: B 35 LYS cc_start: 0.7730 (ttpt) cc_final: 0.7528 (ttpt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 1.5835 time to fit residues: 257.2188 Evaluate side-chains 108 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 142 optimal weight: 0.0870 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 ASN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13659 Z= 0.284 Angle : 0.620 9.485 18577 Z= 0.326 Chirality : 0.045 0.225 1972 Planarity : 0.005 0.055 2284 Dihedral : 13.177 82.510 2280 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.00 % Allowed : 10.31 % Favored : 87.69 % 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: -0.89 (0.21), residues: 1519 helix: 1.25 (0.26), residues: 409 sheet: -0.76 (0.32), residues: 263 loop : -1.51 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1466 HIS 0.007 0.001 HIS A1483 PHE 0.021 0.002 PHE A1220 TYR 0.015 0.002 TYR A 360 ARG 0.006 0.001 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.485 Fit side-chains REVERT: A 353 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6263 (mm-30) REVERT: A 460 ASP cc_start: 0.7172 (t0) cc_final: 0.6865 (t0) REVERT: A 484 THR cc_start: 0.9110 (m) cc_final: 0.8907 (m) REVERT: A 559 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.8828 (mtt) REVERT: A 768 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7702 (ttm-80) REVERT: A 1097 TRP cc_start: 0.8025 (m100) cc_final: 0.7302 (m100) REVERT: A 1196 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: A 1216 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 1267 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: A 1504 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6250 (mpt-90) outliers start: 27 outliers final: 9 residues processed: 144 average time/residue: 1.5727 time to fit residues: 245.5882 Evaluate side-chains 120 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1267 GLU Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1504 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 154 optimal weight: 0.0980 chunk 127 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN A1003 GLN A1078 ASN B 9 GLN B 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13659 Z= 0.197 Angle : 0.528 8.784 18577 Z= 0.279 Chirality : 0.042 0.249 1972 Planarity : 0.005 0.054 2284 Dihedral : 12.938 81.239 2280 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.08 % Allowed : 12.54 % Favored : 85.39 % 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: -0.60 (0.21), residues: 1519 helix: 1.51 (0.27), residues: 409 sheet: -0.45 (0.32), residues: 264 loop : -1.39 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1466 HIS 0.005 0.001 HIS A1483 PHE 0.023 0.001 PHE A1277 TYR 0.010 0.001 TYR A 492 ARG 0.004 0.000 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.304 Fit side-chains REVERT: A 112 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8045 (pptt) REVERT: A 125 PHE cc_start: 0.8155 (t80) cc_final: 0.7871 (t80) REVERT: A 460 ASP cc_start: 0.7125 (t0) cc_final: 0.6795 (t0) REVERT: A 559 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8649 (mtt) REVERT: A 1097 TRP cc_start: 0.7920 (m100) cc_final: 0.7590 (m100) REVERT: A 1099 LYS cc_start: 0.7482 (mmpt) cc_final: 0.6817 (ttpt) REVERT: A 1504 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6427 (mpt-90) outliers start: 28 outliers final: 10 residues processed: 144 average time/residue: 1.5445 time to fit residues: 241.5733 Evaluate side-chains 114 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1270 LYS Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1504 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13659 Z= 0.180 Angle : 0.514 8.896 18577 Z= 0.271 Chirality : 0.041 0.264 1972 Planarity : 0.004 0.053 2284 Dihedral : 12.900 80.942 2280 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.15 % Allowed : 13.80 % Favored : 84.05 % 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: -0.45 (0.21), residues: 1519 helix: 1.67 (0.27), residues: 405 sheet: -0.34 (0.32), residues: 264 loop : -1.32 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1466 HIS 0.004 0.001 HIS A1483 PHE 0.021 0.001 PHE A1220 TYR 0.011 0.001 TYR A1228 