Starting phenix.real_space_refine on Thu Jul 31 04:25:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8asg_15615/07_2025/8asg_15615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asg_15615/07_2025/8asg_15615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8asg_15615/07_2025/8asg_15615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asg_15615/07_2025/8asg_15615.map" model { file = "/net/cci-nas-00/data/ceres_data/8asg_15615/07_2025/8asg_15615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asg_15615/07_2025/8asg_15615.cif" } resolution = 3.2 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= 0.002 sd= 0.033 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 P 16 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 7988 2.51 5 N 2202 2.21 5 O 2409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12687 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1544, 12311 Classifications: {'peptide': 1544} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1484} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 1544, 12311 Classifications: {'peptide': 1544} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1484} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 12558 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 213 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.26, per 1000 atoms: 0.97 Number of scatterers: 12687 At special positions: 0 Unit cell: (101.15, 113.05, 122.4, 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) S 71 16.00 P 16 15.00 Mg 1 11.99 O 2409 8.00 N 2202 7.00 C 7988 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: 2.91 Conformation dependent library (CDL) restraints added in 2.7 seconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2908 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 54.2% alpha, 8.0% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.646A pdb=" N PHE A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.545A pdb=" N VAL A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 removed outlier: 3.515A pdb=" N LEU A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 removed outlier: 4.224A pdb=" N ILE A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 209 Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.535A pdb=" N LEU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.750A pdb=" N PHE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 262 through 286 Processing helix chain 'A' and resid 292 through 319 removed outlier: 3.777A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.554A pdb=" N SER A 354 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET A 356 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 357 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.601A pdb=" N LEU A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.751A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.980A pdb=" N ASP A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 438 through 447 removed outlier: 3.683A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.681A pdb=" N PHE A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 604 through 611 removed outlier: 4.227A pdb=" N ASN A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 656 through 665 removed outlier: 3.666A pdb=" N GLU A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 671 removed outlier: 3.541A pdb=" N THR A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 682 through 690 removed outlier: 3.652A pdb=" N LYS A 685 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 687 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 716 Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.827A pdb=" N TRP A 750 " --> pdb=" O MET A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 removed outlier: 3.532A pdb=" N LYS A 756 " --> pdb=" O GLY A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 779 removed outlier: 4.096A pdb=" N TYR A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 4.305A pdb=" N PHE A 787 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 removed outlier: 3.710A pdb=" N ARG A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 840 removed outlier: 3.677A pdb=" N ASN A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS A 840 " --> pdb=" O GLU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 860 through 865 removed outlier: 3.819A pdb=" N VAL A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 885 removed outlier: 3.998A pdb=" N LYS A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 904 Processing helix chain 'A' and resid 926 through 945 removed outlier: 3.987A pdb=" N VAL A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 942 " --> pdb=" O THR A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 957 through 973 removed outlier: 4.300A