Starting phenix.real_space_refine on Thu Nov 20 10:38:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m3m_4148/11_2025/5m3m_4148.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m3m_4148/11_2025/5m3m_4148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5m3m_4148/11_2025/5m3m_4148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m3m_4148/11_2025/5m3m_4148.map" model { file = "/net/cci-nas-00/data/ceres_data/5m3m_4148/11_2025/5m3m_4148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m3m_4148/11_2025/5m3m_4148.cif" } resolution = 4.0 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= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 190 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 172 5.16 5 C 21028 2.51 5 N 5746 2.21 5 O 6280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33233 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 11558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1462, 11558 Classifications: {'peptide': 1462} Link IDs: {'CIS': 1, 'PCIS': 5, 'PTRANS': 53, 'TRANS': 1402} Chain breaks: 6 Chain: "B" Number of atoms: 9266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9266 Classifications: {'peptide': 1166} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1106} Chain breaks: 3 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2423 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 285} Chain: "E" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1735 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain: "F" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 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: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 793 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "M" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 771 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "N" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1035 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 9, 'TRANS': 121} Chain breaks: 2 Chain: "D" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 459 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Chain: "G" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1518 Classifications: {'peptide': 192} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 179} Chain breaks: 2 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" 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: "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 480 SG CYS A 65 71.825 68.343 56.013 1.00 55.24 S ATOM 535 SG CYS A 72 73.206 69.454 58.922 1.00 61.70 S ATOM 20134 SG CYS B1104 60.225 56.551 61.368 1.00 49.88 S ATOM 26904 SG CYS I 10 124.409 50.286 144.048 1.00 78.72 S ATOM 27474 SG CYS I 86 46.951 83.675 126.754 1.00 77.79 S ATOM 27778 SG CYS J 7 72.515 127.084 102.573 1.00 59.10 S ATOM 27801 SG CYS J 10 69.493 129.065 103.461 1.00 55.25 S ATOM 28081 SG CYS J 45 70.045 126.042 104.584 1.00 99.91 S ATOM 28087 SG CYS J 46 72.528 130.461 103.786 1.00 61.84 S ATOM 29129 SG CYS L 31 110.893 113.337 81.503 1.00 82.42 S ATOM 29149 SG CYS L 34 112.650 116.198 81.510 1.00 85.12 S ATOM 29253 SG CYS L 48 113.750 113.622 79.610 1.00 79.14 S ATOM 29276 SG CYS L 51 114.827 113.915 83.366 1.00147.14 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN I3002 " occ=0.75 Time building chain proxies: 7.13, per 1000 atoms: 0.21 Number of scatterers: 33233 At special positions: 0 Unit cell: (158.55, 162.75, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 172 16.00 O 6280 8.00 N 5746 7.00 C 21028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 65 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 72 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1104 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb=" ZN I3002 " pdb="ZN ZN I3002 " - pdb=" SG CYS I 86 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " Number of angles added : 12 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7872 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 49 sheets defined 38.5% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.555A pdb=" N LEU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.541A pdb=" N VAL A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 4.332A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 199 removed outlier: 3.600A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 228 removed outlier: 4.038A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 Processing helix chain 'A' and resid 316 through 339 removed outlier: 3.541A pdb=" N LEU A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N CYS A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.679A pdb=" N SER A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 406 removed outlier: 3.796A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 438 removed outlier: 3.612A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 removed outlier: 3.908A pdb=" N GLU A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.649A pdb=" N ALA A 502 " --> pdb=" O PRO A 498 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 561 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 618 through 625 removed outlier: 4.165A pdb=" N GLY A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 4.394A 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 681 removed outlier: 3.884A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 Processing helix chain 'A' and resid 727 through 740 removed outlier: 3.555A pdb=" N ILE A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 802 through 825 removed outlier: 3.529A pdb=" N LEU A 813 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 836 through 850 removed outlier: 3.628A pdb=" N ASN A 840 " --> pdb=" O THR A 836 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 846 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.571A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.513A