ARG 0.005 0.000 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.476 Fit side-chains REVERT: A 125 PHE cc_start: 0.8158 (t80) cc_final: 0.7879 (t80) REVERT: A 177 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: A 215 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7594 (mtp85) REVERT: A 460 ASP cc_start: 0.7094 (t0) cc_final: 0.6790 (t0) REVERT: A 559 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8630 (mtt) REVERT: A 879 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7380 (mptm) REVERT: A 896 ARG cc_start: 0.7338 (ttm-80) cc_final: 0.6969 (mtp180) REVERT: A 1099 LYS cc_start: 0.7516 (mmpt) cc_final: 0.6726 (ttpt) REVERT: A 1196 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: A 1504 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7081 (mtt-85) outliers start: 29 outliers final: 13 residues processed: 140 average time/residue: 1.5419 time to fit residues: 234.7714 Evaluate side-chains 119 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1221 ASP Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1270 LYS Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1504 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 104 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A1003 GLN A1020 HIS ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13659 Z= 0.270 Angle : 0.573 9.213 18577 Z= 0.301 Chirality : 0.044 0.269 1972 Planarity : 0.005 0.062 2284 Dihedral : 12.903 82.859 2280 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.45 % Allowed : 14.32 % Favored : 83.23 % 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: -0.59 (0.21), residues: 1519 helix: 1.51 (0.27), residues: 403 sheet: -0.33 (0.32), residues: 265 loop : -1.40 (0.19), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1466 HIS 0.005 0.001 HIS A1483 PHE 0.016 0.002 PHE A1220 TYR 0.014 0.002 TYR A 492 ARG 0.006 0.000 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8140 (t80) cc_final: 0.7899 (t80) REVERT: A 177 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: A 215 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7620 (mtp85) REVERT: A 460 ASP cc_start: 0.7177 (t0) cc_final: 0.6867 (t0) REVERT: A 559 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8770 (mtt) REVERT: A 879 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7460 (mptm) REVERT: A 1042 PHE cc_start: 0.7708 (m-80) cc_final: 0.7475 (m-80) REVERT: A 1097 TRP cc_start: 0.7812 (m100) cc_final: 0.6716 (m100) REVERT: A 1099 LYS cc_start: 0.7852 (mmpt) cc_final: 0.7209 (ttpt) REVERT: A 1504 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7077 (mtt-85) REVERT: A 1535 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7053 (mpp-170) outliers start: 33 outliers final: 12 residues processed: 138 average time/residue: 1.5787 time to fit residues: 236.5375 Evaluate side-chains 121 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1504 ARG Chi-restraints excluded: chain A residue 1535 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.0070 chunk 146 optimal weight: 0.4980 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A1003 GLN A1483 HIS ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13659 Z= 0.154 Angle : 0.494 8.314 18577 Z= 0.263 Chirality : 0.040 0.259 1972 Planarity : 0.004 0.052 2284 Dihedral : 12.775 80.400 2280 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.78 % Allowed : 15.58 % Favored : 82.64 % 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: -0.34 (0.21), residues: 1519 helix: 1.74 (0.27), residues: 405 sheet: -0.19 (0.32), residues: 265 loop : -1.26 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1097 HIS 0.003 0.001 HIS A1095 PHE 0.025 0.001 PHE A1220 TYR 0.013 0.001 TYR A1228 ARG 0.005 0.000 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7881 (pptt) REVERT: A 125 PHE cc_start: 0.8121 (t80) cc_final: 0.7847 (t80) REVERT: A 215 ARG cc_start: 0.7834 (mtt90) cc_final: 0.7520 (mtp85) REVERT: A 460 ASP cc_start: 0.7069 (t0) cc_final: 0.6826 (t0) REVERT: A 559 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8532 (mtt) REVERT: A 593 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8723 (tttp) REVERT: A 879 