pdb=" N ILE A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLU A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 removed outlier: 3.766A pdb=" N HIS A 993 " --> pdb=" O TRP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 4.043A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1009 removed outlier: 6.061A pdb=" N LYS A1009 " --> pdb=" O MET A1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1006 through 1009' Processing helix chain 'A' and resid 1010 through 1018 Processing helix chain 'A' and resid 1019 through 1022 removed outlier: 3.679A pdb=" N ARG A1022 " --> pdb=" O SER A1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1019 through 1022' Processing helix chain 'A' and resid 1029 through 1040 removed outlier: 3.657A pdb=" N LEU A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A1039 " --> pdb=" O HIS A1035 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1058 removed outlier: 3.616A pdb=" N GLU A1050 " --> pdb=" O ASP A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1109 removed outlier: 3.543A pdb=" N SER A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1155 removed outlier: 4.213A pdb=" N VAL A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A1144 " --> pdb=" O MET A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1161 through 1164 Processing helix chain 'A' and resid 1194 through 1200 removed outlier: 4.073A pdb=" N TRP A1198 " --> pdb=" O PRO A1194 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A1200 " --> pdb=" O LEU A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1228 removed outlier: 3.558A pdb=" N GLU A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 Processing helix chain 'A' and resid 1257 through 1268 removed outlier: 3.786A pdb=" N SER A1267 " --> pdb=" O GLY A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 3.818A pdb=" N ALA A1284 " --> pdb=" O PRO A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1300 removed outlier: 3.546A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1311 removed outlier: 3.656A pdb=" N LYS A1305 " --> pdb=" O ASP A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1353 Processing helix chain 'A' and resid 1360 through 1367 removed outlier: 3.668A pdb=" N GLN A1364 " --> pdb=" O ASP A1360 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A1365 " --> pdb=" O TRP A1361 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP A1366 " --> pdb=" O VAL A1362 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A1367 " --> pdb=" O GLU A1363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1360 through 1367' Processing helix chain 'A' and resid 1368 through 1373 removed outlier: 3.531A pdb=" N VAL A1371 " --> pdb=" O ASN A1368 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A1372 " --> pdb=" O PRO A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1391 Processing helix chain 'A' and resid 1392 through 1400 removed outlier: 3.968A pdb=" N THR A1396 " --> pdb=" O SER A1392 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A1397 " --> pdb=" O PRO A1393 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A1400 " --> pdb=" O THR A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1403 No H-bonds generated for 'chain 'A' and resid 1401 through 1403' Processing helix chain 'A' and resid 1404 through 1411 Processing helix chain 'A' and resid 1412 through 1414 No H-bonds generated for 'chain 'A' and resid 1412 through 1414' Processing helix chain 'A' and resid 1438 through 1448 Processing helix chain 'A' and resid 1457 through 1465 removed outlier: 3.529A pdb=" N ARG A1462 " --> pdb=" O PRO A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1478 Processing helix chain 'A' and resid 1514 through 1519 Processing helix chain 'A' and resid 1539 through 1546 removed outlier: 3.664A pdb=" N ALA A1543 " --> pdb=" O ASP A1539 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1572 Processing helix chain 'A' and resid 1597 through 1604 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25 removed outlier: 3.546A pdb=" N SER A 179 " --> pdb=" O GLY A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39 removed outlier: 3.726A pdb=" N ASP A 37 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 46 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 336 removed outlier: 3.503A pdb=" N ARG A 577 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 removed outlier: 3.525A pdb=" N PHE A 565 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 411 removed outlier: 3.525A pdb=" N PHE A 565 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 922 through 925 removed outlier: 3.720A pdb=" N ILE A 922 " --> pdb=" O PHE A 911 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 911 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N MET A 906 " --> pdb=" O LYS A1025 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET A1027 " --> pdb=" O MET A 906 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 908 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 6.654A pdb=" N SER A 983 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A1173 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 986 through 987 removed outlier: 4.257A pdb=" N TYR A1166 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1178 through 1181 Processing sheet with id=AB1, first strand: chain 'A' and resid 1338 through 1339 Processing sheet with id=AB2, first strand: chain 'A' and resid 1486 through 1488 removed outlier: 3.568A pdb=" N LYS A1487 " --> pdb=" O SER A1610 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1496 through 1497 removed outlier: 3.552A pdb=" N GLY A1585 " --> pdb=" O VAL A1496 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 3.47 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: 3882 1.34 - 1.46: 2252 1.46 - 1.58: 6708 1.58 - 1.70: 32 1.70 - 1.82: 117 Bond restraints: 12991 Sorted by residual: bond pdb=" CB PRO A1466 " pdb=" CG PRO A1466 " ideal model delta sigma weight residual 1.492 1.653 -0.161 5.00e-02 4.00e+02 1.04e+01 bond pdb=" N PRO A1466 " pdb=" CD PRO A1466 " ideal model delta sigma weight residual 1.473 1.517 -0.044 1.40e-02 5.10e+03 9.86e+00 bond pdb=" N PRO A1466 " pdb=" CA PRO A1466 " ideal model delta sigma weight residual 1.466 1.434 0.033 1.13e-02 7.83e+03 8.35e+00 bond pdb=" CB PRO A 396 " pdb=" CG PRO A 396 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.93e+00 bond pdb=" CA PRO A1466 " pdb=" C PRO A1466 " ideal model delta sigma weight residual 1.520 1.537 -0.016 9.50e-03 1.11e+04 2.96e+00 ... (remaining 12986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 17416 2.95 - 5.89: 166 5.89 - 8.84: 19 8.84 - 11.79: 9 11.79 - 14.73: 2 Bond angle restraints: 17612 Sorted by residual: angle pdb=" CA PRO A1466 " pdb=" N PRO A1466 " pdb=" CD PRO A1466 " ideal model delta sigma weight residual 112.00 97.27 14.73 1.40e+00 5.10e-01 1.11e+02 angle pdb=" N PRO A1466 " pdb=" CD PRO A1466 " pdb=" CG PRO A1466 " ideal model delta sigma weight residual 103.20 95.94 7.26 1.50e+00 4.44e-01 2.34e+01 angle pdb=" CA PRO A 396 " pdb=" N PRO A 396 " pdb=" CD PRO A 396 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C LEU A 118 " pdb=" N ASP A 119 " pdb=" CA ASP A 119 " ideal model delta sigma weight residual 124.31 131.27 -6.96 1.67e+00 3.59e-01 1.74e+01 angle pdb=" N THR A 499 " pdb=" CA THR A 499 " pdb=" C THR A 499 " ideal model delta sigma weight residual 113.12 107.96 5.16 1.25e+00 6.40e-01 1.70e+01 ... (remaining 17607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 7666 34.89 - 69.77: 173 69.77 - 104.66: 21 104.66 - 139.55: 1 139.55 - 174.43: 3 Dihedral angle restraints: 7864 sinusoidal: 3374 harmonic: 4490 Sorted by residual: dihedral pdb=" O4' U T 5 " pdb=" C1' U T 5 " pdb=" N1 U T 5 " pdb=" C2 U T 5 " ideal model delta sinusoidal sigma weight residual 200.00 45.38 154.62 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" CA TYR A1110 " pdb=" C TYR A1110 " pdb=" N MET A1111 " pdb=" CA MET A1111 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLN A1095 " pdb=" C GLN A1095 " pdb=" N SER A1096 " pdb=" CA SER A1096 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1786 0.075 - 0.150: 153 0.150 - 0.224: 8 0.224 - 0.299: 3 0.299 - 0.374: 4 Chirality restraints: 1954 Sorted by residual: chirality pdb=" P G P 8 " pdb=" OP1 G P 8 " pdb=" OP2 G P 8 " pdb=" O5' G P 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" P U D 29 " pdb=" OP1 U D 29 " pdb=" OP2 U D 29 " pdb=" O5' U D 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA PRO A1466 " pdb=" N PRO A1466 " pdb=" C PRO A1466 " pdb=" CB PRO A1466 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1951 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1465 " 0.098 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO A1466 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO A1466 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A1466 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1383 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LEU A1383 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU A1383 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU A1384 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 395 " -0.054 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO A 396 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.044 5.00e-02 4.00e+02 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 224 2.67 - 3.23: 12006 3.23 - 3.79: 19629 3.79 - 4.34: 26571 4.34 - 4.90: 43524 Nonbonded interactions: 101954 Sorted by model distance: nonbonded pdb=" OD1 ASP A1127 " pdb="MG MG A2101 " model vdw 2.114 2.170 nonbonded pdb=" OE1 GLU A 643 " pdb=" OG SER A 737 " model vdw 2.198 3.040 nonbonded pdb=" O ILE A 663 " pdb=" OG1 THR A 666 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU A 625 " pdb=" OG SER A1231 " model vdw 2.248 3.040 nonbonded pdb=" OG SER A 173 " pdb=" O GLY A 176 " model vdw 2.264 3.040 ... (remaining 101949 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=0.50 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 39.080 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.161 12991 Z= 0.153 Angle : 0.772 14.734 17612 Z= 0.412 Chirality : 0.046 0.374 1954 Planarity : 0.006 0.135 2188 Dihedral : 15.816 174.435 4956 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.29 % Allowed : 0.37 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 (0.20), residues: 1528 helix: 0.08 (0.19), residues: 720 sheet: -0.48 (0.55), residues: 102 loop : -1.67 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1547 HIS 0.007 0.001 HIS A 563 PHE 0.030 0.001 PHE A 649 TYR 0.021 0.001 TYR A 142 ARG 0.011 0.001 ARG A 871 Details of bonding type rmsd hydrogen bonds : bond 0.20342 ( 543) hydrogen bonds : angle 6.94173 ( 1581) covalent geometry : bond 0.00338 (12991) covalent geometry : angle 0.77245 (17612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 186 time to evaluate : 1.351 Fit side-chains REVERT: A 156 ARG cc_start: 0.6874 (mmt90) cc_final: 0.6420 (mmm-85) REVERT: A 1308 TYR cc_start: 0.7998 (t80) cc_final: 0.7705 (t80) outliers start: 3 outliers final: 0 residues processed: 187 average time/residue: 0.2870 time to fit residues: 77.2967 Evaluate side-chains 153 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 8.9990 chunk 117 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS A 993 HIS ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN A1604 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.189909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143845 restraints weight = 17505.343| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.33 r_work: 0.3274 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12991 Z= 0.135 Angle : 0.627 9.717 17612 Z= 0.320 Chirality : 0.042 0.202 1954 Planarity : 0.005 0.060 2188 Dihedral : 12.169 167.950 1927 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.59 % Allowed : 7.36 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.51 (0.21), residues: 1528 helix: 0.77 (0.19), residues: 736 sheet: -0.17 (0.55), residues: 101 loop : -1.61 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1547 HIS 0.008 0.001 HIS A1091 PHE 0.025 0.001 PHE A 649 TYR 0.027 0.002 TYR A1110 ARG 0.008 0.001 ARG A 971 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 543) hydrogen bonds : angle 4.76012 ( 1581) covalent geometry : bond 0.00319 (12991) covalent geometry : angle 0.62686 (17612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 489 LYS cc_start: 0.8416 (tptt) cc_final: 0.8190 (tptt) REVERT: A 888 TRP cc_start: 0.8403 (m100) cc_final: 0.7910 (m100) REVERT: A 1308 TYR cc_start: 0.8503 (t80) cc_final: 0.8166 (t80) REVERT: A 1434 GLN cc_start: 0.6537 (pm20) cc_final: 0.6332 (pm20) REVERT: A 1462 ARG cc_start: 0.6761 (ttm-80) cc_final: 0.6453 (ttp-110) outliers start: 7 outliers final: 3 residues processed: 167 average time/residue: 0.2907 time to fit residues: 71.2996 Evaluate side-chains 152 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 936 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 101 optimal weight: 0.0000 chunk 99 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 141 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 GLN A 563 HIS ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN B ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 HIS A1378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.185170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127455 restraints weight = 26465.331| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.57 r_work: 0.3239 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12991 Z= 0.190 Angle : 0.647 9.604 17612 Z= 0.331 Chirality : 0.043 0.212 1954 Planarity : 0.005 0.049 2188 Dihedral : 12.182 167.452 1927 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.59 % Allowed : 8.69 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.46 (0.21), residues: 1528 helix: 0.96 (0.19), residues: 731 sheet: -0.33 (0.54), residues: 101 loop : -1.74 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1064 HIS 0.009 0.001 HIS A1091 PHE 0.022 0.002 PHE A 649 TYR 0.024 0.002 TYR A1181 ARG 0.006 0.000 ARG A 971 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 543) hydrogen bonds : angle 4.60479 ( 1581) covalent geometry : bond 0.00457 (12991) covalent geometry : angle 0.64740 (17612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 