pdb=" N SER A 889 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 895 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 908 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.743A pdb=" N VAL A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1010 removed outlier: 3.613A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1028 Processing helix chain 'A' and resid 1060 through 1064 removed outlier: 3.793A pdb=" N THR A1064 " --> pdb=" O SER A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1071 removed outlier: 3.686A pdb=" N CYS A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 Processing helix chain 'A' and resid 1081 through 1086 removed outlier: 4.605A pdb=" N LEU A1085 " --> pdb=" O ASN A1081 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A1086 " --> pdb=" O PRO A1082 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1081 through 1086' Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1092 through 1108 removed outlier: 3.534A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.564A pdb=" N LYS A1150 " --> pdb=" O SER A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1158 removed outlier: 4.052A pdb=" N PHE A1155 " --> pdb=" O ASN A1151 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 3.505A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.910A pdb=" N ILE A1188 " --> pdb=" O ALA A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1202 removed outlier: 4.177A pdb=" N LEU A1202 " --> pdb=" O GLN A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1262 through 1266 removed outlier: 3.868A pdb=" N VAL A1266 " --> pdb=" O LEU A1262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1262 through 1266' Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 3.644A pdb=" N TYR A1302 " --> pdb=" O ASP A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1319 Processing helix chain 'A' and resid 1319 through 1336 removed outlier: 3.650A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A1328 " --> pdb=" O LEU A1324 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1454 removed outlier: 3.736A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1495 removed outlier: 3.600A pdb=" N ILE A1488 " --> pdb=" O LEU A1484 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A1494 " --> pdb=" O GLU A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 3.768A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.843A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.770A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.585A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A1590 " --> pdb=" O ALA A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1605 removed outlier: 3.925A pdb=" N THR A1605 " --> pdb=" O GLN A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1614 Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.971A pdb=" N PHE A1621 " --> pdb=" O THR A1617 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A1622 " --> pdb=" O THR A1618 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A1624 " --> pdb=" O GLN A1620 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A1626 " --> pdb=" O LEU A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1643 Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 35 through 51 removed outlier: 3.676A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.619A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.846A pdb=" N GLY B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.120A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.724A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.531A pdb=" N THR B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 removed outlier: 3.688A pdb=" N ASP B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 333 " --> pdb=" O TYR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.749A pdb=" N ILE B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 434 removed outlier: 3.503A pdb=" N GLY B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 456 through 468 removed outlier: 4.144A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 499 removed outlier: 3.743A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 512 removed outlier: 3.651A pdb=" N GLN B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 512' Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 597 through 615 removed outlier: 4.191A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.792A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 removed outlier: 3.619A pdb=" N THR B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 725 removed outlier: 3.532A pdb=" N ASN B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 723 " --> pdb=" O CYS B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 735 removed outlier: 4.503A pdb=" N CYS B 734 " --> pdb=" O VAL B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 removed outlier: 4.127A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 782 through 786 removed outlier: 3.521A pdb=" N ALA B 786 " --> pdb=" O MET B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 835 through 840 removed outlier: 3.996A pdb=" N LYS B 839 " --> pdb=" O GLU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 936 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 959 through 976 removed outlier: 4.466A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.647A pdb=" N GLU B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1083 removed outlier: 3.979A pdb=" N LEU B1079 " --> pdb=" O GLU B1075 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B1081 " --> pdb=" O ASP B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1092 Processing helix chain 'B' and resid 1154 through 1156 No H-bonds generated for 'chain 'B' and resid 1154 through 1156' Processing helix chain 'B' and resid 