Starting phenix.real_space_refine on Tue Sep 15 04:28:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5m64_3449/09_2026/5m64_3449.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m64_3449/09_2026/5m64_3449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5m64_3449/09_2026/5m64_3449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m64_3449/09_2026/5m64_3449.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5m64_3449/09_2026/5m64_3449.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5m64_3449/09_2026/5m64_3449.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5m64_3449/09_2026/5m64_3449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m64_3449/09_2026/5m64_3449.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 51 5.49 5 S 171 5.16 5 C 22559 2.51 5 N 6211 2.21 5 O 6878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.26s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35876 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1466, 11571 Classifications: {'peptide': 1466} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1406} Chain breaks: 7 Chain: "B" Number of atoms: 9301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9301 Classifications: {'peptide': 1170} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1110} Chain breaks: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1600 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 2 Chain: "H" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1075 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 472 Classifications: {'peptide': 64} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 60} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2573 Classifications: {'peptide': 323} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 304} Chain breaks: 2 Chain: "N" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1070 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 125} Chain breaks: 3 Chain: "S" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 397 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "T" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "R" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 145 Classifications: {'RNAv2': 7} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 781 SG CYS A 102 67.570 103.056 31.016 1.00 64.19 S ATOM 806 SG CYS A 105 69.516 102.164 29.309 1.00 63.96 S ATOM 1609 SG CYS A 233 71.552 105.447 31.007 1.00 63.59 S ATOM 1631 SG CYS A 236 69.020 104.799 28.795 1.00 61.24 S ATOM 461 SG CYS A 62 59.976 55.606 50.322 1.00 58.27 S ATOM 480 SG CYS A 65 62.226 54.447 50.681 1.00 56.92 S ATOM 535 SG CYS A 72 63.472 56.046 52.045 1.00 52.20 S ATOM 20152 SG CYS B1104 76.372 61.136 41.152 1.00 55.81 S ATOM 20178 SG CYS B1107 74.825 63.485 42.814 1.00 61.99 S ATOM 20325 SG CYS B1128 71.993 61.580 41.855 1.00 53.13 S ATOM 20353 SG CYS B1131 73.998 63.232 39.182 1.00 60.07 S ATOM 29091 SG CYS I 13 37.587 138.117 80.860 1.00 79.31 S ATOM 29211 SG CYS I 30 38.503 137.095 77.867 1.00 76.48 S ATOM 29532 SG CYS J 7 76.092 57.993 121.713 1.00 56.17 S ATOM 29555 SG CYS J 10 76.783 55.953 124.171 1.00 54.28 S ATOM 29835 SG CYS J 45 78.966 59.154 123.845 1.00 51.99 S ATOM 29841 SG CYS J 46 76.644 57.270 126.146 1.00 53.86 S ATOM 30867 SG CYS L 31 34.767 56.622 104.678 1.00 59.44 S ATOM 30887 SG CYS L 34 33.287 55.493 106.873 1.00 64.11 S ATOM 30991 SG CYS L 48 32.444 54.794 104.354 1.00 71.34 S ATOM 31014 SG CYS L 51 31.167 58.667 104.592 1.00 67.19 S Time building chain proxies: 7.47, per 1000 atoms: 0.21 Number of scatterers: 35876 At special positions: 0 Unit cell: (156.6, 168.75, 166.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 171 16.00 P 51 15.00 O 6878 8.00 N 6211 7.00 C 22559 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 27 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8254 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 54 sheets defined 35.9% alpha, 14.1% beta 15 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 87 through 101 removed outlier: 4.271A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.786A pdb=" N GLN A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 4.038A pdb=" N TYR A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 199 removed outlier: 3.581A pdb=" N MET A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.906A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.783A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.539A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.055A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 398 removed outlier: 3.946A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 4.116A pdb=" N ASP A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.746A pdb=" N ALA A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.090A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.700A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 619 through 625 removed outlier: 3.847A pdb=" N ALA A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 671 through 682 removed outlier: 3.963A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 4.025A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.615A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 Processing helix chain 'A' and resid 815 through 824 removed outlier: 3.728A pdb=" N ASN A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 839 through 849 removed outlier: 3.875A pdb=" N ARG A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.657A pdb=" N ALA A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 883 removed outlier: 3.940A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 892 through 911 Processing helix chain 'A' and resid 923 through 932 Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.968A pdb=" N GLN A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1025 removed outlier: 3.846A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1065 through 1072 removed outlier: 4.236A pdb=" N CYS A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 3.888A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1086 removed outlier: 4.051A pdb=" N ILE A1086 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1109 removed outlier: 3.999A pdb=" N HIS A1108 " --> pdb=" O TYR A1104 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A1109 " --> pdb=" O ARG A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.558A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 4.022A pdb=" N GLN A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.604A pdb=" N ILE A1188 " --> pdb=" O ALA A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1218 through 1228 removed outlier: 3.683A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1259 removed outlier: 4.828A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1265 Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 3.715A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 4.281A pdb=" N ASN A1315 " --> pdb=" O GLU A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1337 removed outlier: 4.026A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A1337 " --> pdb=" O ILE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1452 Processing helix chain 'A' and resid 1484 through 1494 removed outlier: 3.852A pdb=" N ILE A1488 " --> pdb=" O LEU A1484 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1552 Processing helix chain 'A' and resid 1554 through 1572 removed outlier: 3.883A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.886A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1614 Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.771A pdb=" N ASP A1628 " --> pdb=" O LYS A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1653 removed outlier: 3.701A pdb=" N SER A1653 " --> pdb=" O GLY A1650 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 4.261A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.780A pdb=" N ASN B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 286 through 292 Processing helix chain 'B' and resid 300 through 315 removed outlier: 3.910A pdb=" N ARG B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 Processing helix chain 'B' and resid 345 through 356 removed outlier: 4.053A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 365 through 368 removed outlier: 3.869A pdb=" N GLN B 368 " --> pdb=" O ASP B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 369 through 386 Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.605A pdb=" N HIS B 399 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 400 " --> pdb=" O THR B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 417 through 432 removed outlier: 3.833A pdb=" N LEU B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 506 through 511 removed outlier: 4.030A pdb=" N GLN B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 598 through 614 removed outlier: 3.714A pdb=" N ASP B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 removed outlier: 4.386A pdb=" N TYR B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 4.066A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.792A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 723 removed outlier: 3.770A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET B 721 " --> pdb=" O TYR B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.124A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 790 through 797 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 960 through 975 Processing helix chain 'B' and resid 991 through 996 Processing helix chain 'B' and resid 996 through 1004 removed outlier: 3.637A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.710A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS B1082 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1093 removed outlier: 3.704A pdb=" N GLN B1089 " --> pdb=" O SER B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1192 removed outlier: 3.907A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.182A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.653A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.620A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 330 removed outlier: 4.835A pdb=" N ILE C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 48 removed outlier: 4.104A pdb=" N GLN D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.402A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 73 Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.614A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 9 through 18 removed outlier: 3.978A pdb=" N THR G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG G 15 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.581A pdb=" N ASN H 131 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU H 132 " --> pdb=" O TYR H 129 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 128 through 133' Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 16 through 28 removed outlier: 4.522A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.624A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.986A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 141 Processing helix chain 'M' and resid 203 through 207 Processing helix chain 'M' and resid 209 through 214 removed outlier: 3.648A pdb=" N GLN M 214 " --> pdb=" O LYS M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 247 removed outlier: 4.084A pdb=" N LYS M 246 " --> pdb=" O TYR M 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU M 247 " --> pdb=" O VAL M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 250 No H-bonds generated for 'chain 'M' and resid 248 through 250' Processing helix chain 'M' and resid 252 through 254 No H-bonds generated for 'chain 'M' and resid 252 through 254' Processing helix chain 'M' and resid 255 through 274 removed outlier: 3.823A pdb=" N LEU M 261 " --> pdb=" O THR M 257 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU M 262 " --> pdb=" O LYS M 258 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER M 266 " --> pdb=" O LEU M 