1.696 Fit side-chains revert: symmetry clash REVERT: A 848 MET cc_start: 0.8166 (pmm) cc_final: 0.7720 (ptt) REVERT: A 888 TRP cc_start: 0.8534 (m100) cc_final: 0.7980 (m100) REVERT: A 1209 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 1304 ARG cc_start: 0.6968 (mmm160) cc_final: 0.6578 (mmm160) REVERT: A 1462 ARG cc_start: 0.6649 (ttm-80) cc_final: 0.6322 (ttp-110) REVERT: A 1582 ARG cc_start: 0.7534 (ttt-90) cc_final: 0.7099 (ttp-110) outliers start: 7 outliers final: 4 residues processed: 159 average time/residue: 0.3676 time to fit residues: 84.9786 Evaluate side-chains 148 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS A 563 HIS ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.184662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128927 restraints weight = 28819.430| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.36 r_work: 0.3208 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12991 Z= 0.183 Angle : 0.621 8.846 17612 Z= 0.319 Chirality : 0.042 0.202 1954 Planarity : 0.004 0.049 2188 Dihedral : 12.110 166.116 1927 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.03 % Allowed : 10.53 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.46 (0.21), residues: 1528 helix: 0.97 (0.19), residues: 739 sheet: -0.44 (0.53), residues: 102 loop : -1.76 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 433 HIS 0.009 0.001 HIS A1091 PHE 0.021 0.002 PHE A 649 TYR 0.021 0.002 TYR A1110 ARG 0.006 0.000 ARG A 971 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 543) hydrogen bonds : angle 4.44325 ( 1581) covalent geometry : bond 0.00439 (12991) covalent geometry : angle 0.62108 (17612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 193 TYR cc_start: 0.7837 (t80) cc_final: 0.7479 (t80) REVERT: A 489 LYS cc_start: 0.8462 (tptt) cc_final: 0.8224 (tptt) REVERT: A 888 TRP cc_start: 0.8521 (m100) cc_final: 0.7986 (m100) REVERT: A 1031 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7780 (mtm-85) REVERT: A 1140 MET cc_start: 0.7955 (tmm) cc_final: 0.7717 (tmm) REVERT: A 1304 ARG cc_start: 0.6964 (mmm160) cc_final: 0.6680 (mtp180) REVERT: A 1462 ARG cc_start: 0.6679 (ttm-80) cc_final: 0.6344 (ttp-110) outliers start: 13 outliers final: 7 residues processed: 160 average time/residue: 0.2688 time to fit residues: 62.0543 Evaluate side-chains 152 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 41 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 0.0270 chunk 69 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 HIS A1378 ASN ** A1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.187857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135273 restraints weight = 17970.658| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.49 r_work: 0.3316 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12991 Z= 0.117 Angle : 0.584 11.153 17612 Z= 0.293 Chirality : 0.040 0.205 1954 Planarity : 0.004 0.049 2188 Dihedral : 11.934 165.409 1927 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.81 % Allowed : 11.71 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.22 (0.21), residues: 1528 helix: 1.26 (0.19), residues: 735 sheet: -0.50 (0.52), residues: 102 loop : -1.69 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 520 HIS 0.006 0.001 HIS A1091 PHE 0.022 0.001 PHE A 649 TYR 0.021 0.001 TYR A1110 ARG 0.006 0.000 ARG A 971 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 543) hydrogen bonds : angle 4.20140 ( 1581) covalent geometry : bond 0.00270 (12991) covalent geometry : angle 0.58361 (17612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 193 TYR cc_start: 0.7716 (t80) cc_final: 0.7415 (t80) REVERT: A 888 TRP cc_start: 0.8445 (m100) cc_final: 0.7970 (m100) REVERT: A 1056 PHE cc_start: 0.8214 (t80) cc_final: 0.7743 (t80) REVERT: A 1140 MET cc_start: 0.7980 (tmm) cc_final: 0.7701 (tmm) REVERT: A 1304 ARG cc_start: 0.6882 (mmm160) cc_final: 0.6627 (mtp180) REVERT: A 1462 ARG cc_start: 0.6586 (ttm-80) cc_final: 0.6288 (ttp-110) outliers start: 10 outliers final: 7 residues processed: 157 average time/residue: 0.2637 time to fit residues: 59.9098 Evaluate side-chains 150 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 107 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS A 563 HIS ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.187384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130392 restraints weight = 26545.475| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.56 r_work: 0.3222 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12991 Z= 0.131 Angle : 0.593 10.605 17612 Z= 0.299 Chirality : 0.041 0.212 1954 Planarity : 0.004 0.048 2188 Dihedral : 11.895 164.596 1927 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.03 % Allowed : 12.37 