1180 through 1192 removed outlier: 4.039A pdb=" N TYR B1184 " --> pdb=" O PHE B1180 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B1191 " --> pdb=" O SER B1187 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.667A pdb=" N PHE C 36 " --> pdb=" O ASN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.539A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.947A pdb=" N LEU C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.627A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 173 through 182 removed outlier: 3.631A pdb=" N THR C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS C 182 " --> pdb=" O THR C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 240 through 250 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 282 through 288 removed outlier: 3.726A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.700A pdb=" N LYS C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 26 removed outlier: 3.890A pdb=" N LYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU E 21 " --> pdb=" O ARG E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.793A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 119 through 123 Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.895A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 58 through 73 removed outlier: 4.114A pdb=" N ARG F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'I' and resid 40 through 42 No H-bonds generated for 'chain 'I' and resid 40 through 42' Processing helix chain 'I' and resid 58 through 65 removed outlier: 3.832A pdb=" N ALA I 62 " --> pdb=" O SER I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 77 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.154A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.413A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.894A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.860A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN K 83 " --> pdb=" O VAL K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.685A pdb=" N ASP K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 72 removed outlier: 3.504A pdb=" N ALA M 72 " --> pdb=" O SER M 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'N' and resid 92 through 97 Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 81 through 96 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 66 through 70 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 18 removed outlier: 4.783A pdb=" N ILE A 11 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1201 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 85 removed outlier: 6.283A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 372 Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA6, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 8.478A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.924A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 719 through 721 removed outlier: 5.502A pdb=" N ILE A 719 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR H 98 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR H 141 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA H 60 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR H 39 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG H 124 " --> pdb=" O THR H 39 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.743A pdb=" N LYS A 772 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 948 through 949 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 1239 through 1241 Processing sheet with id=AB4, first strand: chain 'A' and resid 1461 through 1462 removed outlier: 3.743A pdb=" N VAL A1272 " --> pdb=" O THR I 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1654 through 1656 Processing sheet with id=AB6, first strand: chain 'B' and resid 70 through 74 removed outlier: 3.538A pdb=" N ILE B 73 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 139 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 156 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB9, first strand: chain 'B' and resid 401 through 403 removed outlier: 6.959A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.821A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS B 251 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC3, first strand: chain 'B' and resid 571 through 572 removed outlier: 3.759A pdb=" N ALA B 571 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP B 595 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 625 through 626 Processing sheet with id=AC5, first strand: chain 'B' and resid 674 through 675 Processing sheet with id=AC6, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.578A pdb=" N LYS B 805 " --> pdb=" O TYR B 905 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 807 through 810 removed outlier: 4.028A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS L 58 " --> pdb=" O VAL B 885 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1010 through 1011 removed outlier: 7.421A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 769 " --> pdb=" O TYR B1033 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 825 removed outlier: 6.416A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) 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 1098 through 1104 Processing sheet with id=AD3, first strand: chain 'B' and resid 1113 through 1115 removed outlier: 3.813A pdb=" N GLN B1114 " --> pdb=" O CYS B1127 " (cutoff:3.500A) 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 47 removed outlier: 6.968A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 157 through 158 removed outlier: 4.620A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 135 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 168 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.512A pdb=" N GLN C 200 " --> pdb=" O CYS C 140 