262 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU M 267 " --> pdb=" O TYR M 263 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY M 270 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL M 271 " --> pdb=" O LEU M 267 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR M 272 " --> pdb=" O LEU M 268 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU M 273 " --> pdb=" O LEU M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 285 Processing helix chain 'M' and resid 291 through 303 removed outlier: 3.547A pdb=" N VAL M 295 " --> pdb=" O PRO M 291 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE M 298 " --> pdb=" O LEU M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 315 removed outlier: 3.967A pdb=" N LYS M 314 " --> pdb=" O PHE M 310 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 340 removed outlier: 3.760A pdb=" N LEU M 329 " --> pdb=" O GLU M 325 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS M 330 " --> pdb=" O ASP M 326 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR M 331 " --> pdb=" O LYS M 327 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE M 335 " --> pdb=" O TYR M 331 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE M 336 " --> pdb=" O ILE M 332 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET M 337 " --> pdb=" O LEU M 333 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS M 338 " --> pdb=" O ALA M 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 353 Processing helix chain 'M' and resid 356 through 368 removed outlier: 3.513A pdb=" N PHE M 364 " --> pdb=" O VAL M 360 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG M 365 " --> pdb=" O VAL M 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL M 366 " --> pdb=" O SER M 362 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 383 removed outlier: 3.757A pdb=" N GLU M 380 " --> pdb=" O VAL M 376 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE M 382 " --> pdb=" O GLN M 378 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 389 removed outlier: 3.600A pdb=" N THR M 388 " --> pdb=" O PRO M 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 4.809A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B1199 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.698A pdb=" N ASP A 39 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 85 removed outlier: 10.490A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.535A pdb=" N LEU A 373 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 476 removed outlier: 4.044A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 495 removed outlier: 3.569A pdb=" N ASN A 590 " --> pdb=" O ASN A 634 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 507 through 510 removed outlier: 7.141A pdb=" N LYS A 576 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ILE A 536 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR A 578 " --> pdb=" O THR A 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB1, first strand: chain 'A' and resid 750 through 751 removed outlier: 6.621A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1031 through 1032 Processing sheet with id=AB3, first strand: chain 'A' and resid 1504 through 1507 removed outlier: 4.277A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 5.574A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A1271 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A1295 " --> pdb=" O LYS A1269 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A1269 " --> pdb=" O ARG A1295 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1275 through 1276 Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.818A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.818A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY G 83 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 74 removed outlier: 6.176A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 71 through 74 removed outlier: 3.836A pdb=" N GLU B 154 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP B 143 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC2, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC3, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.725A pdb=" N VAL B 249 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 550 through 552 removed outlier: 4.212A pdb=" N ARG B 648 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 550 through 552 removed outlier: 4.212A pdb=" N ARG B 648 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 592 through 597 removed outlier: 4.215A pdb=" N GLY B 594 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY B 639 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL B 629 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.715A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 769 through 775 removed outlier: 9.362A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 948 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B1031 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA B 771 " --> pdb=" O VAL B1031 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 769 " --> pdb=" O TYR B1033 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 824 Processing sheet with id=AD1, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD2, first strand: chain 'B' and resid 1099 through 1104 Processing sheet with id=AD3, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD4, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AD5, first strand: chain 'C' and resid 41 through 43 removed outlier: 4.172A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 10.338A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.534A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 86 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 168 through 169 removed outlier: 6.886A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.960A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN C 158 " --> pdb=" O THR C 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.902A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 234 through 235 removed outlier: 3.531A pdb=" N ASN C 234 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS C 290 " --> pdb=" O ASN C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 61 removed outlier: 7.110A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 156 removed outlier: 4.237A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 132 through 135 Processing sheet with id=AE6, first strand: chain 'G' and resid 154 through 156 Processing sheet with id=AE7, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=AE8, first strand: chain 'H' and resid 37 through 40 removed outlier: 6.805A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 100 through 103 removed outlier: 3.549A pdb=" N TYR H 102 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.510A pdb=" N ASP I 15 " --> pdb=" O CYS I 10 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 49 removed outlier: 3.744A pdb=" N ASN K 102 " --> pdb=" O SER K 92 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 37 through 38 Processing sheet with id=AF5, first strand: chain 'N' and resid 30 through 31 removed outlier: 6.067A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA M 22 " --> pdb=" O LEU N 110 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 91 through 92 removed outlier: 4.054A pdb=" N GLN M 75 " --> pdb=" O PHE N 58 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE N 58 " --> pdb=" O GLN M 75 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL M 77 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE N 56 " --> pdb=" O VAL M 77 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 80 through 81 removed outlier: 3.534A pdb=" N GLN N 52 " --> pdb=" O PHE M 81 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 344 through 345 removed outlier: 3.582A pdb=" N LYS M 372 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR M 396 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 88 through 92 1204 hydrogen bonds defined for protein. 3276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 10.23 Time building geometry restraints manager: 4.17 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: 10784 1.34 - 1.45: 5304 1.45 - 1.57: 20205 1.57 - 1.69: 103 1.69 - 1.81: 272 Bond restraints: 36668 Sorted by residual: bond pdb=" N ASP K 57 " pdb=" CA ASP K 57 " ideal model delta sigma weight residual 1.458 1.659 -0.201 1.28e-02 6.10e+03 2.48e+02 bond pdb=" CA GLY A 445 " pdb=" C GLY A 445 " ideal model delta sigma weight residual 1.514 1.350 0.164 1.41e-02 5.03e+03 1.35e+02 bond pdb=" N GLY A 449 " pdb=" CA GLY A 449 " ideal model delta sigma weight residual 1.449 1.599 -0.150 1.45e-02 4.76e+03 1.07e+02 bond pdb=" N LYS B1064 " pdb=" CA LYS B1064 " ideal model delta sigma weight residual 1.456 1.567 -0.111 1.36e-02 5.41e+03 6.70e+01 bond pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 1.531 1.651 -0.120 1.59e-02 3.96e+03 5.72e+01 ... (remaining 36663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.89: 49730 7.89 - 15.78: 17 15.78 - 23.67: 4 23.67 - 31.56: 2 31.56 - 39.45: 3 Bond angle restraints: 49756 Sorted by residual: angle pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" C ASP K 57 " ideal model delta sigma weight residual 112.45 73.00 39.45 1.39e+00 5.18e-01 8.06e+02 angle pdb=" N LYS B1064 " pdb=" CA LYS B1064 " pdb=" C LYS B1064 " ideal model delta sigma weight residual 114.04 79.22 34.82 1.24e+00 6.50e-01 7.88e+02 angle pdb=" N GLY A 449 " pdb=" CA GLY A 449 " pdb=" C GLY A 449 " ideal model delta sigma weight residual 113.18 79.14 34.04 2.37e+00 1.78e-01 2.06e+02 angle pdb=" C ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 110.11 87.07 23.04 1.89e+00 2.80e-01 1.49e+02 angle pdb=" N GLY K 58 " pdb=" CA GLY K 58 " pdb=" C GLY K 58 " ideal model delta sigma weight residual 113.18 88.05 25.13 2.37e+00 1.78e-01 1.12e+02 ... (remaining 49751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 20364 17.65 - 35.30: 1415 35.30 - 52.95: 408 52.95 - 70.60: 62 70.60 - 88.25: 12 Dihedral angle restraints: 22261 sinusoidal: 9500 harmonic: 12761 Sorted by residual: dihedral pdb=" C ASP K 57 " pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta harmonic sigma weight residual -122.60 -85.10 -37.50 0 2.50e+00 1.60e-01 2.25e+02 dihedral pdb=" C LYS B1064 " pdb=" N LYS B1064 " pdb=" CA LYS B1064 " pdb=" CB LYS B1064 " ideal model delta harmonic sigma weight residual -122.60 -96.53 -26.07 0 2.50e+00 1.60e-01 1.09e+02 dihedral pdb=" N ASP K 57 " pdb=" C ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta harmonic sigma weight residual 122.80 97.09 25.71 0 2.50e+00 1.60e-01 1.06e+02 ... (remaining 22258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 5575 0.290 - 0.579: 4 0.579 - 0.869: 0 0.869 - 1.158: 1 1.158 - 1.448: 1 Chirality restraints: 5581 Sorted by residual: chirality pdb=" CA ASP K 57 " pdb=" N ASP K 57 " pdb=" C ASP K 57 " pdb=" CB ASP K 57 " both_signs ideal model delta sigma weight residual False 2.51 3.96 -1.45 2.00e-01 2.50e+01 5.24e+01 chirality pdb=" CA LYS B1064 " pdb=" N LYS B1064 " pdb=" C LYS B1064 " pdb=" CB LYS B1064 " both_signs ideal model delta sigma weight residual False 2.51 3.58 -1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" CA LYS A 866 " pdb=" N LYS A 866 " pdb=" C LYS A 866 " pdb=" CB LYS A 866 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 5578 not shown) Planarity restraints: 6243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY K 58 " -0.030 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C GLY K 58 " 0.102 2.00e-02 2.50e+03 pdb=" O GLY K 58 " -0.038 2.00e-02 2.50e+03 pdb=" N THR K 59 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 247 " 0.030 2.00e-02 2.50e+03 5.86e-02 3.43e+01 pdb=" C GLY A 247 " -0.101 2.00e-02 2.50e+03 pdb=" O GLY A 247 " 0.038 2.00e-02 2.50e+03 pdb=" N PHE A 248 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 445 " 0.031 2.00e-02 2.50e+03 5.84e-02 3.41e+01 pdb=" C GLY A 445 " -0.101 2.00e-02 