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1528 helix: 1.31 (0.20), residues: 733 sheet: -0.57 (0.51), residues: 102 loop : -1.64 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 520 HIS 0.006 0.001 HIS A1091 PHE 0.021 0.001 PHE A 649 TYR 0.023 0.001 TYR A1110 ARG 0.006 0.000 ARG A 971 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 543) hydrogen bonds : angle 4.16845 ( 1581) covalent geometry : bond 0.00307 (12991) covalent geometry : angle 0.59263 (17612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: A 193 TYR cc_start: 0.7703 (t80) cc_final: 0.7440 (t80) REVERT: A 254 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: A 888 TRP cc_start: 0.8457 (m100) cc_final: 0.7951 (m100) REVERT: A 1031 ARG cc_start: 0.7970 (mtm180) cc_final: 0.7695 (mtm-85) REVERT: A 1080 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8073 (mt0) REVERT: A 1140 MET cc_start: 0.7980 (tmm) cc_final: 0.7679 (tmm) REVERT: A 1304 ARG cc_start: 0.6944 (mmm160) cc_final: 0.6660 (mtp180) REVERT: A 1462 ARG cc_start: 0.6577 (ttm-80) cc_final: 0.6257 (ttp-110) outliers start: 13 outliers final: 8 residues processed: 159 average time/residue: 0.2587 time to fit residues: 59.4670 Evaluate side-chains 156 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1080 GLN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 102 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 447 HIS A 563 HIS ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.184688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126841 restraints weight = 24915.270| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.39 r_work: 0.3173 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12991 Z= 0.186 Angle : 0.641 12.236 17612 Z= 0.322 Chirality : 0.042 0.208 1954 Planarity : 0.004 0.048 2188 Dihedral : 11.994 164.590 1927 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.18 % Allowed : 12.59 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.33 (0.21), residues: 1528 helix: 1.14 (0.19), residues: 741 sheet: -0.62 (0.51), residues: 102 loop : -1.75 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 433 HIS 0.007 0.001 HIS A1091 PHE 0.021 0.002 PHE A 649 TYR 0.021 0.002 TYR A1110 ARG 0.007 0.000 ARG A 971 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 543) hydrogen bonds : angle 4.33459 ( 1581) covalent geometry : bond 0.00446 (12991) covalent geometry : angle 0.64072 (17612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: A 193 TYR cc_start: 0.7742 (t80) cc_final: 0.7390 (t80) REVERT: A 888 TRP cc_start: 0.8525 (m100) cc_final: 0.7975 (m100) REVERT: A 1140 MET cc_start: 0.7982 (tmm) cc_final: 0.7677 (tmm) REVERT: A 1304 ARG cc_start: 0.7005 (mmm160) cc_final: 0.6710 (mtp180) REVERT: A 1462 ARG cc_start: 0.6672 (ttm-80) cc_final: 0.6291 (ttp-110) outliers start: 15 outliers final: 7 residues processed: 158 average time/residue: 0.2695 time to fit residues: 61.8777 Evaluate side-chains 154 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 7 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.186083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.131197 restraints weight = 23301.463| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.14 r_work: 0.3221 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12991 Z= 0.146 Angle : 0.622 12.397 17612 Z= 0.310 Chirality : 0.041 0.217 1954 Planarity : 0.004 0.043 2188 Dihedral : 11.955 164.191 1927 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.96 % Allowed : 13.18 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.31 (0.21), residues: 1528 helix: 1.15 (0.19), residues: 741 sheet: -0.54 (0.52), residues: 102 loop : -1.73 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 520 HIS 0.006 0.001 HIS A1091 PHE 0.019 0.001 PHE A 649 TYR 0.021 0.002 TYR A1110 ARG 0.009 0.000 ARG A 971 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 543) hydrogen bonds : angle 4.21571 ( 1581) covalent geometry : bond 0.00346 (12991) covalent geometry : angle 0.62194 (17612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 2.056 Fit side-chains revert: symmetry clash REVERT: A 193 TYR cc_start: 0.7750 (t80) cc_final: 0.7403 (t80) REVERT: A 254 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 489 LYS cc_start: 0.8432 (tptt) cc_final: 0.8169 (tptt) REVERT: A 888 TRP cc_start: 0.8452 (m100) cc_final: 0.7948 (m100) REVERT: A 1140 MET cc_start: 0.8006 (tmm) cc_final: 0.7688 (tmm) REVERT: A 1304 ARG cc_start: 0.6962 (mmm160) cc_final: 0.6676 (mtp180) REVERT: A 1462 ARG cc_start: 0.6528 (ttm-80) cc_final: 0.6180 (ttp-110) outliers start: 12 outliers final: 7 residues processed: 160 average time/residue: 0.3226 time to fit residues: 75.9214 Evaluate side-chains 156 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Chi-restraints excluded: chain