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS C 205 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE C 85 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N HIS C 207 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL C 83 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE C 209 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU C 81 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY C 211 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA C 79 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.974A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.216A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AE3, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.818A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 212 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 27 through 29 Processing sheet with id=AE6, first strand: chain 'I' and resid 81 through 83 removed outlier: 3.709A pdb=" N ILE I 82 " --> pdb=" O MET I 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 47 through 50 removed outlier: 3.924A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 11 through 16 removed outlier: 6.278A pdb=" N ILE M 88 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER M 14 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER M 87 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 30 through 31 removed outlier: 6.625A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.863A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.863A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY G 79 " --> pdb=" O ASN G 74 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 132 through 140 removed outlier: 6.714A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 167 through 169 1299 hydrogen bonds defined for protein. 3597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.75 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10410 1.33 - 1.45: 5467 1.45 - 1.57: 17724 1.57 - 1.69: 1 1.69 - 1.81: 269 Bond restraints: 33871 Sorted by residual: bond pdb=" CA LEU D 99 " pdb=" C LEU D 99 " ideal model delta sigma weight residual 1.524 1.584 -0.060 1.26e-02 6.30e+03 2.29e+01 bond pdb=" CA ASN B 168 " pdb=" C ASN B 168 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.29e-02 6.01e+03 2.14e+01 bond pdb=" CA LEU E 123 " pdb=" C LEU E 123 " ideal model delta sigma weight residual 1.523 1.458 0.064 1.41e-02 5.03e+03 2.09e+01 bond pdb=" CA TYR A1595 " pdb=" CB TYR A1595 " ideal model delta sigma weight residual 1.528 1.479 0.048 1.39e-02 5.18e+03 1.20e+01 bond pdb=" CA ASP B 708 " pdb=" C ASP B 708 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.45e-02 4.76e+03 1.15e+01 ... (remaining 33866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 44853 2.84 - 5.68: 805 5.68 - 8.52: 89 8.52 - 11.36: 10 11.36 - 14.20: 4 Bond angle restraints: 45761 Sorted by residual: angle pdb=" N ASN A1648 " pdb=" CA ASN A1648 " pdb=" C ASN A1648 " ideal model delta sigma weight residual 112.45 122.65 -10.20 1.39e+00 5.18e-01 5.38e+01 angle pdb=" C ASN A1648 " pdb=" N VAL A1649 " pdb=" CA VAL A1649 " ideal model delta sigma weight residual 121.70 134.13 -12.43 1.80e+00 3.09e-01 4.77e+01 angle pdb=" CD ARG G 241 " pdb=" NE ARG G 241 " pdb=" CZ ARG G 241 " ideal model delta sigma weight residual 124.40 132.11 -7.71 1.40e+00 5.10e-01 3.04e+01 angle pdb=" N ASP N 127 " pdb=" CA ASP N 127 " pdb=" C ASP N 127 " ideal model delta sigma weight residual 114.16 106.21 7.95 1.48e+00 4.57e-01 2.89e+01 angle pdb=" N ASP G 219 " pdb=" CA ASP G 219 " pdb=" C ASP G 219 " ideal model delta sigma weight residual 109.31 116.80 -7.49 1.42e+00 4.96e-01 2.78e+01 ... (remaining 45756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 19957 17.80 - 35.60: 517 35.60 - 53.40: 140 53.40 - 71.20: 41 71.20 - 89.00: 28 Dihedral angle restraints: 20683 sinusoidal: 8507 harmonic: 12176 Sorted by residual: dihedral pdb=" CA VAL A1649 " pdb=" C VAL A1649 " pdb=" N GLY A1650 " pdb=" CA GLY A1650 " ideal model delta harmonic sigma weight residual 180.00 -143.81 -36.19 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA ASN C 130 " pdb=" C ASN C 130 " pdb=" N THR C 131 " pdb=" CA THR C 131 " ideal model delta harmonic sigma weight residual -180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ASP A1545 " pdb=" C ASP A1545 " pdb=" N VAL A1546 " pdb=" CA VAL A1546 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 20680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4194 0.068 - 0.136: 840 0.136 - 0.204: 65 0.204 - 0.272: 12 0.272 - 0.340: 4 Chirality restraints: 5115 Sorted by residual: chirality pdb=" CA LEU D 99 " pdb=" N LEU D 99 " pdb=" C LEU D 99 " pdb=" CB LEU D 99 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ASP N 86 " pdb=" N ASP N 86 " pdb=" C ASP N 86 " pdb=" CB ASP N 86 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ASN M 57 " pdb=" N ASN M 57 " pdb=" C ASN M 57 " pdb=" CB ASN M 57 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 5112 not shown) Planarity restraints: 5915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE N 145 " 0.090 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO N 146 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO N 146 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO N 146 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 903 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C ILE A 903 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE A 903 " 0.018 2.00e-02 2.50e+03 pdb=" N THR A 904 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU N 70 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO N 71 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO N 71 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO N 71 " 0.036 5.00e-02 4.00e+02 ... (remaining 5912 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.84: 3 