2.50e+03 pdb=" O GLY A 445 " 0.034 2.00e-02 2.50e+03 pdb=" N ARG A 446 " 0.036 2.00e-02 2.50e+03 ... (remaining 6240 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 15 2.20 - 2.88: 13014 2.88 - 3.55: 50981 3.55 - 4.23: 83606 4.23 - 4.90: 133998 Nonbonded interactions: 281614 Sorted by model distance: nonbonded pdb=" OD2 ASP M 197 " pdb=" OE1 GLU M 199 " model vdw 1.529 3.040 nonbonded pdb=" CA ALA M 369 " pdb=" SD MET M 397 " model vdw 1.783 3.830 nonbonded pdb=" N ASP K 57 " pdb=" N GLY K 58 " model vdw 1.969 2.560 nonbonded pdb=" N LYS B1064 " pdb=" N ARG B1065 " model vdw 2.002 2.560 nonbonded pdb=" CG ASN A 757 " pdb=" O SER A 764 " model vdw 2.062 3.270 ... (remaining 281609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.050 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 42.280 Find NCS groups from input model: 0.180 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 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 : 0.004 0.363 36691 Z= 0.279 Angle : 0.963 50.264 49783 Z= 0.431 Chirality : 0.050 1.448 5581 Planarity : 0.004 0.074 6243 Dihedral : 13.010 88.250 14007 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.89 % Favored : 94.99 % Rotamer: Outliers : 2.03 % Allowed : 15.27 % Favored : 82.70 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.10), residues: 4313 helix: -3.36 (0.09), residues: 1332 sheet: -2.45 (0.20), residues: 544 loop : -3.02 (0.11), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 368 TYR 0.013 0.001 TYR B 717 PHE 0.010 0.001 PHE B 691 TRP 0.012 0.001 TRP B 836 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.20 (36668) covalent geometry : angle 0.69884 / 0.41 (49756) hydrogen bonds : bond 0.18333 / 12.10 ( 1202) hydrogen bonds : angle 10.48313 / 7.06 ( 3340) metal coordination : bond 0.02619 / 1.62 ( 22) metal coordination : angle 28.48445 / 17.04 ( 27) Misc. bond : bond 0.36251 / 19.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1253 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.6539 (m) cc_final: 0.5419 (m) REVERT: A 99 ARG cc_start: 0.8748 (ptp90) cc_final: 0.8346 (ptt180) REVERT: A 103 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7181 (pp) REVERT: A 180 GLU cc_start: 0.7992 (pp20) cc_final: 0.7105 (mm-30) REVERT: A 211 THR cc_start: 0.7993 (t) cc_final: 0.7667 (m) REVERT: A 212 VAL cc_start: 0.9507 (m) cc_final: 0.9077 (m) REVERT: A 338 VAL cc_start: 0.8416 (p) cc_final: 0.8200 (p) REVERT: A 348 LYS cc_start: 0.7168 (mmtt) cc_final: 0.5788 (tmtt) REVERT: A 358 ASP cc_start: 0.6555 (m-30) cc_final: 0.6241 (m-30) REVERT: A 458 GLN cc_start: 0.7770 (pm20) cc_final: 0.6190 (mt0) REVERT: A 562 LEU cc_start: 0.7684 (tp) cc_final: 0.7379 (mm) REVERT: A 646 GLU cc_start: 0.7231 (pp20) cc_final: 0.6962 (mp0) REVERT: A 655 SER cc_start: 0.8987 (m) cc_final: 0.8554 (t) REVERT: A 656 GLN cc_start: 0.8594 (mp-120) cc_final: 0.8302 (mp10) REVERT: A 709 ARG cc_start: 0.3637 (OUTLIER) cc_final: 0.2907 (ptt-90) REVERT: A 764 SER cc_start: 0.7178 (OUTLIER) cc_final: 0.6791 (p) REVERT: A 765 LEU cc_start: 0.7230 (mm) cc_final: 0.6912 (pt) REVERT: A 782 ASP cc_start: 0.6566 (t0) cc_final: 0.6205 (t0) REVERT: A 793 ILE cc_start: 0.9048 (tp) cc_final: 0.7991 (tt) REVERT: A 795 HIS cc_start: 0.6922 (t-90) cc_final: 0.6467 (t-170) REVERT: A 796 SER cc_start: 0.8691 (m) cc_final: 0.8379 (p) REVERT: A 830 MET cc_start: 0.8305 (tpt) cc_final: 0.7961 (tpt) REVERT: A 876 LEU cc_start: 0.7781 (tt) cc_final: 0.7139 (mm) REVERT: A 960 MET cc_start: 0.7460 (ppp) cc_final: 0.7205 (ppp) REVERT: A 995 TYR cc_start: 0.7320 (t80) cc_final: 0.6265 (t80) REVERT: A 1016 SER cc_start: 0.8882 (p) cc_final: 0.8621 (t) REVERT: A 1072 ASN cc_start: 0.8030 (m-40) cc_final: 0.7635 (m-40) REVERT: A 1136 VAL cc_start: 0.7496 (m) cc_final: 0.6556 (m) REVERT: A 1200 MET cc_start: 0.8248 (ptt) cc_final: 0.8013 (ptt) REVERT: A 1293 HIS cc_start: 0.8699 (t-170) cc_final: 0.8130 (t-170) REVERT: B 50 ASN cc_start: 0.8418 (t0) cc_final: 0.8084 (t0) REVERT: B 60 LEU cc_start: 0.8705 (mm) cc_final: 0.8049 (tt) REVERT: B 153 PHE cc_start: 0.7035 (t80) cc_final: 0.6430 (p90) REVERT: B 209 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: B 275 MET cc_start: 0.6280 (ptm) cc_final: 0.5879 (ptm) REVERT: B 285 ASP cc_start: 0.7362 (p0) cc_final: 0.7077 (p0) REVERT: B 334 PHE cc_start: 0.8391 (m-80) cc_final: 0.8079 (m-80) REVERT: B 425 ILE cc_start: 0.8418 (pt) cc_final: 0.8191 (tp) REVERT: B 430 MET cc_start: 0.8082 (tmm) cc_final: 0.7290 (tmm) REVERT: B 613 VAL cc_start: 0.8547 (m) cc_final: 0.8326 (p) REVERT: B 646 HIS cc_start: 0.7819 (m90) cc_final: 0.6881 (m-70) REVERT: B 673 ASN cc_start: 0.9156 (p0) cc_final: 0.8822 (p0) REVERT: B 708 ASP cc_start: 0.7264 (m-30) cc_final: 0.6418 (m-30) REVERT: B 790 ASN cc_start: 0.7986 (t160) cc_final: 0.7211 (t0) REVERT: B 856 ASP cc_start: 0.8659 (t0) cc_final: 0.8173 (m-30) REVERT: B 936 MET cc_start: 0.6703 (mtm) cc_final: 0.6318 (mtm) REVERT: B 963 PHE cc_start: 0.8041 (m-80) cc_final: 0.7277 (m-80) REVERT: B 974 LEU cc_start: 0.7728 (tm) cc_final: 0.7356 (tm) REVERT: B 980 ASP cc_start: 0.6800 (t0) cc_final: 0.5646 (p0) REVERT: B 1039 MET cc_start: 0.7155 (tmt) cc_final: 0.5850 (tmt) REVERT: B 1080 ILE cc_start: 0.8981 (tp) cc_final: 0.8725 (tt) REVERT: B 1092 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7522 (tm) REVERT: C 125 LYS cc_start: 0.7812 (tttt) cc_final: 0.7481 (tppt) REVERT: C 152 ASP cc_start: 0.6580 (m-30) cc_final: 0.5829 (t0) REVERT: C 227 TYR cc_start: 0.6474 (m-10) cc_final: 0.6000 (m-80) REVERT: C 330 ASN cc_start: 0.7107 (p0) cc_final: 0.6112 (m-40) REVERT: E 13 TRP cc_start: 0.8348 (t60) cc_final: 0.7769 (t60) REVERT: E 24 LYS cc_start: 0.8852 (tttt) cc_final: 0.8648 (tptt) REVERT: E 41 ASP cc_start: 0.7506 (m-30) cc_final: 0.7247 (m-30) REVERT: E 58 MET cc_start: 0.7126 (mtp) cc_final: 0.6329 (mtp) REVERT: E 97 VAL cc_start: 0.8756 (t) cc_final: 0.8466 (p) REVERT: E 174 GLN cc_start: 0.8806 (tt0) cc_final: 0.8445 (mt0) REVERT: E 186 LEU cc_start: 0.7653 (tt) cc_final: 0.7206 (tt) REVERT: E 208 TYR cc_start: 0.7459 (p90) cc_final: 0.6713 (p90) REVERT: F 122 MET cc_start: 0.7799 (mtp) cc_final: 0.7440 (mtm) REVERT: F 130 ILE cc_start: 0.8653 (tp) cc_final: 0.8326 (mt) REVERT: G 53 TYR cc_start: 0.5770 (m-80) cc_final: 0.5065 (m-80) REVERT: G 67 ASN cc_start: 0.8451 (m-40) cc_final: 0.8010 (t0) REVERT: G 122 LEU cc_start: 0.8160 (mm) cc_final: 0.7950 (mm) REVERT: G 160 ASN cc_start: 0.4757 (t160) cc_final: 0.4453 (t0) REVERT: G 169 VAL cc_start: 0.8288 (t) cc_final: 0.8086 (p) REVERT: G 219 ASP cc_start: 0.4564 (p0) cc_final: 0.4309 (p0) REVERT: H 17 PRO cc_start: 0.8281 (Cg_exo) cc_final: 0.7989 (Cg_endo) REVERT: H 34 ASP cc_start: 0.8034 (m-30) cc_final: 0.7572 (p0) REVERT: H 40 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6378 (mm) REVERT: H 104 PHE cc_start: 0.6712 (m-10) cc_final: 0.5966 (m-10) REVERT: H 131 ASN cc_start: 0.6151 (p0) cc_final: 0.4770 (t0) REVERT: H 133 ASN cc_start: 0.8553 (p0) cc_final: 0.7615 (p0) REVERT: K 59 THR cc_start: 0.8602 (m) cc_final: 0.7922 (m) REVERT: K 63 PHE cc_start: 0.7984 (m-10) cc_final: 0.7684 (m-10) REVERT: K 68 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7260 (mm-30) REVERT: K 142 MET cc_start: 0.6111 (mtm) cc_final: 0.4902 (ttm) REVERT: L 28 LYS cc_start: 0.7938 (pmtt) cc_final: 0.6325 (mmpt) REVERT: L 64 LEU cc_start: 0.8447 (tp) cc_final: 0.8179 (pp) REVERT: L 68 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6373 (pm20) REVERT: M 18 GLN cc_start: 0.7890 (tt0) cc_final: 0.7361 (tt0) REVERT: M 49 ASP cc_start: 0.7969 (m-30) cc_final: 0.7573 (m-30) outliers start: 79 outliers final: 16 residues processed: 1304 average time/residue: 0.2536 time to fit residues: 522.6074 Evaluate side-chains 780 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 758 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 93 GLN A 332 GLN A 344 ASN A 470 HIS A 537 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN A 640 ASN A 691 GLN A 748 ASN A 795 HIS ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 ASN A 939 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1062 HIS A1113 HIS ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1199 GLN A1323 HIS A1454 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS B 248 ASN B 473 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN B1082 HIS ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN B1171 ASN C 88 ASN C 130 ASN D 17 ASN D 26 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS H 134 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 323 GLN M 351 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.168466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.152405 restraints weight = 77254.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.153862 restraints weight = 52878.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.154881 restraints weight = 39875.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155461 restraints weight = 31466.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.155612 restraints weight = 29591.935| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36691 Z= 0.181 Angle : 0.804 48.482 49783 Z= 0.380 Chirality : 0.048 0.287 5581 Planarity : 0.006 0.079 6243 Dihedral : 10.831 89.865 5312 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.32 % Rotamer: Outliers : 0.39 % Allowed : 5.09 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.11), residues: 4313 helix: -2.10 (0.11), residues: 1361 sheet: -2.05 (0.21), residues: 543 loop : -2.64 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 323 TYR 0.038 0.002 TYR A 618 PHE 0.038 0.002 PHE E 82 TRP 0.024 0.002 TRP B 836 HIS 0.011 0.002 HIS B 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (36668) covalent geometry : angle 0.73587 / 0.38 (49756) hydrogen bonds : bond 0.05052 / 3.37 ( 1202) hydrogen bonds : angle 7.16484 / 4.83 ( 3340) metal coordination : bond 0.01749 / 0.97 ( 22) metal coordination : angle 13.90013 / 7.80 ( 27) Misc. bond : bond 0.02299 / 1.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 953 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.8508 (ptp90) cc_final: 0.8055 (ptt180) REVERT: A 130 ILE cc_start: 0.7064 (pt) cc_final: 0.6793 (tp) REVERT: A 181 LEU cc_start: 0.8042 (mt) cc_final: 0.7806 (tp) REVERT: A 211 THR cc_start: 0.7735 (t) cc_final: 0.7184 (m) REVERT: A 212 VAL cc_start: 0.9191 (m) cc_final: 0.8903 (m) REVERT: A 555 LYS cc_start: 0.7735 (mttp) cc_final: 0.7481 (mttm) REVERT: A 562 LEU cc_start: 0.7880 (tp) cc_final: 0.7569 (mm) REVERT: A 580 HIS cc_start: 0.6371 (m90) cc_final: 0.5492 (m170) REVERT: A 747 ILE cc_start: 0.8634 (pt) cc_final: 0.8332 (pt) REVERT: A 765 LEU cc_start: 0.6499 (mm) cc_final: 0.6161 (pt) REVERT: A 773 ASP cc_start: 0.7559 (t70) cc_final: 0.7158 (t0) REVERT: A 830 MET cc_start: 0.8615 (tpt) cc_final: 0.8177 (tpt) REVERT: A 848 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8195 (mttm) REVERT: A 876 LEU cc_start: 0.7654 (tt) cc_final: 0.7257 (mm) REVERT: A 993 GLN cc_start: 0.8879 (mp10) cc_final: 0.8586 (mp10) REVERT: A 1019 LEU cc_start: 0.8947 (tp) cc_final: 0.8724 (tp) REVERT: A 1072 ASN cc_start: 0.7580 (m-40) cc_final: 0.6860 (p0) REVERT: A 1293 HIS cc_start: 0.8491 (t-170) cc_final: 0.7030 (t70) REVERT: A 1565 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 1588 MET cc_start: 0.8841 (tpp) cc_final: 0.8284 (tpp) REVERT: B 60 LEU cc_start: 0.8467 (mm) cc_final: 0.8033 (tt) REVERT: B 131 THR cc_start: 0.7859 (p) cc_final: 0.7602 (p) REVERT: B 153 PHE cc_start: 0.6892 (t80) cc_final: 0.6435 (p90) REVERT: B 275 MET cc_start: 0.6596 (ptm) cc_final: 0.6055 (ptm) REVERT: B 461 MET cc_start: 0.8378 (mmp) cc_final: 0.8012 (mmt) REVERT: B 603 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7531 (tp) REVERT: B 646 HIS cc_start: 0.7132 (m90) cc_final: 0.6374 (m-70) REVERT: B 708 ASP cc_start: 0.7164 (m-30) cc_final: 0.6384 (m-30) REVERT: B 765 PHE cc_start: 0.8897 (m-80) cc_final: 