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7246 (mptm) REVERT: A 1042 PHE cc_start: 0.7751 (m-80) cc_final: 0.7507 (m-80) REVERT: A 1097 TRP cc_start: 0.8004 (m100) cc_final: 0.6751 (m100) REVERT: A 1099 LYS cc_start: 0.7828 (mmpt) cc_final: 0.7255 (ttpt) REVERT: A 1504 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6992 (mtt-85) outliers start: 24 outliers final: 11 residues processed: 136 average time/residue: 1.5300 time to fit residues: 226.5426 Evaluate side-chains 120 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1504 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 151 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13659 Z= 0.287 Angle : 0.591 9.162 18577 Z= 0.310 Chirality : 0.044 0.265 1972 Planarity : 0.005 0.063 2284 Dihedral : 12.819 82.988 2280 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.93 % Allowed : 16.62 % Favored : 81.45 % 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: -0.55 (0.21), residues: 1519 helix: 1.52 (0.27), residues: 403 sheet: -0.24 (0.32), residues: 260 loop : -1.38 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1097 HIS 0.006 0.001 HIS A1483 PHE 0.023 0.002 PHE A1220 TYR 0.016 0.002 TYR A1228 ARG 0.004 0.000 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7872 (pptt) REVERT: A 125 PHE cc_start: 0.8170 (t80) cc_final: 0.7883 (t80) REVERT: A 177 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: A 215 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7595 (mtp85) REVERT: A 460 ASP cc_start: 0.7231 (t0) cc_final: 0.6961 (t0) REVERT: A 559 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8763 (mtt) REVERT: A 573 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: A 593 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8743 (tttp) REVERT: A 1042 PHE cc_start: 0.7732 (m-80) cc_final: 0.7469 (m-80) REVERT: A 1097 TRP cc_start: 0.7999 (m100) cc_final: 0.6649 (m100) REVERT: A 1099 LYS cc_start: 0.7852 (mmpt) cc_final: 0.7334 (ttpt) REVERT: A 1504 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6996 (mtt-85) REVERT: A 1535 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7053 (mpp-170) outliers start: 26 outliers final: 12 residues processed: 133 average time/residue: 1.5682 time to fit residues: 227.2257 Evaluate side-chains 125 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1221 ASP Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1504 ARG Chi-restraints excluded: chain A residue 1535 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13659 Z= 0.191 Angle : 0.527 8.820 18577 Z= 0.279 Chirality : 0.041 0.253 1972 Planarity : 0.005 0.058 2284 Dihedral : 12.796 81.751 2280 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.71 % Allowed : 16.77 % Favored : 81.53 % 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: -0.40 (0.21), residues: 1519 helix: 1.68 (0.27), residues: 403 sheet: -0.15 (0.33), residues: 260 loop : -1.31 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1097 HIS 0.004 0.001 HIS A1483 PHE 0.026 0.001 PHE A1220 TYR 0.016 0.001 TYR A1228 ARG 0.004 0.000 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8141 (t80) cc_final: 0.7843 (t80) REVERT: A 184 HIS cc_start: 0.7667 (p-80) cc_final: 0.6974 (m-70) REVERT: A 215 ARG cc_start: 0.7876 (mtt90) cc_final: 0.7614 (mtp85) REVERT: A 460 ASP cc_start: 0.7113 (t0) cc_final: 0.6840 (t0) REVERT: A 559 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8633 (mtt) REVERT: A 578 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6498 (tp30) REVERT: A 1042 PHE cc_start: 0.7745 (m-80) cc_final: 0.7477 (m-80) REVERT: A 1097 TRP cc_start: 0.8062 (m100) cc_final: 0.6661 (m100) REVERT: A 1099 LYS cc_start: 0.7829 (mmpt) cc_final: 0.7299 (ttpt) REVERT: A 1187 ASP cc_start: 0.6708 (t0) cc_final: 0.6282 (t0) REVERT: A 1504 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6959 (mtt-85) outliers start: 23 outliers final: 12 residues processed: 134 average time/residue: 1.5561 time to fit residues: 227.3680 Evaluate side-chains 121 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1504 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13659 Z= 0.153 Angle : 0.507 9.037 18577 Z= 0.269 Chirality : 0.040 0.244 1972 Planarity : 