1.84 - 2.60: 663 2.60 - 3.37: 48106 3.37 - 4.13: 82702 4.13 - 4.90: 145129 Nonbonded interactions: 276603 Sorted by model distance: nonbonded pdb=" ND2 ASN B 683 " pdb=" NH2 ARG N 154 " model vdw 1.074 3.200 nonbonded pdb=" OD1 ASN B 893 " pdb=" CE2 PHE B 895 " model vdw 1.173 3.340 nonbonded pdb=" CE MET F 103 " pdb=" CG PRO G 51 " model vdw 1.665 3.860 nonbonded pdb=" OD1 ASN B 893 " pdb=" CD2 PHE B 895 " model vdw 1.881 3.340 nonbonded pdb=" O GLU B1172 " pdb="ZN ZN B1302 " model vdw 1.945 2.230 ... (remaining 276598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.050 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 36.330 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 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 : 0.009 0.635 33884 Z= 0.423 Angle : 1.073 55.400 45773 Z= 0.602 Chirality : 0.053 0.340 5115 Planarity : 0.006 0.140 5915 Dihedral : 10.361 89.000 12811 Min Nonbonded Distance : 1.074 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.66 % Allowed : 4.88 % Favored : 94.47 % Rotamer: Outliers : 1.21 % Allowed : 1.99 % Favored : 96.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.41 (0.10), residues: 4122 helix: -3.65 (0.09), residues: 1187 sheet: -1.55 (0.17), residues: 631 loop : -1.65 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 155 TYR 0.034 0.003 TYR F 137 PHE 0.034 0.003 PHE B 895 TRP 0.030 0.003 TRP B 143 HIS 0.013 0.002 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00767 (33871) covalent geometry : angle 0.99669 (45761) hydrogen bonds : bond 0.31243 ( 1289) hydrogen bonds : angle 10.21261 ( 3597) metal coordination : bond 0.21147 ( 13) metal coordination : angle 24.48437 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 1131 time to evaluate : 1.215 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: A 345 LEU cc_start: 0.7244 (mt) cc_final: 0.6878 (tp) REVERT: A 368 ARG cc_start: 0.6498 (mtm110) cc_final: 0.6004 (mmm-85) REVERT: A 498 PRO cc_start: 0.8642 (Cg_endo) cc_final: 0.8420 (Cg_exo) REVERT: A 646 GLU cc_start: 0.6371 (mt-10) cc_final: 0.6006 (mt-10) REVERT: A 777 LEU cc_start: 0.9274 (mt) cc_final: 0.8953 (mt) REVERT: A 783 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8185 (tttt) REVERT: A 831 ASP cc_start: 0.8488 (p0) cc_final: 0.7991 (p0) REVERT: A 836 THR cc_start: 0.7465 (t) cc_final: 0.6198 (t) REVERT: A 865 ASP cc_start: 0.7921 (t70) cc_final: 0.7254 (m-30) REVERT: A 911 CYS cc_start: 0.7974 (m) cc_final: 0.7435 (p) REVERT: A 912 VAL cc_start: 0.9065 (t) cc_final: 0.8664 (p) REVERT: A 914 ASP cc_start: 0.7469 (m-30) cc_final: 0.7090 (t0) REVERT: A 1136 VAL cc_start: 0.8805 (t) cc_final: 0.8134 (t) REVERT: A 1537 ASP cc_start: 0.7633 (t0) cc_final: 0.7325 (p0) REVERT: A 1611 MET cc_start: 0.7024 (ttp) cc_final: 0.6645 (tmm) REVERT: B 74 PHE cc_start: 0.7140 (m-10) cc_final: 0.6860 (m-80) REVERT: B 90 TYR cc_start: 0.6530 (t80) cc_final: 0.5931 (m-10) REVERT: B 96 SER cc_start: 0.8457 (m) cc_final: 0.8013 (t) REVERT: B 136 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7477 (mptt) REVERT: B 184 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8053 (mtmt) REVERT: B 229 TYR cc_start: 0.8240 (m-80) cc_final: 0.7960 (m-10) REVERT: B 494 TYR cc_start: 0.6832 (m-10) cc_final: 0.6349 (m-10) REVERT: B 509 PHE cc_start: 0.7388 (m-10) cc_final: 0.7113 (m-80) REVERT: B 604 ILE cc_start: 0.8826 (mt) cc_final: 0.8359 (mt) REVERT: B 731 VAL cc_start: 0.8246 (t) cc_final: 0.7804 (t) REVERT: B 758 ASP cc_start: 0.8271 (m-30) cc_final: 0.7686 (t0) REVERT: B 762 MET cc_start: 0.7580 (mmp) cc_final: 0.7285 (mmt) REVERT: B 784 ASP cc_start: 0.7176 (m-30) cc_final: 0.6893 (m-30) REVERT: B 822 THR cc_start: 0.6332 (m) cc_final: 0.5994 (p) REVERT: B 876 SER cc_start: 0.8461 (t) cc_final: 0.8164 (m) REVERT: B 883 GLU cc_start: 0.8202 (tp30) cc_final: 0.7804 (tp30) REVERT: B 919 SER cc_start: 0.8778 (p) cc_final: 0.8340 (t) REVERT: B 958 MET cc_start: 0.8971 (mtm) cc_final: 0.8508 (mtt) REVERT: B 1159 TRP cc_start: 0.5945 (p-90) cc_final: 0.5441 (p-90) REVERT: C 58 ASN cc_start: 0.7623 (m-40) cc_final: 0.7281 (m-40) REVERT: C 81 GLU cc_start: 0.7331 (tp30) cc_final: 0.7116 (tt0) REVERT: C 124 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8616 (mm-30) REVERT: C 140 CYS cc_start: 0.7637 (t) cc_final: 0.7278 (t) REVERT: C 168 LYS cc_start: 0.8370 (mptt) cc_final: 0.7933 (pttm) REVERT: C 177 THR cc_start: 0.8512 (m) cc_final: 0.8246 (p) REVERT: C 273 ASP cc_start: 0.8801 (t70) cc_final: 0.8093 (p0) REVERT: E 42 PHE cc_start: 0.7383 (t80) cc_final: 0.6953 (t80) REVERT: E 105 PHE cc_start: 0.6212 (m-80) cc_final: 0.5973 (m-10) REVERT: E 112 TYR cc_start: 0.6964 (p90) cc_final: 0.6719 (p90) REVERT: H 38 LEU cc_start: 0.8004 (tp) cc_final: 0.7547 (tp) REVERT: H 103 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7723 (tppt) REVERT: H 117 SER cc_start: 0.8355 (t) cc_final: 0.8112 (t) REVERT: H 130 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7780 (tpt90) REVERT: H 145 ARG cc_start: 0.7940 (ptt-90) cc_final: 0.7235 (ttp80) REVERT: I 15 ASP cc_start: 0.7860 (m-30) cc_final: 0.7313 (t0) REVERT: I 38 PRO cc_start: 0.6465 (Cg_exo) cc_final: 0.5944 (Cg_endo) REVERT: J 55 ASP cc_start: 0.6983 (t0) cc_final: 0.6548 (t0) REVERT: K 50 LEU cc_start: 0.7240 (mt) cc_final: 0.6700 (mt) REVERT: M 18 GLN cc_start: 0.0718 (OUTLIER) cc_final: 0.0065 (tm-30) REVERT: N 162 LYS cc_start: 0.4669 (mptt) cc_final: 0.4355 (tptp) outliers start: 45 outliers final: 9 residues processed: 1169 average time/residue: 0.2383 time to fit residues: 429.5634 Evaluate side-chains 606 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 596 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 65 TYR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 241 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.0570 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 213 ASN A 340 HIS A 344 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 537 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 HIS A 738 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS A1503 HIS ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS B 182 GLN B 213 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 504 HIS B 669 GLN B 683 ASN B 684 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 GLN B1008 HIS B1010 ASN B1034 GLN B1082 HIS ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN C 58 ASN C 99 HIS C 119 ASN C 248 GLN E 32 GLN E 179 GLN L 53 HIS ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.188400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.158719 restraints weight = 58231.