0.8157 (m-80) REVERT: B 856 ASP cc_start: 0.8168 (t0) cc_final: 0.7281 (m-30) REVERT: B 882 ILE cc_start: 0.8125 (pt) cc_final: 0.7790 (mp) REVERT: B 980 ASP cc_start: 0.7078 (t0) cc_final: 0.5537 (p0) REVERT: B 1065 ARG cc_start: 0.8629 (mtt90) cc_final: 0.8379 (mpp-170) REVERT: B 1080 ILE cc_start: 0.8809 (tp) cc_final: 0.8456 (tt) REVERT: C 227 TYR cc_start: 0.6766 (m-10) cc_final: 0.6297 (m-80) REVERT: C 326 GLU cc_start: 0.8634 (pt0) cc_final: 0.8325 (pt0) REVERT: C 330 ASN cc_start: 0.6912 (p0) cc_final: 0.6490 (m-40) REVERT: D 29 GLN cc_start: 0.7309 (tm-30) cc_final: 0.7088 (tm-30) REVERT: D 37 LEU cc_start: 0.6556 (mm) cc_final: 0.5930 (tt) REVERT: E 24 LYS cc_start: 0.8888 (tttt) cc_final: 0.8549 (tptt) REVERT: E 41 ASP cc_start: 0.8068 (m-30) cc_final: 0.7469 (m-30) REVERT: E 58 MET cc_start: 0.8533 (mtp) cc_final: 0.8081 (ttm) REVERT: E 97 VAL cc_start: 0.8894 (t) cc_final: 0.8565 (p) REVERT: E 113 GLN cc_start: 0.8056 (mp10) cc_final: 0.7765 (mm-40) REVERT: E 137 GLU cc_start: 0.7278 (pm20) cc_final: 0.7071 (pm20) REVERT: E 152 LYS cc_start: 0.8370 (tmtt) cc_final: 0.7976 (tptm) REVERT: G 15 ARG cc_start: 0.8009 (mmp-170) cc_final: 0.7694 (mmp80) REVERT: G 53 TYR cc_start: 0.5641 (m-80) cc_final: 0.5104 (m-80) REVERT: G 149 ILE cc_start: 0.8341 (tt) cc_final: 0.8025 (tt) REVERT: G 160 ASN cc_start: 0.5144 (t0) cc_final: 0.4881 (t0) REVERT: G 169 VAL cc_start: 0.8390 (t) cc_final: 0.8167 (p) REVERT: G 219 ASP cc_start: 0.5337 (p0) cc_final: 0.5127 (p0) REVERT: H 34 ASP cc_start: 0.7973 (m-30) cc_final: 0.7663 (p0) REVERT: H 40 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6456 (mm) REVERT: H 104 PHE cc_start: 0.6446 (m-10) cc_final: 0.5954 (m-10) REVERT: H 114 VAL cc_start: 0.7646 (m) cc_final: 0.7111 (m) REVERT: H 131 ASN cc_start: 0.5884 (p0) cc_final: 0.4449 (t0) REVERT: H 133 ASN cc_start: 0.8999 (p0) cc_final: 0.7767 (p0) REVERT: K 65 ILE cc_start: 0.8636 (pt) cc_final: 0.8408 (pt) REVERT: K 142 MET cc_start: 0.5992 (mtm) cc_final: 0.4566 (ttm) REVERT: M 49 ASP cc_start: 0.7334 (m-30) cc_final: 0.7062 (m-30) REVERT: M 351 HIS cc_start: 0.6527 (m170) cc_final: 0.5864 (t-90) outliers start: 15 outliers final: 2 residues processed: 962 average time/residue: 0.2393 time to fit residues: 370.2948 Evaluate side-chains 688 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 684 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 397 optimal weight: 0.9990 chunk 412 optimal weight: 10.0000 chunk 111 optimal weight: 0.3980 chunk 99 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 428 optimal weight: 9.9990 chunk 427 optimal weight: 2.9990 chunk 257 optimal weight: 0.0770 chunk 337 optimal weight: 0.8980 chunk 303 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1199 GLN A1323 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 128 GLN B 182 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 682 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN B1171 ASN C 58 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN J 53 HIS ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.169179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.152573 restraints weight = 76954.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.154250 restraints weight = 53066.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.155468 restraints weight = 40784.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.156290 restraints weight = 30315.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.156498 restraints weight = 27287.797| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 36691 Z= 0.139 Angle : 0.742 46.109 49783 Z= 0.347 Chirality : 0.046 0.262 5581 Planarity : 0.005 0.074 6243 Dihedral : 10.865 89.781 5312 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.93 % Favored : 93.04 % Rotamer: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.11), residues: 4313 helix: -1.64 (0.12), residues: 1360 sheet: -1.92 (0.21), residues: 558 loop : -2.46 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 379 TYR 0.026 0.002 TYR B 717 PHE 0.039 0.002 PHE B 496 TRP 0.018 0.002 TRP A 530 HIS 0.014 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (36668) covalent geometry : angle 0.68290 / 0.34 (49756) hydrogen bonds : bond 0.04691 / 3.13 ( 1202) hydrogen bonds : angle 6.63066 / 4.48 ( 3340) metal coordination : bond 0.01260 / 0.68 ( 22) metal coordination : angle 12.47201 / 6.96 ( 27) Misc. bond : bond 0.00111 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 901 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7496 (pt0) cc_final: 0.6788 (pt0) REVERT: A 99 ARG cc_start: 0.8471 (ptp90) cc_final: 0.7797 (ptt180) REVERT: A 211 THR cc_start: 0.7912 (t) cc_final: 0.7401 (m) REVERT: A 212 VAL cc_start: 0.9176 (m) cc_final: 0.8826 (m) REVERT: A 222 GLU cc_start: 0.7269 (tp30) cc_final: 0.6872 (tp30) REVERT: A 228 LEU cc_start: 0.5920 (mp) cc_final: 0.5680 (mp) REVERT: A 555 LYS cc_start: 0.7609 (mttp) cc_final: 0.7357 (mttm) REVERT: A 562 LEU cc_start: 0.7821 (tp) cc_final: 0.7545 (mm) REVERT: A 646 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6795 (mt-10) REVERT: A 703 GLU cc_start: 0.7950 (mp0) cc_final: 0.6823 (mm-30) REVERT: A 747 ILE cc_start: 0.8703 (pt) cc_final: 0.8386 (pt) REVERT: A 765 LEU cc_start: 0.6455 (mm) cc_final: 0.6132 (pt) REVERT: A 773 ASP cc_start: 0.7544 (t70) cc_final: 0.7078 (t0) REVERT: A 830 MET cc_start: 0.8573 (tpt) cc_final: 0.8215 (tpt) REVERT: A 842 TRP cc_start: 0.5768 (m-90) cc_final: 0.5446 (m-90) REVERT: A 848 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8034 (mttm) REVERT: A 876 LEU cc_start: 0.7673 (tt) cc_final: 0.7240 (mm) REVERT: A 993 GLN cc_start: 0.8844 (mp10) cc_final: 0.8627 (mp10) REVERT: A 1072 ASN cc_start: 0.7867 (m-40) cc_final: 0.7345 (m-40) REVERT: A 1185 VAL cc_start: 0.9038 (t) cc_final: 0.8826 (p) REVERT: A 1293 HIS cc_start: 0.7939 (t-170) cc_final: 0.7410 (t70) REVERT: A 1308 VAL cc_start: 0.9441 (m) cc_final: 0.9147 (t) REVERT: A 1473 LYS cc_start: 0.7984 (pttt) cc_final: 0.7485 (pttt) REVERT: B 50 ASN cc_start: 0.8120 (t0) cc_final: 0.7557 (t0) REVERT: B 60 LEU cc_start: 0.8400 (mm) cc_final: 0.8040 (tt) REVERT: B 131 THR cc_start: 0.7844 (p) cc_final: 0.7519 (p) REVERT: B 153 PHE cc_start: 0.6775 (t80) cc_final: 0.6501 (p90) REVERT: B 275 MET cc_start: 0.6465 (ptm) cc_final: 0.6009 (ptm) REVERT: B 327 LEU cc_start: 0.7914 (tp) cc_final: 0.7332 (pp) REVERT: B 411 MET cc_start: 0.7352 (mtm) cc_final: 0.6838 (mtp) REVERT: B 421 LEU cc_start: 0.7296 (tp) cc_final: 0.6785 (tp) REVERT: B 461 MET cc_start: 0.8355 (mmp) cc_final: 0.7375 (mmt) REVERT: B 519 LYS cc_start: 0.6460 (mmmt) cc_final: 0.6129 (mtmm) REVERT: B 646 HIS cc_start: 0.6991 (m90) cc_final: 0.6267 (m-70) REVERT: B 668 GLU cc_start: 0.8255 (mp0) cc_final: 0.8046 (mp0) REVERT: B 708 ASP cc_start: 0.7122 (m-30) cc_final: 0.6411 (m-30) REVERT: B 765 PHE cc_start: 0.8887 (m-80) cc_final: 0.8092 (m-80) REVERT: B 856 ASP cc_start: 0.8311 (t0) cc_final: 0.7260 (m-30) REVERT: B 882 ILE cc_start: 0.8223 (pt) cc_final: 0.7868 (mp) REVERT: B 980 ASP cc_start: 0.7113 (t0) cc_final: 0.5540 (p0) REVERT: B 1080 ILE cc_start: 0.8812 (tp) cc_final: 0.8597 (tt) REVERT: C 227 TYR cc_start: 0.6772 (m-10) cc_final: 0.6295 (m-80) REVERT: C 326 GLU cc_start: 0.8654 (pt0) cc_final: 0.8414 (pt0) REVERT: C 330 ASN cc_start: 0.7421 (p0) cc_final: 0.6664 (m-40) REVERT: D 29 GLN cc_start: 0.7432 (tm-30) cc_final: 0.7153 (tm-30) REVERT: D 37 LEU cc_start: 0.6679 (mm) cc_final: 0.5875 (tt) REVERT: E 24 LYS cc_start: 0.8801 (tttt) cc_final: 0.8520 (tptt) REVERT: E 41 ASP cc_start: 0.8139 (m-30) cc_final: 0.7815 (m-30) REVERT: E 58 MET cc_start: 0.8755 (mtp) cc_final: 0.8466 (mtm) REVERT: E 97 VAL cc_start: 0.8880 (t) cc_final: 0.8539 (p) REVERT: E 112 TYR cc_start: 0.8644 (p90) cc_final: 0.8047 (p90) REVERT: E 133 GLU cc_start: 0.7405 (pm20) cc_final: 0.7131 (pm20) REVERT: E 137 GLU cc_start: 0.7381 (pm20) cc_final: 0.7132 (pm20) REVERT: E 152 LYS cc_start: 0.8339 (tmtt) cc_final: 0.7999 (tptm) REVERT: E 177 ARG cc_start: 0.8521 (ptt90) cc_final: 0.8055 (ptm-80) REVERT: F 66 ARG cc_start: 0.7156 (mmp80) cc_final: 0.6860 (mmp80) REVERT: G 15 ARG cc_start: 0.8100 (mmp-170) cc_final: 0.7640 (mmp80) REVERT: G 53 TYR cc_start: 0.5343 (m-80) cc_final: 0.5011 (m-80) REVERT: G 149 ILE cc_start: 0.8285 (tt) cc_final: 0.7821 (tt) REVERT: G 160 ASN cc_start: 0.5087 (t0) cc_final: 0.4859 (t0) REVERT: G 169 VAL cc_start: 0.8423 (t) cc_final: 0.8196 (p) REVERT: G 219 ASP cc_start: 0.5602 (p0) cc_final: 0.5296 (p0) REVERT: H 34 ASP cc_start: 0.7923 (m-30) cc_final: 0.7437 (p0) REVERT: H 104 PHE cc_start: 0.6601 (m-10) cc_final: 0.6346 (m-10) REVERT: H 131 ASN cc_start: 0.5885 (p0) cc_final: 0.4532 (t0) REVERT: H 133 ASN cc_start: 0.8877 (p0) cc_final: 0.7669 (p0) REVERT: J 1 MET cc_start: 0.5249 (tmm) cc_final: 0.5010 (ttt) REVERT: K 62 SER cc_start: 0.6370 (m) cc_final: 0.3969 (m) REVERT: K 64 GLN cc_start: 0.4108 (tp40) cc_final: 0.3725 (tp40) REVERT: K 65 ILE cc_start: 0.8564 (pt) cc_final: 0.8344 (pt) REVERT: K 67 GLU cc_start: 0.7201 (tp30) cc_final: 0.6247 (tp30) REVERT: K 68 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6580 (mm-30) REVERT: K 142 MET cc_start: 0.5996 (mtm) cc_final: 0.4564 (ttm) REVERT: M 18 GLN cc_start: 0.7726 (tt0) cc_final: 0.7323 (tt0) REVERT: M 39 ASP cc_start: 0.6038 (p0) cc_final: 0.5301 (t0) REVERT: M 49 ASP cc_start: 0.7181 (m-30) cc_final: 0.6944 (m-30) REVERT: M 351 HIS cc_start: 0.6658 (m170) cc_final: 0.6030 (t-90) outliers start: 4 outliers final: 3 residues processed: 905 average time/residue: 0.2336 time to fit residues: 348.0521 Evaluate side-chains 672 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 669 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 74 optimal weight: 5.9990 chunk 379 optimal weight: 3.9990 chunk 225 optimal weight: 0.0020 chunk 157 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 340 optimal weight: 7.9990 chunk 315 optimal weight: 0.0870 chunk 318 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 798 HIS A 880 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1199 GLN A1314 GLN ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 182 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 ASN C 58 ASN C 323 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN M 57 ASN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.167357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150874 restraints weight = 77197.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.152822 restraints weight = 54729.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153482 restraints weight = 40037.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.154156 restraints weight = 33083.