0.004 0.052 2284 Dihedral : 12.774 80.190 2280 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.41 % Allowed : 17.14 % Favored : 81.45 % 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: -0.23 (0.21), residues: 1519 helix: 1.80 (0.27), residues: 405 sheet: 0.01 (0.32), residues: 270 loop : -1.24 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1097 HIS 0.003 0.001 HIS A1483 PHE 0.027 0.001 PHE A1220 TYR 0.017 0.001 TYR A1228 ARG 0.004 0.000 ARG A 855 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8069 (t80) cc_final: 0.7831 (t80) REVERT: A 184 HIS cc_start: 0.7609 (p-80) cc_final: 0.6945 (m-70) REVERT: A 460 ASP cc_start: 0.7082 (t0) cc_final: 0.6849 (t0) REVERT: A 559 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8569 (mtt) REVERT: A 879 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7269 (mptm) REVERT: A 1042 PHE cc_start: 0.7825 (m-80) cc_final: 0.7581 (m-80) REVERT: A 1097 TRP cc_start: 0.8081 (m100) cc_final: 0.6738 (m100) REVERT: A 1099 LYS cc_start: 0.7782 (mmpt) cc_final: 0.7296 (tmmt) REVERT: A 1187 ASP cc_start: 0.6607 (t0) cc_final: 0.6185 (t0) REVERT: A 1504 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.7011 (mtt-85) REVERT: A 1585 LYS cc_start: 0.8028 (ptpp) cc_final: 0.7782 (mttm) outliers start: 19 outliers final: 9 residues processed: 131 average time/residue: 1.5313 time to fit residues: 217.7415 Evaluate side-chains 123 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 879 LYS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1504 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13659 Z= 0.361 Angle : 0.635 9.240 18577 Z= 0.335 Chirality : 0.046 0.247 1972 Planarity : 0.005 0.066 2284 Dihedral : 12.890 84.596 2280 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.56 % Allowed : 17.28 % Favored : 81.16 % 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: -0.62 (0.21), residues: 1519 helix: 1.32 (0.27), residues: 403 sheet: -0.20 (0.32), residues: 278 loop : -1.41 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1097 HIS 0.007 0.001 HIS A1483 PHE 0.028 0.002 PHE A1220 TYR 0.018 0.002 TYR A1228 ARG 0.004 0.000 ARG A 951 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.524 Fit side-chains revert: symmetry clash REVERT: A 108 ARG cc_start: 0.7114 (ptm160) cc_final: 0.6810 (ptp90) REVERT: A 125 PHE cc_start: 0.8163 (t80) cc_final: 0.7855 (t80) REVERT: A 177 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: A 460 ASP cc_start: 0.7200 (t0) cc_final: 0.6935 (t0) REVERT: A 559 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8869 (mtt) REVERT: A 578 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6577 (tp30) REVERT: A 1042 PHE cc_start: 0.7791 (m-80) cc_final: 0.7563 (m-80) REVERT: A 1097 TRP cc_start: 0.8056 (m100) cc_final: 0.6768 (m100) REVERT: A 1099 LYS cc_start: 0.7753 (mmpt) cc_final: 0.7291 (tmmt) REVERT: A 1504 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7085 (mtt-85) outliers start: 21 outliers final: 13 residues processed: 124 average time/residue: 1.4676 time to fit residues: 198.8948 Evaluate side-chains 122 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1357 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1504 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.171069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129407 restraints weight = 16214.757| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.77 r_work: 0.3287 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13659 Z= 0.184 Angle : 0.536 8.647 18577 Z= 0.285 Chirality : 0.041 0.228 1972 Planarity : 0.005 0.058 2284 Dihedral : 12.836 82.138 2280 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.26 % Allowed : 17.66 % Favored : 81.08 % 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: -0.38 (0.21), residues: 1519 helix: 1.61 (0.27), residues: 403 sheet: -0.05 (0.33), residues: 260 loop : -1.28 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1097 HIS 0.004 0.001 HIS A1483 PHE 0.027 0.001 PHE A1220 TYR 0.017 0.001 TYR A1228 ARG 0.006 0.000 ARG A1193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4400.40 seconds wall clock time: 81 minutes 17.15 seconds (4877.15 seconds total)