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157093 restraints weight = 80371.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158859 restraints weight = 63222.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.159397 restraints weight = 41971.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159823 restraints weight = 38401.218| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33884 Z= 0.161 Angle : 0.773 39.201 45773 Z= 0.382 Chirality : 0.046 0.255 5115 Planarity : 0.006 0.079 5915 Dihedral : 6.058 62.368 4552 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.03 % Favored : 96.85 % Rotamer: Outliers : 2.64 % Allowed : 10.88 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.09 (0.12), residues: 4122 helix: -0.60 (0.12), residues: 1375 sheet: -0.85 (0.18), residues: 656 loop : -0.64 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1176 TYR 0.024 0.002 TYR A 478 PHE 0.032 0.002 PHE B 895 TRP 0.024 0.002 TRP A 530 HIS 0.009 0.001 HIS A1453 Details of bonding type rmsd covalent geometry : bond 0.00342 (33871) covalent geometry : angle 0.71380 (45761) hydrogen bonds : bond 0.05739 ( 1289) hydrogen bonds : angle 6.56246 ( 3597) metal coordination : bond 0.00964 ( 13) metal coordination : angle 18.29983 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 745 time to evaluate : 1.243 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: A 63 SER cc_start: 0.7219 (m) cc_final: 0.6794 (t) REVERT: A 345 LEU cc_start: 0.7296 (mt) cc_final: 0.6809 (tt) REVERT: A 368 ARG cc_start: 0.6506 (mtm110) cc_final: 0.6176 (mmm-85) REVERT: A 777 LEU cc_start: 0.9179 (mt) cc_final: 0.8877 (mt) REVERT: A 831 ASP cc_start: 0.7497 (p0) cc_final: 0.7197 (p0) REVERT: A 867 ASP cc_start: 0.7820 (t0) cc_final: 0.7235 (t0) REVERT: A 975 ASP cc_start: 0.8083 (t0) cc_final: 0.7860 (t0) REVERT: A 1018 TYR cc_start: 0.6223 (t80) cc_final: 0.6014 (t80) REVERT: A 1040 ASP cc_start: 0.7281 (t0) cc_final: 0.6974 (p0) REVERT: A 1603 MET cc_start: 0.7652 (tmm) cc_final: 0.7162 (tpp) REVERT: B 90 TYR cc_start: 0.6766 (t80) cc_final: 0.6097 (m-10) REVERT: B 96 SER cc_start: 0.7848 (m) cc_final: 0.7638 (t) REVERT: B 99 VAL cc_start: 0.7575 (t) cc_final: 0.7293 (t) REVERT: B 184 LYS cc_start: 0.8525 (mtmt) cc_final: 0.7806 (mtmt) REVERT: B 205 MET cc_start: 0.7946 (mtm) cc_final: 0.7690 (mtm) REVERT: B 373 MET cc_start: 0.7906 (tpp) cc_final: 0.7653 (tpp) REVERT: B 409 TYR cc_start: 0.7778 (t80) cc_final: 0.7152 (t80) REVERT: B 447 SER cc_start: 0.8284 (m) cc_final: 0.7988 (p) REVERT: B 494 TYR cc_start: 0.6358 (m-10) cc_final: 0.5356 (m-10) REVERT: B 509 PHE cc_start: 0.7148 (m-10) cc_final: 0.6941 (m-80) REVERT: B 588 ILE cc_start: 0.8557 (mt) cc_final: 0.8350 (pt) REVERT: B 658 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7092 (mm) REVERT: B 661 GLU cc_start: 0.7861 (mp0) cc_final: 0.7654 (mp0) REVERT: B 718 GLN cc_start: 0.7540 (tp40) cc_final: 0.7103 (tp40) REVERT: B 759 ASP cc_start: 0.7801 (m-30) cc_final: 0.7241 (m-30) REVERT: B 900 THR cc_start: 0.7363 (OUTLIER) cc_final: 0.7160 (p) REVERT: B 958 MET cc_start: 0.8609 (mtm) cc_final: 0.8395 (mtm) REVERT: C 140 CYS cc_start: 0.7727 (t) cc_final: 0.7267 (t) REVERT: C 168 LYS cc_start: 0.8586 (mptt) cc_final: 0.8125 (pttm) REVERT: E 37 LEU cc_start: 0.8111 (tp) cc_final: 0.7594 (tp) REVERT: E 58 MET cc_start: 0.6663 (mtt) cc_final: 0.6338 (mtt) REVERT: E 145 THR cc_start: 0.8324 (p) cc_final: 0.7988 (t) REVERT: E 156 LEU cc_start: 0.8009 (mt) cc_final: 0.7794 (mt) REVERT: F 130 ILE cc_start: 0.8133 (mt) cc_final: 0.7703 (mm) REVERT: F 135 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7253 (ttp-110) REVERT: I 92 GLU cc_start: 0.6895 (tp30) cc_final: 0.6599 (tp30) REVERT: J 68 LYS cc_start: 0.7369 (pptt) cc_final: 0.6499 (pptt) REVERT: K 55 SER cc_start: 0.7461 (p) cc_final: 0.7166 (t) REVERT: K 68 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7842 (mm-30) REVERT: K 125 MET cc_start: 0.7422 (mtm) cc_final: 0.7198 (mtm) REVERT: K 126 ASP cc_start: 0.7990 (t70) cc_final: 0.7743 (t70) REVERT: M 18 GLN cc_start: 0.1218 (OUTLIER) cc_final: 0.0155 (tm-30) REVERT: M 61 GLU cc_start: 0.5753 (mp0) cc_final: 0.5215 (mt-10) REVERT: N 162 LYS cc_start: 0.4898 (mptt) cc_final: 0.4276 (tptp) REVERT: D 99 LEU cc_start: -0.1363 (OUTLIER) cc_final: -0.1651 (pp) outliers start: 98 outliers final: 44 residues processed: 810 average time/residue: 0.2098 time to fit residues: 274.7977 Evaluate side-chains 597 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 549 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 65 TYR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 295 optimal weight: 20.0000 chunk 333 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 289 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 224 HIS A 344 ASN A 378 HIS ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN A 639 GLN ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN A1447 GLN A1629 ASN B 151 ASN B 231 HIS B 246 GLN B 427 GLN B 686 HIS B 702 ASN B 745 GLN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN B1171 ASN C 58 ASN H 64 ASN H 83 GLN L 53 HIS N 51 GLN N 128 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.176402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144998 restraints weight = 57854.