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.154294 restraints weight = 30517.980| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36691 Z= 0.142 Angle : 0.728 46.188 49783 Z= 0.343 Chirality : 0.046 0.264 5581 Planarity : 0.005 0.080 6243 Dihedral : 10.914 89.721 5312 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.13 % Allowed : 4.37 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.12), residues: 4313 helix: -1.23 (0.13), residues: 1357 sheet: -1.74 (0.21), residues: 544 loop : -2.28 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 366 TYR 0.030 0.002 TYR G 123 PHE 0.048 0.002 PHE D 39 TRP 0.022 0.002 TRP E 79 HIS 0.011 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (36668) covalent geometry : angle 0.66815 / 0.34 (49756) hydrogen bonds : bond 0.04557 / 3.02 ( 1202) hydrogen bonds : angle 6.27255 / 4.24 ( 3340) metal coordination : bond 0.01129 / 0.62 ( 22) metal coordination : angle 12.46732 / 6.88 ( 27) Misc. bond : bond 0.00069 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 874 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7053 (pt) cc_final: 0.6713 (tp) REVERT: A 211 THR cc_start: 0.8056 (t) cc_final: 0.7400 (m) REVERT: A 212 VAL cc_start: 0.9161 (m) cc_final: 0.8878 (m) REVERT: A 222 GLU cc_start: 0.6904 (tp30) cc_final: 0.6534 (tp30) REVERT: A 495 ILE cc_start: 0.8631 (mm) cc_final: 0.8379 (mm) REVERT: A 555 LYS cc_start: 0.7735 (mttp) cc_final: 0.7497 (mttm) REVERT: A 562 LEU cc_start: 0.7782 (tp) cc_final: 0.7471 (mm) REVERT: A 646 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6775 (mt-10) REVERT: A 747 ILE cc_start: 0.8668 (pt) cc_final: 0.8344 (pt) REVERT: A 749 LEU cc_start: 0.7434 (mm) cc_final: 0.7144 (mm) REVERT: A 765 LEU cc_start: 0.6712 (mm) cc_final: 0.6422 (pt) REVERT: A 773 ASP cc_start: 0.7571 (t70) cc_final: 0.7135 (t0) REVERT: A 830 MET cc_start: 0.8561 (tpt) cc_final: 0.8184 (tpt) REVERT: A 876 LEU cc_start: 0.7805 (tt) cc_final: 0.7317 (mm) REVERT: A 1072 ASN cc_start: 0.7981 (m-40) cc_final: 0.7099 (p0) REVERT: A 1138 GLU cc_start: 0.6811 (tp30) cc_final: 0.6325 (tp30) REVERT: A 1293 HIS cc_start: 0.7722 (t-170) cc_final: 0.7081 (t-90) REVERT: A 1294 MET cc_start: 0.7950 (mmp) cc_final: 0.7694 (mmp) REVERT: A 1308 VAL cc_start: 0.9432 (m) cc_final: 0.9161 (t) REVERT: B 50 ASN cc_start: 0.8243 (t0) cc_final: 0.6636 (t0) REVERT: B 60 LEU cc_start: 0.8468 (mm) cc_final: 0.8117 (tt) REVERT: B 131 THR cc_start: 0.7809 (p) cc_final: 0.7527 (p) REVERT: B 153 PHE cc_start: 0.6802 (t80) cc_final: 0.6571 (p90) REVERT: B 275 MET cc_start: 0.6336 (ptm) cc_final: 0.6019 (ptm) REVERT: B 323 ARG cc_start: 0.7831 (mpp-170) cc_final: 0.6288 (ppt170) REVERT: B 327 LEU cc_start: 0.7962 (tp) cc_final: 0.7283 (pp) REVERT: B 421 LEU cc_start: 0.7096 (tp) cc_final: 0.6427 (tp) REVERT: B 646 HIS cc_start: 0.6917 (m90) cc_final: 0.6250 (m-70) REVERT: B 668 GLU cc_start: 0.8182 (mp0) cc_final: 0.7943 (mp0) REVERT: B 708 ASP cc_start: 0.7326 (m-30) cc_final: 0.6619 (m-30) REVERT: B 765 PHE cc_start: 0.8943 (m-80) cc_final: 0.8209 (m-80) REVERT: B 856 ASP cc_start: 0.8235 (t0) cc_final: 0.7133 (m-30) REVERT: B 882 ILE cc_start: 0.8369 (pt) cc_final: 0.7995 (mp) REVERT: B 980 ASP cc_start: 0.7252 (t0) cc_final: 0.5552 (p0) REVERT: B 1065 ARG cc_start: 0.8426 (mpp-170) cc_final: 0.8164 (mtm-85) REVERT: B 1074 MET cc_start: 0.7061 (mpp) cc_final: 0.6681 (mpp) REVERT: C 216 HIS cc_start: 0.7423 (m90) cc_final: 0.6878 (m90) REVERT: C 227 TYR cc_start: 0.6965 (m-10) cc_final: 0.6474 (m-80) REVERT: C 326 GLU cc_start: 0.8638 (pt0) cc_final: 0.8354 (pt0) REVERT: C 330 ASN cc_start: 0.7643 (p0) cc_final: 0.6923 (m-40) REVERT: D 29 GLN cc_start: 0.7381 (tm-30) cc_final: 0.7085 (tm-30) REVERT: D 37 LEU cc_start: 0.6848 (mm) cc_final: 0.6015 (tt) REVERT: D 90 LYS cc_start: 0.5917 (pptt) cc_final: 0.5509 (pptt) REVERT: E 24 LYS cc_start: 0.8797 (tttt) cc_final: 0.8495 (tptt) REVERT: E 133 GLU cc_start: 0.7263 (pm20) cc_final: 0.6999 (pm20) REVERT: E 148 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6517 (tm-30) REVERT: E 152 LYS cc_start: 0.8442 (tmtt) cc_final: 0.7945 (tptm) REVERT: E 177 ARG cc_start: 0.8435 (ptt90) cc_final: 0.8092 (ptm-80) REVERT: F 66 ARG cc_start: 0.6870 (mmp80) cc_final: 0.6632 (mmp80) REVERT: F 144 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7392 (tm-30) REVERT: G 149 ILE cc_start: 0.8373 (tt) cc_final: 0.7957 (tt) REVERT: G 160 ASN cc_start: 0.5133 (t0) cc_final: 0.4886 (t0) REVERT: G 219 ASP cc_start: 0.5557 (p0) cc_final: 0.5255 (p0) REVERT: H 34 ASP cc_start: 0.8000 (m-30) cc_final: 0.7517 (p0) REVERT: H 98 TYR cc_start: 0.7821 (t80) cc_final: 0.7536 (t80) REVERT: H 104 PHE cc_start: 0.6682 (m-10) cc_final: 0.6451 (m-10) REVERT: H 131 ASN cc_start: 0.6055 (p0) cc_final: 0.4583 (t0) REVERT: H 133 ASN cc_start: 0.8941 (p0) cc_final: 0.8397 (p0) REVERT: K 68 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6901 (mm-30) REVERT: K 126 ASP cc_start: 0.8191 (m-30) cc_final: 0.7910 (m-30) REVERT: K 142 MET cc_start: 0.5870 (mtm) cc_final: 0.4520 (ttm) REVERT: M 18 GLN cc_start: 0.7726 (tt0) cc_final: 0.7467 (tt0) REVERT: M 39 ASP cc_start: 0.6038 (p0) cc_final: 0.5264 (t0) REVERT: M 49 ASP cc_start: 0.7257 (m-30) cc_final: 0.7024 (m-30) REVERT: M 319 PHE cc_start: 0.7318 (t80) cc_final: 0.6431 (t80) REVERT: M 338 HIS cc_start: 0.5298 (t70) cc_final: 0.4880 (m90) REVERT: M 351 HIS cc_start: 0.6592 (m170) cc_final: 0.5977 (t-90) REVERT: N 41 ASN cc_start: 0.6701 (p0) cc_final: 0.6408 (p0) outliers start: 5 outliers final: 1 residues processed: 878 average time/residue: 0.2284 time to fit residues: 328.9396 Evaluate side-chains 656 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 655 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 15 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 370 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 240 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1199 GLN A1320 GLN A1500 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN ** B 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.161982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145602 restraints weight = 77730.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147142 restraints weight = 54662.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147875 restraints weight = 42090.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148659 restraints weight = 35696.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149139 restraints weight = 28364.800| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36691 Z= 0.180 Angle : 0.765 46.817 49783 Z= 0.365 Chirality : 0.047 0.274 5581 Planarity : 0.005 0.088 6243 Dihedral : 10.989 89.724 5312 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.12), residues: 4313 helix: -1.01 (0.13), residues: 1340 sheet: -1.66 (0.21), residues: 563 loop : -2.13 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG F 119 TYR 0.025 0.002 TYR M 242 PHE 0.032 0.002 PHE B 496 TRP 0.026 0.002 TRP A 842 HIS 0.009 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (36668) covalent geometry : angle 0.71176 / 0.36 (49756) hydrogen bonds : bond 0.04508 / 3.00 ( 1202) hydrogen bonds : angle 6.05711 / 4.10 ( 3340) metal coordination : bond 0.00828 / 0.51 ( 22) metal coordination : angle 12.05854 / 6.65 ( 27) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 846 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.7707 (ptp-170) REVERT: A 211 THR cc_start: 0.8033 (t) cc_final: 0.7333 (m) REVERT: A 212 VAL cc_start: 0.9100 (m) cc_final: 0.8843 (m) REVERT: A 222 GLU cc_start: 0.7040 (tp30) cc_final: 0.6811 (tp30) REVERT: A 358 ASP cc_start: 0.6222 (m-30) cc_final: 0.5928 (m-30) REVERT: A 383 ASN cc_start: 0.7950 (m110) cc_final: 0.7480 (t0) REVERT: A 472 MET cc_start: 0.8311 (mmt) cc_final: 0.7792 (mmt) REVERT: A 555 LYS cc_start: 0.7879 (mttp) cc_final: 0.7638 (mttm) REVERT: A 616 LEU cc_start: 0.8375 (tp) cc_final: 0.7816 (tt) REVERT: A 646 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7111 (mt-10) REVERT: A 703 GLU cc_start: 0.7494 (mp0) cc_final: 0.7217 (mp0) REVERT: A 747 ILE cc_start: 0.8640 (pt) cc_final: 0.8323 (pt) REVERT: A 765 LEU cc_start: 0.7069 (mm) cc_final: 0.6709 (pp) REVERT: A 773 ASP cc_start: 0.7645 (t70) cc_final: 0.7192 (t0) REVERT: A 830 MET cc_start: 0.8558 (tpt) cc_final: 0.8257 (tpt) REVERT: A 842 TRP cc_start: 0.4577 (m-90) cc_final: 0.4336 (m-10) REVERT: A 876 LEU cc_start: 0.7980 (tt) cc_final: 0.7502 (mm) REVERT: A 993 GLN cc_start: 0.8930 (mp10) cc_final: 0.8448 (mp10) REVERT: A 1024 THR cc_start: 0.7395 (m) cc_final: 0.7031 (m) REVERT: A 1072 ASN cc_start: 0.7892 (m-40) cc_final: 0.7275 (p0) REVERT: A 1200 MET cc_start: 0.8214 (ptt) cc_final: 0.7993 (ptt) REVERT: A 1293 HIS cc_start: 0.8285 (t-170) cc_final: 0.7504 (t-90) REVERT: A 1294 MET cc_start: 0.7940 (mmp) cc_final: 0.7687 (mmp) REVERT: A 1315 ASN cc_start: 0.7569 (m-40) cc_final: 0.7364 (m110) REVERT: A 1473 LYS cc_start: 0.7248 (pttp) cc_final: 0.6979 (pttp) REVERT: B 50 ASN cc_start: 0.8084 (t0) cc_final: 0.7677 (t0) REVERT: B 60 LEU cc_start: 0.8649 (mm) cc_final: 0.8201 (tt) REVERT: B 131 THR cc_start: 0.7850 (p) cc_final: 0.7636 (p) REVERT: B 153 PHE cc_start: 0.6833 (t80) cc_final: 0.6582 (p90) REVERT: B 278 LYS cc_start: 0.8681 (ptmm) cc_final: 0.7923 (ptmm) REVERT: B 323 ARG cc_start: 0.7686 (mpp-170) cc_final: 0.6122 (ppt170) REVERT: B 421 LEU cc_start: 0.7385 (tp) cc_final: 0.7060 (tp) REVERT: B 519 LYS cc_start: 0.7003 (mmmt) cc_final: 0.6543 (mtmm) REVERT: B 646 HIS cc_start: 0.7143 (m90) cc_final: 0.6270 (m-70) REVERT: B 708 ASP cc_start: 0.7119 (m-30) cc_final: 0.6868 (m-30) REVERT: B 755 ASN cc_start: 0.6607 (p0) cc_final: 0.5617 (p0) REVERT: B 765 PHE cc_start: 0.9055 (m-80) cc_final: 0.8292 (m-80) REVERT: B 803 MET cc_start: 0.6486 (ptt) cc_final: 0.6275 (ptt) REVERT: B 843 ASP cc_start: 0.7290 (p0) cc_final: 0.6544 (m-30) REVERT: B 882 ILE cc_start: 0.8449 (pt) cc_final: 0.8179 (mp) REVERT: B 980 ASP cc_start: 0.7505 (t0) cc_final: 0.5730 (p0) REVERT: B 1026 ILE cc_start: 0.6899 (pt) cc_final: 0.6633 (pt) REVERT: C 85 PHE cc_start: 0.8594 (m-10) cc_final: 0.8145 (m-10) REVERT: C 227 TYR cc_start: 0.7246 (m-10) cc_final: 0.6771 (m-80) REVERT: C 326 GLU cc_start: 0.8536 (pt0) cc_final: 0.8104 (pt0) REVERT: C 330 ASN cc_start: 0.7195 (p0) cc_final: 0.6643 (m-40) REVERT: D 29 GLN cc_start: 0.7569 (tm-30) cc_final: 0.7247 (tm-30) REVERT: E 40 GLU cc_start: 0.7802 (pm20) cc_final: 0.7267 (pp20) REVERT: E 41 ASP cc_start: 0.7691 (m-30) cc_final: 0.6657 (m-30) REVERT: E 112 TYR cc_start: 0.8639 (p90) cc_final: 0.8383 (p90) REVERT: E 148 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6580 (tm-30) REVERT: E 152 LYS cc_start: 0.8562 (tmtt) cc_final: 0.8059 (tptm) REVERT: E 177 ARG cc_start: 0.8481 (ptt90) cc_final: 0.7873 (ttt-90) REVERT: F 66 ARG cc_start: 0.6692 (mmp80) cc_final: 0.6196 (mmp80) REVERT: F 144 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7340 (tm-30) REVERT: F 150 GLU cc_start: 0.7759 (pt0) cc_final: 0.7550 (pt0) REVERT: G 149 ILE cc_start: 0.8587 (tt) cc_final: 0.8219 (tt) REVERT: G 219 ASP cc_start: 0.5756 (p0) cc_final: 0.5408 (p0) REVERT: H 34 ASP cc_start: 0.7835 (m-30) cc_final: 0.7421 (p0) REVERT: H 98 TYR cc_start: 0.7873 (t80) cc_final: 0.7635 (t80) REVERT: H 104 PHE cc_start: 0.6831 (m-10) cc_final: 0.6434 (m-10) REVERT: H 131 ASN cc_start: 0.6125 (p0) cc_final: 0.4521 (t0) REVERT: J 39 LEU cc_start: 0.8834 (mt) cc_final: 0.8585 (mt) REVERT: K 142 MET cc_start: 0.5923 (mtm) cc_final: 0.4652 (ttm) REVERT: L 57 LEU cc_start: 0.7413 (mt) cc_final: 0.7100 (mp) REVERT: M 39 ASP cc_start: 0.6139 (p0) cc_final: 0.5332 (t0) REVERT: M 319 PHE cc_start: 0.7455 (t80) cc_final: 0.6586 (t80) REVERT: M 338 HIS cc_start: 0.5403 (t70) cc_final: 0.4912 (m90) REVERT: M 351 HIS cc_start: 0.6651 (m170) cc_final: 0.6056 (t-90) REVERT: N 41 ASN cc_start: 0.6752 (p0) cc_final: 0.6442 (p0) outliers start: 1 outliers final: 0 residues processed: 847 average time/residue: 0.2250 time to fit residues: 312.4720 Evaluate side-chains 645 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 110 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 273 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 417 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 344 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 263 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS A 880 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1199 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN K 99 ASN M 57 ASN M 274 ASN M 323 GLN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.158562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141835 restraints weight = 78269.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143358 restraints weight = 54657.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144824 restraints weight = 41386.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145314 restraints weight = 31464.