A residue 1399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS A 563 HIS ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128153 restraints weight = 24659.967| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.22 r_work: 0.3152 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12991 Z= 0.168 Angle : 0.640 12.442 17612 Z= 0.320 Chirality : 0.042 0.214 1954 Planarity : 0.004 0.048 2188 Dihedral : 11.977 164.160 1927 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.88 % Allowed : 13.48 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1528 helix: 1.12 (0.19), residues: 739 sheet: -0.55 (0.52), residues: 102 loop : -1.71 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 433 HIS 0.006 0.001 HIS A1091 PHE 0.019 0.001 PHE A 649 TYR 0.022 0.002 TYR A 28 ARG 0.006 0.000 ARG A 971 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 543) hydrogen bonds : angle 4.26651 ( 1581) covalent geometry : bond 0.00405 (12991) covalent geometry : angle 0.64038 (17612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 1.861 Fit side-chains revert: symmetry clash REVERT: A 193 TYR cc_start: 0.7726 (t80) cc_final: 0.7396 (t80) REVERT: A 254 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: A 378 GLU cc_start: 0.6470 (mp0) cc_final: 0.6159 (mp0) REVERT: A 888 TRP cc_start: 0.8460 (m100) cc_final: 0.7905 (m100) REVERT: A 1140 MET cc_start: 0.7973 (tmm) cc_final: 0.7655 (tmm) REVERT: A 1304 ARG cc_start: 0.7088 (mmm160) cc_final: 0.6556 (mtp180) REVERT: A 1462 ARG cc_start: 0.6497 (ttm-80) cc_final: 0.5995 (ttp-110) outliers start: 11 outliers final: 8 residues processed: 153 average time/residue: 0.2798 time to fit residues: 62.4059 Evaluate side-chains 155 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 67 optimal weight: 0.0370 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 75 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 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 = 0.4126 r_free = 0.4126 target = 0.187218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129816 restraints weight = 26259.368| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.51 r_work: 0.3179 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12991 Z= 0.126 Angle : 0.626 12.999 17612 Z= 0.310 Chirality : 0.040 0.218 1954 Planarity : 0.004 0.049 2188 Dihedral : 11.932 163.731 1927 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.74 % Allowed : 13.77 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.21 (0.21), residues: 1528 helix: 1.19 (0.19), residues: 741 sheet: -0.48 (0.52), residues: 102 loop : -1.63 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 520 HIS 0.008 0.001 HIS A 447 PHE 0.021 0.001 PHE A 465 TYR 0.021 0.001 TYR A 28 ARG 0.011 0.000 ARG A1582 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 543) hydrogen bonds : angle 4.17272 ( 1581) covalent geometry : bond 0.00294 (12991) covalent geometry : angle 0.62589 (17612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 193 TYR cc_start: 0.7621 (t80) cc_final: 0.7345 (t80) REVERT: A 195 PHE cc_start: 0.8218 (t80) cc_final: 0.7980 (t80) REVERT: A 254 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: A 888 TRP cc_start: 0.8411 (m100) cc_final: 0.7867 (m100) REVERT: A 1140 MET cc_start: 0.7956 (tmm) cc_final: 0.7638 (tmm) REVERT: A 1462 ARG cc_start: 0.6419 (ttm-80) cc_final: 0.5981 (ttp-110) outliers start: 9 outliers final: 7 residues processed: 155 average time/residue: 0.2563 time to fit residues: 57.8539 Evaluate side-chains 150 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.1980 chunk 70 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 85 optimal weight: 0.2980 chunk 140 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.186641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129463 restraints weight = 24918.596| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.26 r_work: 0.3188 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12991 Z= 0.141 Angle : 0.627 13.434 17612 Z= 0.313 Chirality : 0.041 0.217 1954 Planarity : 0.004 0.050 2188 Dihedral : 11.914 163.726 1927 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.88 % Allowed : 13.55 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1528 helix: 1.18 (0.19), residues: 740 sheet: -0.45 (0.53), residues: 102 loop : -1.65 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 520 HIS 0.006 0.001 HIS A1091 PHE 0.021 0.001 PHE A 649 TYR 0.021 0.002 TYR A 28 ARG 0.009 0.000 ARG A 971 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 543) hydrogen bonds : angle 4.18898 ( 1581) covalent geometry : bond 0.00336 (12991) covalent geometry : angle 0.62724 (17612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8891.92 seconds wall clock time: 160 minutes 9.81 seconds (9609.81 seconds total)