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142781 restraints weight = 80371.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144353 restraints weight = 69085.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145304 restraints weight = 43281.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145675 restraints weight = 40507.648| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 33884 Z= 0.252 Angle : 0.830 43.296 45773 Z= 0.404 Chirality : 0.049 0.237 5115 Planarity : 0.006 0.058 5915 Dihedral : 5.827 58.750 4544 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.71 % Favored : 96.17 % Rotamer: Outliers : 4.39 % Allowed : 12.92 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.67 (0.12), residues: 4122 helix: 0.04 (0.13), residues: 1371 sheet: -0.71 (0.18), residues: 684 loop : -0.57 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 920 TYR 0.039 0.003 TYR A1573 PHE 0.030 0.003 PHE B 895 TRP 0.026 0.002 TRP E 13 HIS 0.009 0.002 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00582 (33871) covalent geometry : angle 0.77292 (45761) hydrogen bonds : bond 0.05382 ( 1289) hydrogen bonds : angle 5.96964 ( 3597) metal coordination : bond 0.00957 ( 13) metal coordination : angle 18.71643 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 598 time to evaluate : 1.301 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: A 183 SER cc_start: 0.7287 (t) cc_final: 0.6936 (m) REVERT: A 345 LEU cc_start: 0.7240 (mt) cc_final: 0.6738 (tt) REVERT: A 447 THR cc_start: 0.5571 (OUTLIER) cc_final: 0.5318 (p) REVERT: A 571 HIS cc_start: 0.7634 (p-80) cc_final: 0.7135 (t-90) REVERT: A 656 GLN cc_start: 0.7591 (mt0) cc_final: 0.7116 (tp40) REVERT: A 777 LEU cc_start: 0.9427 (mt) cc_final: 0.9084 (mt) REVERT: A 867 ASP cc_start: 0.7807 (t0) cc_final: 0.7554 (t0) REVERT: A 1136 VAL cc_start: 0.8137 (t) cc_final: 0.7901 (m) REVERT: A 1191 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.6791 (mt0) REVERT: B 74 PHE cc_start: 0.7329 (m-80) cc_final: 0.7036 (m-80) REVERT: B 90 TYR cc_start: 0.7024 (t80) cc_final: 0.6030 (m-80) REVERT: B 150 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7002 (mm-30) REVERT: B 184 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8351 (ptmt) REVERT: B 447 SER cc_start: 0.8418 (m) cc_final: 0.8133 (p) REVERT: B 469 ASN cc_start: 0.8447 (m-40) cc_final: 0.8063 (t0) REVERT: B 588 ILE cc_start: 0.8722 (mt) cc_final: 0.8245 (pt) REVERT: B 589 ASP cc_start: 0.6906 (m-30) cc_final: 0.6030 (t0) REVERT: B 718 GLN cc_start: 0.7935 (tp40) cc_final: 0.7304 (tp40) REVERT: B 759 ASP cc_start: 0.7881 (m-30) cc_final: 0.7522 (m-30) REVERT: B 919 SER cc_start: 0.9162 (p) cc_final: 0.8475 (t) REVERT: B 1180 PHE cc_start: 0.7622 (t80) cc_final: 0.7405 (t80) REVERT: C 156 LEU cc_start: 0.8911 (mt) cc_final: 0.8637 (tp) REVERT: C 168 LYS cc_start: 0.8921 (mptt) cc_final: 0.8054 (pttm) REVERT: E 11 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5809 (ptm160) REVERT: E 37 LEU cc_start: 0.8226 (tp) cc_final: 0.7858 (tp) REVERT: F 135 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7412 (ttp80) REVERT: H 12 VAL cc_start: 0.7945 (t) cc_final: 0.7593 (m) REVERT: H 53 ASP cc_start: 0.6635 (t0) cc_final: 0.6288 (t0) REVERT: K 55 SER cc_start: 0.7924 (p) cc_final: 0.7492 (t) REVERT: M 18 GLN cc_start: 0.1723 (OUTLIER) cc_final: 0.0899 (tm-30) REVERT: M 91 TYR cc_start: 0.5105 (m-80) cc_final: 0.4523 (m-10) REVERT: M 104 SER cc_start: 0.6478 (m) cc_final: 0.6002 (t) REVERT: G 15 ARG cc_start: 0.1410 (OUTLIER) cc_final: 0.1159 (tpp-160) REVERT: G 218 VAL cc_start: 0.2291 (OUTLIER) cc_final: 0.2054 (t) outliers start: 163 outliers final: 100 residues processed: 704 average time/residue: 0.1976 time to fit residues: 231.5623 Evaluate side-chains 605 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 498 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1191 GLN Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1331 LYS Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1161 ASP Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 65 TYR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain G residue 15 ARG Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 243 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 348 optimal weight: 9.9990 chunk 363 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 380 optimal weight: 3.9990 chunk 391 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 374 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A1026 GLN ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN B1089 GLN ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.177737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147913 restraints weight = 58255.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147299 restraints weight = 71648.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148445 restraints weight = 68503.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148907 restraints weight = 41724.