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.145425 restraints weight = 27609.849| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36691 Z= 0.197 Angle : 0.789 46.169 49783 Z= 0.380 Chirality : 0.048 0.239 5581 Planarity : 0.006 0.108 6243 Dihedral : 11.090 88.651 5312 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.03 % Allowed : 4.24 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.12), residues: 4313 helix: -0.88 (0.13), residues: 1334 sheet: -1.64 (0.22), residues: 548 loop : -2.08 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 323 TYR 0.038 0.002 TYR E 46 PHE 0.038 0.002 PHE B 493 TRP 0.020 0.002 TRP A 842 HIS 0.018 0.002 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (36668) covalent geometry : angle 0.73959 / 0.38 (49756) hydrogen bonds : bond 0.04579 / 3.05 ( 1202) hydrogen bonds : angle 5.91996 / 4.02 ( 3340) metal coordination : bond 0.01037 / 0.60 ( 22) metal coordination : angle 11.81127 / 6.50 ( 27) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 835 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.8705 (mm) cc_final: 0.8389 (mm) REVERT: A 99 ARG cc_start: 0.8514 (ptm-80) cc_final: 0.7696 (ptp-170) REVERT: A 211 THR cc_start: 0.8048 (t) cc_final: 0.7530 (m) REVERT: A 222 GLU cc_start: 0.7282 (tp30) cc_final: 0.6436 (tp30) REVERT: A 358 ASP cc_start: 0.6040 (m-30) cc_final: 0.5838 (m-30) REVERT: A 383 ASN cc_start: 0.7761 (m110) cc_final: 0.7529 (t0) REVERT: A 472 MET cc_start: 0.8241 (mmt) cc_final: 0.7804 (mmt) REVERT: A 646 GLU cc_start: 0.7832 (mt-10) cc_final: 0.6828 (mm-30) REVERT: A 703 GLU cc_start: 0.7422 (mp0) cc_final: 0.6945 (mp0) REVERT: A 747 ILE cc_start: 0.8634 (pt) cc_final: 0.8213 (pt) REVERT: A 765 LEU cc_start: 0.7279 (mm) cc_final: 0.6732 (pp) REVERT: A 768 GLU cc_start: 0.6694 (mp0) cc_final: 0.6405 (mp0) REVERT: A 773 ASP cc_start: 0.7731 (t70) cc_final: 0.7268 (t0) REVERT: A 816 LEU cc_start: 0.8382 (tt) cc_final: 0.8178 (tt) REVERT: A 830 MET cc_start: 0.8519 (tpt) cc_final: 0.8252 (tpt) REVERT: A 842 TRP cc_start: 0.4817 (m-90) cc_final: 0.3129 (m-10) REVERT: A 876 LEU cc_start: 0.7901 (tt) cc_final: 0.7398 (mm) REVERT: A 928 MET cc_start: 0.7783 (ppp) cc_final: 0.7507 (ppp) REVERT: A 977 MET cc_start: 0.6948 (tpp) cc_final: 0.6652 (tpt) REVERT: A 993 GLN cc_start: 0.9071 (mp10) cc_final: 0.8311 (mp10) REVERT: A 995 TYR cc_start: 0.8640 (t80) cc_final: 0.8190 (t80) REVERT: A 1069 CYS cc_start: 0.8367 (t) cc_final: 0.8113 (p) REVERT: A 1072 ASN cc_start: 0.8006 (m-40) cc_final: 0.7291 (p0) REVERT: A 1200 MET cc_start: 0.7889 (ptt) cc_final: 0.7650 (ptt) REVERT: A 1293 HIS cc_start: 0.8376 (t-170) cc_final: 0.7656 (t-90) REVERT: A 1294 MET cc_start: 0.8057 (mmp) cc_final: 0.7684 (mmp) REVERT: A 1484 LEU cc_start: 0.5351 (mm) cc_final: 0.5082 (mm) REVERT: A 1564 ASN cc_start: 0.7779 (m-40) cc_final: 0.7521 (t0) REVERT: B 50 ASN cc_start: 0.8091 (t0) cc_final: 0.7307 (t0) REVERT: B 60 LEU cc_start: 0.8717 (mm) cc_final: 0.8199 (tt) REVERT: B 153 PHE cc_start: 0.6921 (t80) cc_final: 0.6633 (p90) REVERT: B 215 MET cc_start: 0.6812 (mmm) cc_final: 0.6573 (mmm) REVERT: B 278 LYS cc_start: 0.8699 (ptmm) cc_final: 0.8007 (ptmm) REVERT: B 421 LEU cc_start: 0.7559 (tp) cc_final: 0.7186 (tp) REVERT: B 646 HIS cc_start: 0.6840 (m170) cc_final: 0.6203 (m-70) REVERT: B 668 GLU cc_start: 0.8294 (mp0) cc_final: 0.8052 (mp0) REVERT: B 708 ASP cc_start: 0.7383 (m-30) cc_final: 0.6904 (m-30) REVERT: B 755 ASN cc_start: 0.6782 (p0) cc_final: 0.6055 (p0) REVERT: B 765 PHE cc_start: 0.8584 (m-80) cc_final: 0.8359 (m-80) REVERT: B 803 MET cc_start: 0.6377 (ptt) cc_final: 0.6132 (ptt) REVERT: B 931 TRP cc_start: 0.5541 (t60) cc_final: 0.5253 (t60) REVERT: B 1074 MET cc_start: 0.7032 (mpp) cc_final: 0.6556 (mpp) REVERT: B 1086 PHE cc_start: 0.6791 (t80) cc_final: 0.6567 (t80) REVERT: B 1200 VAL cc_start: 0.8885 (m) cc_final: 0.8616 (t) REVERT: C 74 GLU cc_start: 0.7971 (mp0) cc_final: 0.7751 (mp0) REVERT: C 85 PHE cc_start: 0.8565 (m-10) cc_final: 0.8192 (m-10) REVERT: C 326 GLU cc_start: 0.8459 (pt0) cc_final: 0.8148 (pt0) REVERT: C 330 ASN cc_start: 0.7216 (p0) cc_final: 0.6785 (m-40) REVERT: D 29 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7261 (tm-30) REVERT: E 40 GLU cc_start: 0.7959 (pm20) cc_final: 0.7333 (pp20) REVERT: E 41 ASP cc_start: 0.7895 (m-30) cc_final: 0.6968 (m-30) REVERT: E 137 GLU cc_start: 0.7875 (pm20) cc_final: 0.7540 (pm20) REVERT: E 148 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6531 (tm-30) REVERT: E 152 LYS cc_start: 0.8591 (tmtt) cc_final: 0.8025 (tptm) REVERT: E 177 ARG cc_start: 0.8482 (ptt90) cc_final: 0.7825 (ttt-90) REVERT: F 66 ARG cc_start: 0.6564 (mmp80) cc_final: 0.5909 (mmp80) REVERT: F 144 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7428 (tm-30) REVERT: G 160 ASN cc_start: 0.4610 (t0) cc_final: 0.4243 (t0) REVERT: H 34 ASP cc_start: 0.7860 (m-30) cc_final: 0.7619 (p0) REVERT: H 104 PHE cc_start: 0.6925 (m-10) cc_final: 0.6541 (m-10) REVERT: H 131 ASN cc_start: 0.6286 (p0) cc_final: 0.4583 (t0) REVERT: J 39 LEU cc_start: 0.8748 (mt) cc_final: 0.8475 (mt) REVERT: K 64 GLN cc_start: 0.4436 (tp40) cc_final: 0.4147 (tp40) REVERT: K 102 ASN cc_start: 0.7854 (p0) cc_final: 0.7434 (p0) REVERT: K 142 MET cc_start: 0.6149 (mtm) cc_final: 0.4723 (ttm) REVERT: L 57 LEU cc_start: 0.7350 (mt) cc_final: 0.7145 (mp) REVERT: M 18 GLN cc_start: 0.7470 (tt0) cc_final: 0.7089 (tt0) REVERT: M 48 LYS cc_start: 0.7378 (ptmt) cc_final: 0.7111 (mttm) REVERT: M 49 ASP cc_start: 0.7192 (m-30) cc_final: 0.6551 (m-30) REVERT: M 319 PHE cc_start: 0.7422 (t80) cc_final: 0.6671 (t80) REVERT: M 338 HIS cc_start: 0.5330 (t70) cc_final: 0.4890 (m90) REVERT: M 351 HIS cc_start: 0.6877 (m170) cc_final: 0.6134 (t-90) REVERT: N 41 ASN cc_start: 0.6802 (p0) cc_final: 0.6447 (p0) REVERT: N 80 MET cc_start: -0.0883 (mmt) cc_final: -0.1367 (mmt) outliers start: 1 outliers final: 0 residues processed: 836 average time/residue: 0.2263 time to fit residues: 308.6257 Evaluate side-chains 634 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 239 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 355 optimal weight: 0.0470 chunk 135 optimal weight: 3.9990 chunk 30 optimal weight: 0.0060 chunk 184 optimal weight: 5.9990 chunk 375 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 overall best weight: 2.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN A 880 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1199 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 ASN E 8 ASN E 153 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.158363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141781 restraints weight = 77674.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143192 restraints weight = 54736.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144165 restraints weight = 41634.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145336 restraints weight = 32848.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145437 restraints weight = 28708.578| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 36691 Z= 0.173 Angle : 0.788 44.507 49783 Z= 0.379 Chirality : 0.048 0.349 5581 Planarity : 0.005 0.085 6243 Dihedral : 11.112 89.027 5312 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.18 % Favored : 91.79 % Rotamer: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.12), residues: 4313 helix: -0.85 (0.13), residues: 1350 sheet: -1.57 (0.22), residues: 539 loop : -2.05 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 59 TYR 0.053 0.002 TYR A 314 PHE 0.039 0.002 PHE B 496 TRP 0.019 0.002 TRP A 842 HIS 0.011 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (36668) covalent geometry : angle 0.74073 / 0.38 (49756) hydrogen bonds : bond 0.04385 / 2.93 ( 1202) hydrogen bonds : angle 5.83138 / 3.97 ( 3340) metal coordination : bond 0.00815 / 0.48 ( 22) metal coordination : angle 11.59117 / 6.39 ( 27) Misc. bond : bond 0.01416 / 0.75 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 814 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.8088 (t) cc_final: 0.7476 (m) REVERT: A 222 GLU cc_start: 0.7333 (tp30) cc_final: 0.6640 (tp30) REVERT: A 358 ASP cc_start: 0.5957 (m-30) cc_final: 0.5622 (m-30) REVERT: A 383 ASN cc_start: 0.7971 (m110) cc_final: 0.7587 (t0) REVERT: A 397 ARG cc_start: 0.7319 (ttp-170) cc_final: 0.6681 (ttt180) REVERT: A 472 MET cc_start: 0.8153 (mmp) cc_final: 0.7827 (mmt) REVERT: A 492 THR cc_start: 0.6858 (m) cc_final: 0.6609 (m) REVERT: A 646 GLU cc_start: 0.7857 (mt-10) cc_final: 0.6845 (mm-30) REVERT: A 703 GLU cc_start: 0.7478 (mp0) cc_final: 0.7142 (mp0) REVERT: A 747 ILE cc_start: 0.8597 (pt) cc_final: 0.8244 (pt) REVERT: A 750 ILE cc_start: 0.7595 (mp) cc_final: 0.7370 (tp) REVERT: A 765 LEU cc_start: 0.7273 (mm) cc_final: 0.6722 (pp) REVERT: A 768 GLU cc_start: 0.6676 (mp0) cc_final: 0.6367 (mp0) REVERT: A 773 ASP cc_start: 0.7774 (t70) cc_final: 0.7274 (t0) REVERT: A 816 LEU cc_start: 0.8359 (tt) cc_final: 0.8142 (tt) REVERT: A 830 MET cc_start: 0.8459 (tpt) cc_final: 0.8250 (tpt) REVERT: A 842 TRP cc_start: 0.4829 (m-90) cc_final: 0.3585 (m-10) REVERT: A 876 LEU cc_start: 0.7887 (tt) cc_final: 0.7300 (mm) REVERT: A 960 MET cc_start: 0.8207 (ppp) cc_final: 0.7989 (ppp) REVERT: A 977 MET cc_start: 0.6891 (tpp) cc_final: 0.6475 (tpt) REVERT: A 995 TYR cc_start: 0.8496 (t80) cc_final: 0.8266 (t80) REVERT: A 1049 MET cc_start: 0.8016 (pmm) cc_final: 0.7543 (mtp) REVERT: A 1069 CYS cc_start: 0.8448 (t) cc_final: 0.8184 (p) REVERT: A 1072 ASN cc_start: 0.7890 (m-40) cc_final: 0.7222 (p0) REVERT: A 1200 MET cc_start: 0.7903 (ptt) cc_final: 0.7609 (ptt) REVERT: A 1293 HIS cc_start: 0.8460 (t-170) cc_final: 0.7661 (t70) REVERT: A 1473 LYS cc_start: 0.7234 (pttp) cc_final: 0.7010 (pttp) REVERT: A 1484 LEU cc_start: 0.5327 (mm) cc_final: 0.5124 (mm) REVERT: A 1564 ASN cc_start: 0.7790 (m-40) cc_final: 0.7570 (t0) REVERT: B 50 ASN cc_start: 0.8005 (t0) cc_final: 0.7497 (t0) REVERT: B 60 LEU cc_start: 0.8684 (mm) cc_final: 0.8181 (tt) REVERT: B 153 PHE cc_start: 0.6918 (t80) cc_final: 0.6637 (p90) REVERT: B 175 MET cc_start: 0.5737 (ttt) cc_final: 0.5517 (ptm) REVERT: B 215 MET cc_start: 0.6901 (mmm) cc_final: 0.6650 (mmm) REVERT: B 278 LYS cc_start: 0.8703 (ptmm) cc_final: 0.8093 (ptmm) REVERT: B 347 LEU cc_start: 0.7551 (pp) cc_final: 0.7315 (tp) REVERT: B 389 CYS cc_start: 0.6443 (m) cc_final: 0.6242 (m) REVERT: B 421 LEU cc_start: 0.7663 (tp) cc_final: 0.7313 (tp) REVERT: B 559 SER cc_start: 0.6872 (m) cc_final: 0.6468 (p) REVERT: B 646 HIS cc_start: 0.6759 (m170) cc_final: 0.6118 (m-70) REVERT: B 708 ASP cc_start: 0.7404 (m-30) cc_final: 0.6957 (m-30) REVERT: B 726 MET cc_start: 0.7810 (ptp) cc_final: 0.7385 (ptp) REVERT: B 755 ASN cc_start: 0.6971 (p0) cc_final: 0.6214 (p0) REVERT: B 931 TRP cc_start: 0.5538 (t60) cc_final: 0.5318 (t60) REVERT: B 974 LEU cc_start: 0.7911 (tt) cc_final: 0.7623 (tt) REVERT: B 1074 MET cc_start: 0.6889 (mpp) cc_final: 0.6230 (mpp) REVERT: B 1200 VAL cc_start: 0.8952 (m) cc_final: 0.8672 (t) REVERT: C 68 ARG cc_start: 0.8619 (tmm160) cc_final: 0.8394 (tmm-80) REVERT: C 74 GLU cc_start: 0.7947 (mp0) cc_final: 0.7722 (mp0) REVERT: C 85 PHE cc_start: 0.8629 (m-10) cc_final: 0.8181 (m-10) REVERT: C 326 GLU cc_start: 0.8690 (pt0) cc_final: 0.8413 (pt0) REVERT: C 330 ASN cc_start: 0.7319 (p0) cc_final: 0.6802 (m-40) REVERT: D 29 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7433 (tm-30) REVERT: E 40 GLU cc_start: 0.7977 (pm20) cc_final: 0.7309 (pp20) REVERT: E 41 ASP cc_start: 0.7750 (m-30) cc_final: 0.6745 (m-30) REVERT: E 148 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6771 (tm-30) REVERT: E 152 LYS cc_start: 0.8570 (tmtt) cc_final: 0.8057 (tptm) REVERT: E 177 ARG cc_start: 0.8442 (ptt90) cc_final: 0.7857 (ttt-90) REVERT: F 144 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7548 (tm-30) REVERT: F 150 GLU cc_start: 0.7738 (pt0) cc_final: 0.7364 (pt0) REVERT: G 160 ASN cc_start: 0.5127 (t0) cc_final: 0.4872 (t0) REVERT: G 219 ASP cc_start: 0.5725 (p0) cc_final: 0.5437 (p0) REVERT: H 34 ASP cc_start: 0.7896 (m-30) cc_final: 0.7595 (p0) REVERT: H 104 PHE cc_start: 0.6914 (m-10) cc_final: 0.6551 (m-10) REVERT: H 123 MET cc_start: 0.6587 (tpp) cc_final: 0.6098 (tpp) REVERT: H 131 ASN cc_start: 0.6222 (p0) cc_final: 0.4525 (t0) REVERT: J 39 LEU cc_start: 0.8733 (mt) cc_final: 0.8472 (mt) REVERT: K 64 GLN cc_start: 0.4622 (tp40) cc_final: 0.4375 (tp40) REVERT: K 125 MET cc_start: 0.8648 (mmm) cc_final: 0.8397 (mmm) REVERT: K 126 ASP cc_start: 0.8069 (m-30) cc_final: 0.7598 (m-30) REVERT: K 142 MET cc_start: 0.6374 (mtm) cc_final: 0.4912 (ttm) REVERT: M 18 GLN cc_start: 0.7444 (tt0) cc_final: 0.7065 (tt0) REVERT: M 39 ASP cc_start: 0.5404 (p0) cc_final: 0.5022 (t0) REVERT: M 319 PHE cc_start: 0.7411 (t80) cc_final: 0.6855 (t80) REVERT: M 338 HIS cc_start: 0.5250 (t70) cc_final: 0.4801 (m90) REVERT: M 351 HIS cc_start: 0.6873 (m170) cc_final: 0.6118 (t70) REVERT: N 40 LEU cc_start: 0.7911 (mp) cc_final: 0.7665 (mm) REVERT: N 41 ASN cc_start: 0.6779 (p0) cc_final: 0.6345 (p0) REVERT: N 80 MET cc_start: -0.0568 (mmt) cc_final: -0.1153 (mmt) outliers start: 1 outliers final: 0 residues processed: 814 average time/residue: 0.2186 time to fit residues: 292.6824 Evaluate side-chains 632 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 57 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 340 optimal weight: 30.0000 chunk 165 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 309 optimal weight: 3.9990 chunk 354 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN A 880 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1199 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 ASN C 216 HIS ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.155786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139085 restraints weight = 77862.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140667 restraints weight = 54817.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141385 restraints weight = 42033.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.142468 restraints weight = 35961.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142760 restraints weight = 27974.163| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36691 Z= 0.188 Angle : 0.811 44.017 49783 Z= 0.392 Chirality : 0.049 0.309 5581 Planarity : 0.006 0.132 6243 Dihedral : 11.172 89.622 5312 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.12), residues: 4313 helix: -0.83 (0.13), residues: 1346 sheet: -1.45 (0.22), residues: 541 loop : -2.04 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 323 TYR 0.031 0.002 TYR A1073 PHE 0.035 0.002 PHE B 496 TRP 0.021 0.002 TRP A 842 HIS 0.016 0.002 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (36668) covalent geometry : angle 0.76502 / 0.39 (49756) hydrogen bonds : bond 0.04508 / 3.01 ( 1202) hydrogen bonds : angle 5.77288 / 3.95 ( 3340) metal coordination : bond 0.00957 / 0.55 ( 22) metal coordination : angle 11.52480 / 6.32 ( 27) Misc. bond : bond 0.00622 / 0.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 801 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.8320 (ptm-80) cc_final: 0.8071 (ptp-170) REVERT: A 211 THR cc_start: 0.8098 (t) cc_final: 0.7520 (m) REVERT: A 358 ASP cc_start: 0.6113 (m-30) cc_final: 0.5768 (m-30) REVERT: A 383 ASN cc_start: 0.7785 (m110) cc_final: 0.7544 (t0) REVERT: A 646 GLU cc_start: 0.7780 (mt-10) cc_final: 0.6754 (mm-30) REVERT: A 703 GLU cc_start: 0.7666 (mp0) cc_final: 0.7377 (mp0) REVERT: A 747 ILE cc_start: 0.8583 (pt) cc_final: 0.8280 (pt) REVERT: A 768 GLU cc_start: 0.7012 (mp0) cc_final: 0.6665 (mp0) REVERT: A 773 ASP cc_start: 0.7772 (t70) cc_final: 0.7174 (t0) REVERT: A 816 LEU cc_start: 0.8418 (tt) cc_final: 0.8188 (tt) REVERT: A 830 MET cc_start: 0.8438 (tpt) cc_final: 0.8232 (tpt) REVERT: A 842 TRP cc_start: 0.4621 (m-90) cc_final: 0.3561 (m-10) REVERT: A 876 LEU cc_start: 0.7961 (tt) cc_final: 0.7340 (mm) REVERT: A 995 TYR cc_start: 0.8559 (t80) cc_final: 0.8291 (t80) REVERT: A 1049 MET cc_start: 0.8381 (pmm) cc_final: 0.8103 (pmm) REVERT: A 1069 CYS cc_start: 0.8485 (t) cc_final: 0.7938 (p) REVERT: A 1072 ASN cc_start: 0.7972 (m-40) cc_final: 0.7540 (m-40) REVERT: A 1200 MET cc_start: 0.7912 (ptt) cc_final: 0.7569 (ptt) REVERT: A 1293 HIS cc_start: 0.8504 (t-170) cc_final: 0.7707 (t70) REVERT: A 1564 ASN cc_start: 0.7832 (m-40) cc_final: 0.7585 (t0) REVERT: A 1588 MET cc_start: 0.8635 (tpp) cc_final: 0.8252 (tpp) REVERT: B 50 ASN cc_start: 0.7879 (t0) cc_final: 0.7471 (t0) REVERT: B 60 LEU cc_start: 0.8769 (mm) cc_final: 0.8276 (tt) REVERT: B 127 ARG cc_start: 0.8109 (ptp90) cc_final: 0.7291 (ttm170) REVERT: B 153 PHE cc_start: 0.6933 (t80) cc_final: 0.6654 (p90) REVERT: B 207 ILE cc_start: 0.6655 (mt) cc_final: 0.6002 (mt) REVERT: B 215 MET cc_start: 0.7027 (mmm) cc_final: 0.6727 (mmm) REVERT: B 278 LYS cc_start: 0.8679 (ptmm) cc_final: 0.8156 (ptmm) REVERT: B 347 LEU cc_start: 0.7754 (pp) cc_final: 0.7472 (tp) REVERT: B 421 LEU cc_start: 0.7619 (tp) cc_final: 0.7288 (tp) REVERT: B 559 SER cc_start: 0.7215 (m) cc_final: 0.6755 (p) REVERT: B 646 HIS cc_start: 0.6743 (m170) cc_final: 0.5957 (m90) REVERT: B 672 MET cc_start: 0.8268 (ptt) cc_final: 0.8062 (ptt) REVERT: B 708 ASP cc_start: 0.7658 (m-30) cc_final: 0.7231 (m-30) REVERT: B 755 ASN cc_start: 0.7057 (p0) cc_final: 0.6298 (p0) REVERT: B 896 GLN cc_start: 0.6161 (pm20) cc_final: 0.4680 (mm110) REVERT: C 68 ARG cc_start: 0.8576 (tmm160) cc_final: 0.8340 (tmm-80) REVERT: C 74 GLU cc_start: 0.7763 (mp0) cc_final: 0.7336 (mp0) REVERT: C 85 PHE cc_start: 0.8605 (m-10) cc_final: 0.8290 (m-10) REVERT: C 295 ARG cc_start: 0.8179 (mtt90) cc_final: 0.7929 (mmt180) REVERT: C 300 PHE cc_start: 0.8336 (m-10) cc_final: 0.8126 (m-10) REVERT: C 326 GLU cc_start: 0.8587 (pt0) cc_final: 0.8319 (pt0) REVERT: C 330 ASN cc_start: 0.7356 (p0) cc_final: 0.6872 (m-40) REVERT: D 29 GLN cc_start: 0.7374 (tm-30) cc_final: 0.6952 (tm-30) REVERT: E 40 GLU cc_start: 0.7983 (pm20) cc_final: 0.7325 (pp20) REVERT: E 41 ASP cc_start: 0.7832 (m-30) cc_final: 0.6877 (m-30) REVERT: E 148 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6829 (tm-30) REVERT: E 152 LYS cc_start: 0.8530 (tmtt) cc_final: 0.7976 (tptm) REVERT: F 144 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7598 (tm-30) REVERT: F 150 GLU cc_start: 0.7794 (pt0) cc_final: 0.7429 (pt0) REVERT: G 37 CYS cc_start: 0.7560 (p) cc_final: 0.6483 (m) REVERT: G 160 ASN cc_start: 0.5293 (t0) cc_final: 0.4991 (t0) REVERT: H 34 ASP cc_start: 0.7834 (m-30) cc_final: 0.7582 (p0) REVERT: H 45 GLU cc_start: 0.7756 (pp20) cc_final: 0.7342 (tm-30) REVERT: H 46 LEU cc_start: 0.6456 (tp) cc_final: 0.5957 (tp) REVERT: H 104 PHE cc_start: 0.6874 (m-10) cc_final: 0.6594 (m-10) REVERT: H 131 ASN cc_start: 0.6906 (p0) cc_final: 0.5271 (t0) REVERT: I 59 SER cc_start: 0.6305 (p) cc_final: 0.5611 (t) REVERT: J 39 LEU cc_start: 0.8671 (mt) cc_final: 0.8421 (mt) REVERT: K 59 THR cc_start: 0.8946 (m) cc_final: 0.8108 (m) REVERT: K 65 ILE cc_start: 0.8572 (pt) cc_final: 0.8291 (pt) REVERT: K 102 ASN cc_start: 0.7895 (p0) cc_final: 0.7119 (p0) REVERT: K 125 MET cc_start: 0.8712 (mmm) cc_final: 0.8467 (mmm) REVERT: K 142 MET cc_start: 0.6692 (mtm) cc_final: 0.4933 (ttm) REVERT: M 39 ASP cc_start: 0.5567 (p0) cc_final: 0.5099 (t0) REVERT: M 319 PHE cc_start: 0.7627 (t80) cc_final: 0.6725 (t80) REVERT: M 338 HIS cc_start: 0.5246 (t70) cc_final: 0.4737 (m90) REVERT: M 351 HIS cc_start: 0.6858 (m170) cc_final: 0.6307 (t70) REVERT: N 40 LEU cc_start: 0.7815 (mp) cc_final: 0.7527 (mm) REVERT: N 41 ASN cc_start: 0.6751 (p0) cc_final: 0.6307 (p0) outliers start: 1 outliers final: 1 residues processed: 802 average time/residue: 0.2289 time to fit residues: 299.8609 Evaluate side-chains 607 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 606 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 31 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 282 optimal weight: 10.0000 chunk 423 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 341 optimal weight: 20.0000 chunk 66 optimal weight: 0.1980 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1199 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 ASN ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS B1171 ASN C 216 HIS ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141560 restraints weight = 78359.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142809 restraints weight = 54660.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.143663 restraints weight = 43113.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144629 restraints weight = 34578.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.144769 restraints weight = 30548.678| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36691 Z= 0.148 Angle : 0.782 42.019 49783 Z= 0.374 Chirality : 0.047 0.285 5581 Planarity : 0.005 0.127 6243 Dihedral : 11.143 89.952 5312 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.03 % Allowed : 1.11 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.12), residues: 4313 helix: -0.74 (0.14), residues: 1350 sheet: -1.40 (0.22), residues: 540 loop : -1.98 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 59 TYR 0.031 0.002 TYR A1073 PHE 0.036 0.002 PHE B 496 TRP 0.031 0.002 TRP G 217 HIS 0.017 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (36668) covalent geometry : angle 0.73725 / 0.37 (49756) hydrogen bonds : bond 0.04281 / 2.85 ( 1202) hydrogen bonds : angle 5.61476 / 3.85 ( 3340) metal coordination : bond 0.00681 / 0.40 ( 22) metal coordination : angle 11.23896 / 6.13 ( 27) Misc. bond : bond 0.00660 / 0.35 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 794 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.8058 (t) cc_final: 0.7445 (m) REVERT: A 355 PHE cc_start: 0.7532 (m-80) cc_final: 0.7133 (m-10) REVERT: A 358 ASP cc_start: 0.5951 (m-30) cc_final: 0.5637 (m-30) REVERT: A 492 THR cc_start: 0.7134 (m) cc_final: 0.6757 (m) REVERT: A 646 GLU cc_start: 0.7688 (mt-10) cc_final: 0.6767 (mm-30) REVERT: A 703 GLU cc_start: 0.7616 (mp0) cc_final: 0.7405 (mp0) REVERT: A 747 ILE cc_start: 0.8602 (pt) cc_final: 0.8164 (pt) REVERT: A 768 GLU cc_start: 0.6916 (mp0) cc_final: 0.6445 (mp0) REVERT: A 773 ASP cc_start: 0.7765 (t70) cc_final: 0.7202 (t0) REVERT: A 830 MET cc_start: 0.8541 (tpt) cc_final: 0.8321 (tpt) REVERT: A 842 TRP cc_start: 0.4488 (m-90) cc_final: 0.3420 (m-10) REVERT: A 876 LEU cc_start: 0.7855 (tt) cc_final: 0.7229 (mm) REVERT: A 1049 MET cc_start: 0.8402 (pmm) cc_final: 0.8024 (pmm) REVERT: A 1069 CYS cc_start: 0.8449 (t) cc_final: 0.8150 (p) REVERT: A 1072 ASN cc_start: 0.8244 (m-40) cc_final: 0.7200 (p0) REVERT: A 1185 VAL cc_start: 0.9391 (p) cc_final: 0.9182 (p) REVERT: A 1200 MET cc_start: 0.7830 (ptt) cc_final: 0.7594 (ptt) REVERT: A 1293 HIS cc_start: 0.8445 (t-170) cc_final: 0.7301 (t-90) REVERT: A 1308 VAL cc_start: 0.9480 (m) cc_final: 0.9262 (t) REVERT: A 1473 LYS cc_start: 0.7785 (pttp) cc_final: 0.7356 (pttp) REVERT: A 1564 ASN cc_start: 0.7747 (m-40) cc_final: 0.7530 (t0) REVERT: A 1588 MET cc_start: 0.8711 (tpp) cc_final: 0.8407 (tpp) REVERT: B 50 ASN cc_start: 0.7928 (t0) cc_final: 0.7131 (t0) REVERT: B 60 LEU cc_start: 0.8735 (mm) cc_final: 0.8333 (tt) REVERT: B 127 ARG cc_start: 0.8069 (ptp90) cc_final: 0.7850 (ptp90) REVERT: B 215 MET cc_start: 0.6997 (mmm) cc_final: 0.6646 (mmm) REVERT: B 278 LYS cc_start: 0.8723 (ptmm) cc_final: 0.8157 (ptmm) REVERT: B 347 LEU cc_start: 0.7816 (pp) cc_final: 0.7552 (tp) REVERT: B 421 LEU cc_start: 0.7423 (tp) cc_final: 0.6838 (tp) REVERT: B 525 TRP cc_start: 0.7947 (t-100) cc_final: 0.7509 (t-100) REVERT: B 559 SER cc_start: 0.7407 (m) cc_final: 0.7013 (p) REVERT: B 646 HIS cc_start: 0.6564 (m170) cc_final: 0.5931 (m-70) REVERT: B 668 GLU cc_start: 0.8050 (mp0) cc_final: 0.7542 (mp0) REVERT: B 672 MET cc_start: 0.8185 (ptt) cc_final: 0.7908 (ptt) REVERT: B 686 HIS cc_start: 0.8057 (m-70) cc_final: 0.7735 (m-70) REVERT: B 708 ASP cc_start: 0.7671 (m-30) cc_final: 0.7214 (m-30) REVERT: B 755 ASN cc_start: 0.6994 (p0) cc_final: 0.6241 (p0) REVERT: B 896 GLN cc_start: 0.6190 (pm20) cc_final: 0.4806 (mm110) REVERT: B 931 TRP cc_start: 0.5641 (t60) cc_final: 0.5387 (t60) REVERT: B 974 LEU cc_start: 0.7861 (tt) cc_final: 0.7548 (tt) REVERT: C 85 PHE cc_start: 0.8564 (m-10) cc_final: 0.8264 (m-10) REVERT: C 295 ARG cc_start: 0.8278 (mpp-170) cc_final: 0.7641 (mmt180) REVERT: C 326 GLU cc_start: 0.8555 (pt0) cc_final: 0.8302 (pt0) REVERT: C 330 ASN cc_start: 0.7260 (p0) cc_final: 0.6787 (m-40) REVERT: D 29 GLN cc_start: 0.7386 (tm-30) cc_final: 0.7032 (tm-30) REVERT: E 40 GLU cc_start: 0.7951 (pm20) cc_final: 0.7295 (pp20) REVERT: E 41 ASP cc_start: 0.7796 (m-30) cc_final: 0.6992 (m-30) REVERT: E 148 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6813 (tm-30) REVERT: E 152 LYS cc_start: 0.8523 (tmtt) cc_final: 0.7984 (tptm) REVERT: E 177 ARG cc_start: 0.8610 (ptt90) cc_final: 0.8187 (ttp80) REVERT: E 191 LYS cc_start: 0.8117 (pptt) cc_final: 0.7896 (pttp) REVERT: F 144 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7681 (tm-30) REVERT: F 150 GLU cc_start: 0.7696 (pt0) cc_final: 0.7412 (pt0) REVERT: G 37 CYS cc_start: 0.7515 (p) cc_final: 0.6481 (m) REVERT: G 160 ASN cc_start: 0.4869 (t0) cc_final: 0.4630 (t0) REVERT: G 219 ASP cc_start: 0.5372 (p0) cc_final: 0.5166 (p0) REVERT: H 34 ASP cc_start: 0.7826 (m-30) cc_final: 0.7588 (p0) REVERT: H 45 GLU cc_start: 0.7662 (pp20) cc_final: 0.6908 (tm-30) REVERT: H 46 LEU cc_start: 0.6450 (tp) cc_final: 0.5781 (tp) REVERT: H 104 PHE cc_start: 0.6880 (m-10) cc_final: 0.6623 (m-10) REVERT: H 131 ASN cc_start: 0.6996 (p0) cc_final: 0.5338 (t0) REVERT: H 135 LEU cc_start: 0.6659 (pt) cc_final: 0.6370 (pt) REVERT: I 59 SER cc_start: 0.6031 (p) cc_final: 0.5340 (t) REVERT: J 39 LEU cc_start: 0.8590 (mt) cc_final: 0.8356 (mt) REVERT: K 102 ASN cc_start: 0.7835 (p0) cc_final: 0.7082 (p0) REVERT: K 142 MET cc_start: 0.6690 (mtm) cc_final: 0.4913 (ttm) REVERT: M 18 GLN cc_start: 0.7092 (tt0) cc_final: 0.6880 (tt0) REVERT: M 39 ASP cc_start: 0.5315 (p0) cc_final: 0.4938 (t0) REVERT: M 319 PHE cc_start: 0.7203 (t80) cc_final: 0.6715 (t80) REVERT: M 338 HIS cc_start: 0.5236 (t70) cc_final: 0.4917 (m90) REVERT: M 351 HIS cc_start: 0.6825 (m170) cc_final: 0.6073 (t70) REVERT: N 40 LEU cc_start: 0.7800 (mp) cc_final: 0.7507 (mm) REVERT: N 41 ASN cc_start: 0.6671 (p0) cc_final: 0.6210 (p0) outliers start: 1 outliers final: 0 residues processed: 795 average time/residue: 0.2233 time to fit residues: 292.0937 Evaluate side-chains 624 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 302 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 chunk 418 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 311 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 95 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN A 798 HIS A 880 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1199 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 ASN ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN B1171 ASN C 216 HIS ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.157494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140536 restraints weight = 77446.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142330 restraints weight = 52162.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143786 restraints weight = 38007.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145126 restraints weight = 27590.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145076 restraints weight = 22716.256| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36691 Z= 0.156 Angle : 0.802 41.007 49783 Z= 0.385 Chirality : 0.048 0.264 5581 Planarity : 0.005 0.122 6243 Dihedral : 11.148 89.336 5312 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.03 % Allowed : 0.87 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.12), residues: 4313 helix: -0.69 (0.14), residues: 1353 sheet: -1.38 (0.22), residues: 536 loop : -1.93 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 908 TYR 0.029 0.002 TYR A1073 PHE 0.045 0.002 PHE C 300 TRP 0.026 0.002 TRP G 217 HIS 0.014 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (36668) covalent geometry : angle 0.76030 / 0.38 (49756) hydrogen bonds : bond 0.04307 / 2.87 ( 1202) hydrogen bonds : angle 5.63775 / 3.85 ( 3340) metal coordination : bond 0.00700 / 0.42 ( 22) metal coordination : angle 11.01135 / 6.02 ( 27) Misc. bond : bond 0.00669 / 0.35 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 782 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.6768 (ttp80) cc_final: 0.6540 (tpt90) REVERT: A 211 THR cc_start: 0.8179 (t) cc_final: 0.7486 (m) REVERT: A 358 ASP cc_start: 0.6070 (m-30) cc_final: 0.5766 (m-30) REVERT: A 383 ASN cc_start: 0.7877 (m110) cc_final: 0.7369 (t0) REVERT: A 492 THR cc_start: 0.6963 (m) cc_final: 0.6527 (m) REVERT: A 646 GLU cc_start: 0.7723 (mt-10) cc_final: 0.6744 (mm-30) REVERT: A 747 ILE cc_start: 0.8555 (pt) cc_final: 0.8092 (pt) REVERT: A 768 GLU cc_start: 0.6734 (mp0) cc_final: 0.6265 (mp0) REVERT: A 773 ASP cc_start: 0.7747 (t70) cc_final: 0.7191 (t0) REVERT: A 816 LEU cc_start: 0.8339 (tt) cc_final: 0.8081 (tt) REVERT: A 830 MET cc_start: 0.8597 (tpt) cc_final: 0.8110 (tpt) REVERT: A 842 TRP cc_start: 0.4188 (m-90) cc_final: 0.3201 (m-10) REVERT: A 876 LEU cc_start: 0.7973 (tt) cc_final: 0.7343 (mm) REVERT: A 1049 MET cc_start: 0.8411 (pmm) cc_final: 0.8071 (pmm) REVERT: A 1069 CYS cc_start: 0.8439 (t) cc_final: 0.8182 (p) REVERT: A 1072 ASN cc_start: 0.8221 (m-40) cc_final: 0.7201 (p0) REVERT: A 1138 GLU cc_start: 0.6952 (tp30) cc_final: 0.6703 (tp30) REVERT: A 1200 MET cc_start: 0.7833 (ptt) cc_final: 0.7597 (ptt) REVERT: A 1293 HIS cc_start: 0.8410 (t-170) cc_final: 0.7302 (t-90) REVERT: A 1308 VAL cc_start: 0.9519 (m) cc_final: 0.9280 (t) REVERT: A 1564 ASN cc_start: 0.7809 (m-40) cc_final: 0.7553 (t0) REVERT: A 1588 MET cc_start: 0.8842 (tpp) cc_final: 0.7973 (tpp) REVERT: A 1645 LYS cc_start: 0.6847 (tptt) cc_final: 0.6609 (pttt) REVERT: B 50 ASN cc_start: 0.7962 (t0) cc_final: 0.7540 (t0) REVERT: B 60 LEU cc_start: 0.8802 (mm) cc_final: 0.8378 (tt) REVERT: B 215 MET cc_start: 0.7027 (mmm) cc_final: 0.6721 (mmm) REVERT: B 265 ARG cc_start: 0.7323 (mpt-90) cc_final: 0.6711 (mpt-90) REVERT: B 278 LYS cc_start: 0.8758 (ptmm) cc_final: 0.8220 (ptmm) REVERT: B 296 ASP cc_start: 0.4814 (m-30) cc_final: 0.4432 (t0) REVERT: B 347 LEU cc_start: 0.7838 (pp) cc_final: 0.7529 (tp) REVERT: B 354 LEU cc_start: 0.8773 (tp) cc_final: 0.8520 (tp) REVERT: B 421 LEU cc_start: 0.7630 (tp) cc_final: 0.7091 (tp) REVERT: B 476 LEU cc_start: 0.6856 (tt) cc_final: 0.6281 (mm) REVERT: B 525 TRP cc_start: 0.7964 (t-100) cc_final: 0.7535 (t-100) REVERT: B 559 SER cc_start: 0.7591 (m) cc_final: 0.7175 (p) REVERT: B 566 TYR cc_start: 0.6591 (p90) cc_final: 0.6152 (p90) REVERT: B 646 HIS cc_start: 0.6688 (m170) cc_final: 0.5990 (m-70) REVERT: B 650 LEU cc_start: 0.7788 (mm) cc_final: 0.7462 (mp) REVERT: B 668 GLU cc_start: 0.8224 (mp0) cc_final: 0.7518 (mp0) REVERT: B 672 MET cc_start: 0.8138 (ptt) cc_final: 0.7864 (ptt) REVERT: B 686 HIS cc_start: 0.8099 (m-70) cc_final: 0.7836 (m90) REVERT: B 708 ASP cc_start: 0.7662 (m-30) cc_final: 0.7273 (m-30) REVERT: B 755 ASN cc_start: 0.6994 (p0) cc_final: 0.6241 (p0) REVERT: B 896 GLN cc_start: 0.6321 (pm20) cc_final: 0.4967 (mm110) REVERT: B 931 TRP cc_start: 0.5646 (t60) cc_final: 0.5309 (t60) REVERT: B 1086 PHE cc_start: 0.6670 (t80) cc_final: 0.6424 (t80) REVERT: B 1182 LEU cc_start: 0.7908 (tt) cc_final: 0.7702 (tt) REVERT: C 74 GLU cc_start: 0.8117 (mp0) cc_final: 0.7875 (mm-30) REVERT: C 85 PHE cc_start: 0.8593 (m-10) cc_final: 0.8286 (m-10) REVERT: C 295 ARG cc_start: 0.8249 (mpp-170) cc_final: 0.7698 (mmt180) REVERT: C 326 GLU cc_start: 0.8531 (pt0) cc_final: 0.8277 (pt0) REVERT: C 330 ASN cc_start: 0.7301 (p0) cc_final: 0.6818 (m-40) REVERT: D 29 GLN cc_start: 0.7409 (tm-30) cc_final: 0.6996 (tm-30) REVERT: D 37 LEU cc_start: 0.7858 (mp) cc_final: 0.6978 (pp) REVERT: E 40 GLU cc_start: 0.7841 (pm20) cc_final: 0.7193 (pp20) REVERT: E 41 ASP cc_start: 0.8059 (m-30) cc_final: 0.7112 (m-30) REVERT: E 136 ASN cc_start: 0.8768 (t0) cc_final: 0.8111 (t0) REVERT: E 148 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6824 (tm-30) REVERT: E 152 LYS cc_start: 0.8557 (tmtt) cc_final: 0.8014 (tptm) REVERT: E 177 ARG cc_start: 0.8532 (ptt90) cc_final: 0.8183 (ttp80) REVERT: F 144 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7637 (tm-30) REVERT: F 150 GLU cc_start: 0.7706 (pt0) cc_final: 0.7471 (pt0) REVERT: G 37 CYS cc_start: 0.7584 (p) cc_final: 0.6522 (m) REVERT: G 62 MET cc_start: 0.6260 (ttp) cc_final: 0.5527 (tmm) REVERT: G 160 ASN cc_start: 0.4355 (t0) cc_final: 0.4084 (t0) REVERT: G 219 ASP cc_start: 0.5575 (p0) cc_final: 0.5364 (p0) REVERT: H 34 ASP cc_start: 0.7902 (m-30) cc_final: 0.7638 (p0) REVERT: H 45 GLU cc_start: 0.7619 (pp20) cc_final: 0.6973 (tm-30) REVERT: H 46 LEU cc_start: 0.6395 (tp) cc_final: 0.5828 (tp) REVERT: H 104 PHE cc_start: 0.6815 (m-10) cc_final: 0.6587 (m-10) REVERT: H 131 ASN cc_start: 0.7315 (p0) cc_final: 0.5804 (t0) REVERT: I 59 SER cc_start: 0.6006 (p) cc_final: 0.5359 (t) REVERT: J 39 LEU cc_start: 0.8651 (mt) cc_final: 0.8387 (mt) REVERT: K 65 ILE cc_start: 0.8545 (pt) cc_final: 0.8344 (pt) REVERT: K 102 ASN cc_start: 0.7765 (p0) cc_final: 0.6993 (p0) REVERT: K 142 MET cc_start: 0.6901 (mtm) cc_final: 0.4984 (ttm) REVERT: M 18 GLN cc_start: 0.7256 (tt0) cc_final: 0.7018 (tt0) REVERT: M 39 ASP cc_start: 0.5176 (p0) cc_final: 0.4752 (t0) REVERT: M 319 PHE cc_start: 0.7511 (t80) cc_final: 0.6896 (t80) REVERT: M 338 HIS cc_start: 0.5231 (t70) cc_final: 0.4866 (m90) REVERT: M 351 HIS cc_start: 0.6887 (m170) cc_final: 0.6125 (t70) REVERT: N 40 LEU cc_start: 0.7613 (mp) cc_final: 0.7335 (mm) REVERT: N 41 ASN cc_start: 0.6699 (p0) cc_final: 0.6233 (p0) REVERT: N 80 MET cc_start: 0.0627 (mmm) cc_final: 0.0238 (mmt) REVERT: N 141 GLU cc_start: 0.7600 (mp0) cc_final: 0.7166 (mp0) REVERT: N 167 LYS cc_start: 0.6360 (tptt) cc_final: 0.6144 (tptt) outliers start: 1 outliers final: 1 residues processed: 783 average time/residue: 0.2257 time to fit residues: 290.9742 Evaluate side-chains 626 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 625 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 332 optimal weight: 7.9990 chunk 412 optimal weight: 0.2980 chunk 205 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 396 optimal weight: 8.9990 chunk 385 optimal weight: 9.9990 chunk 280 optimal weight: 6.9990 chunk 310 optimal weight: 0.0970 chunk 343 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1199 GLN A1500 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.159485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142277 restraints weight = 76835.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144474 restraints weight = 52405.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.145652 restraints weight = 37777.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146516 restraints weight = 30755.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147202 restraints weight = 25405.777| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 36691 Z= 0.138 Angle : 0.785 38.573 49783 Z= 0.375 Chirality : 0.047 0.263 5581 Planarity : 0.005 0.108 6243 Dihedral : 11.102 89.566 5312 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.12), residues: 4313 helix: -0.60 (0.14), residues: 1339 sheet: -1.36 (0.22), residues: 547 loop : -1.85 (0.12), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 99 TYR 0.027 0.002 TYR A1073 PHE 0.035 0.002 PHE B 496 TRP 0.026 0.002 TRP G 217 HIS 0.017 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (36668) covalent geometry : angle 0.74509 / 0.37 (49756) hydrogen bonds : bond 0.04126 / 2.75 ( 1202) hydrogen bonds : angle 5.52709 / 3.78 ( 3340) metal coordination : bond 0.00709 / 0.40 ( 22) metal coordination : angle 10.62737 / 5.79 ( 27) Misc. bond : bond 0.00428 / 0.23 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6648.08 seconds wall clock time: 116 minutes 15.08 seconds (6975.08 seconds total)