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149411 restraints weight = 38817.115| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33884 Z= 0.171 Angle : 0.718 40.011 45773 Z= 0.343 Chirality : 0.046 0.318 5115 Planarity : 0.005 0.061 5915 Dihedral : 5.352 55.339 4537 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 3.50 % Allowed : 15.91 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.40 (0.13), residues: 4122 helix: 0.41 (0.14), residues: 1370 sheet: -0.64 (0.19), residues: 708 loop : -0.49 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 154 TYR 0.029 0.002 TYR B1032 PHE 0.029 0.002 PHE B 895 TRP 0.019 0.002 TRP E 13 HIS 0.016 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00393 (33871) covalent geometry : angle 0.65474 (45761) hydrogen bonds : bond 0.04448 ( 1289) hydrogen bonds : angle 5.57457 ( 3597) metal coordination : bond 0.00749 ( 13) metal coordination : angle 18.28127 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 542 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 SER cc_start: 0.7272 (t) cc_final: 0.6960 (m) REVERT: A 345 LEU cc_start: 0.7040 (mt) cc_final: 0.6425 (tp) REVERT: A 447 THR cc_start: 0.5601 (OUTLIER) cc_final: 0.5334 (p) REVERT: A 571 HIS cc_start: 0.7484 (p-80) cc_final: 0.7111 (t-90) REVERT: A 618 TYR cc_start: 0.8226 (m-80) cc_final: 0.8019 (m-80) REVERT: A 656 GLN cc_start: 0.7584 (mt0) cc_final: 0.7064 (tp40) REVERT: A 867 ASP cc_start: 0.7818 (t0) cc_final: 0.7482 (t0) REVERT: A 1191 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.6759 (mt0) REVERT: A 1522 GLU cc_start: 0.7515 (tp30) cc_final: 0.6751 (tt0) REVERT: A 1590 THR cc_start: 0.8184 (p) cc_final: 0.7981 (p) REVERT: A 1603 MET cc_start: 0.7855 (tpp) cc_final: 0.7187 (tpt) REVERT: B 90 TYR cc_start: 0.6975 (t80) cc_final: 0.5984 (m-80) REVERT: B 184 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8387 (ptmt) REVERT: B 447 SER cc_start: 0.8405 (m) cc_final: 0.8097 (p) REVERT: B 588 ILE cc_start: 0.8707 (mt) cc_final: 0.8189 (pt) REVERT: B 589 ASP cc_start: 0.7020 (m-30) cc_final: 0.6031 (t0) REVERT: B 668 GLU cc_start: 0.7558 (pt0) cc_final: 0.7313 (pt0) REVERT: B 672 MET cc_start: 0.8198 (mtt) cc_final: 0.7871 (mtp) REVERT: B 718 GLN cc_start: 0.7768 (tp40) cc_final: 0.7297 (tp40) REVERT: B 759 ASP cc_start: 0.7835 (m-30) cc_final: 0.7477 (m-30) REVERT: B 916 LYS cc_start: 0.8858 (mttt) cc_final: 0.8592 (mttp) REVERT: B 919 SER cc_start: 0.9160 (p) cc_final: 0.8576 (t) REVERT: B 921 HIS cc_start: 0.8294 (m-70) cc_final: 0.7656 (m-70) REVERT: B 965 GLU cc_start: 0.8262 (tt0) cc_final: 0.7296 (pt0) REVERT: B 1047 ARG cc_start: 0.6800 (ttp80) cc_final: 0.5474 (ttm-80) REVERT: C 156 LEU cc_start: 0.9167 (mt) cc_final: 0.8790 (tp) REVERT: C 168 LYS cc_start: 0.8934 (mptt) cc_final: 0.8006 (pttp) REVERT: C 280 LEU cc_start: 0.7486 (mm) cc_final: 0.6615 (tp) REVERT: C 283 GLU cc_start: 0.6867 (mp0) cc_final: 0.6570 (mp0) REVERT: E 11 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.5708 (ptm160) REVERT: E 37 LEU cc_start: 0.8309 (tp) cc_final: 0.8001 (tp) REVERT: E 50 MET cc_start: 0.3320 (ttt) cc_final: 0.3004 (ttt) REVERT: F 135 ARG cc_start: 0.8225 (ttm170) cc_final: 0.7421 (ttp80) REVERT: H 12 VAL cc_start: 0.7844 (t) cc_final: 0.7588 (m) REVERT: H 93 TYR cc_start: 0.7563 (m-80) cc_final: 0.7324 (m-10) REVERT: H 97 MET cc_start: 0.7874 (ptp) cc_final: 0.7664 (ptp) REVERT: J 49 MET cc_start: 0.6951 (mmm) cc_final: 0.6690 (mmm) REVERT: J 68 LYS cc_start: 0.6995 (ptmt) cc_final: 0.6703 (ptpt) REVERT: K 55 SER cc_start: 0.7871 (p) cc_final: 0.7384 (t) REVERT: K 126 ASP cc_start: 0.8258 (t0) cc_final: 0.7984 (t70) REVERT: M 18 GLN cc_start: 0.2046 (OUTLIER) cc_final: 0.0935 (tm-30) REVERT: M 61 GLU cc_start: 0.5639 (mp0) cc_final: 0.4616 (mt-10) REVERT: G 218 VAL cc_start: 0.1898 (OUTLIER) cc_final: 0.1685 (t) outliers start: 130 outliers final: 90 residues processed: 629 average time/residue: 0.1980 time to fit residues: 207.8286 Evaluate side-chains 590 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 495 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1191 GLN Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1578 SER Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 65 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 366 optimal weight: 50.0000 chunk 284 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 313 optimal weight: 20.0000 chunk 255 optimal weight: 0.0040 chunk 170 optimal weight: 5.9990 chunk 397 optimal weight: 5.9990 chunk 263 optimal weight: 0.9980 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN K 70 HIS ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147076 restraints weight = 58390.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145483 restraints weight = 74368.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147740 restraints weight = 62319.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147914 restraints weight = 39423.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148522 restraints weight = 38168.409| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33884 Z= 0.139 Angle : 0.669 36.108 45773 Z= 0.319 Chirality : 0.044 0.188 5115 Planarity : 0.004 0.051 5915 Dihedral : 5.071 52.116 4537 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 3.15 % Allowed : 16.69 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.20 (0.13), residues: 4122 helix: 0.62 (0.14), residues: 1377 sheet: -0.52 (0.19), residues: 684 loop : -0.40 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 468 TYR 0.027 0.002 TYR A 478 PHE 0.027 0.002 PHE B 895 TRP 0.015 0.002 TRP B 832 HIS 0.009 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00315 (33871) covalent geometry : angle 0.60975 (45761) hydrogen bonds : bond 0.04035 ( 1289) hydrogen bonds : angle 5.32142 ( 3597) metal coordination : bond 0.00676 ( 13) metal coordination : angle 17.07009 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 534 time to evaluate : 1.309 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: A 183 SER cc_start: 0.7174 (t) cc_final: 0.6894 (m) REVERT: A 345 LEU cc_start: 0.7036 (mt) cc_final: 0.6410 (tp) REVERT: A 447 THR cc_start: 0.5487 (OUTLIER) cc_final: 0.5209 (p) REVERT: A 656 GLN cc_start: 0.7540 (mt0) cc_final: 0.7048 (tp40) REVERT: A 867 ASP cc_start: 0.7899 (t0) cc_final: 0.7633 (t0) REVERT: A 1191 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.6728 (mt0) REVERT: A 1518 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8803 (p) REVERT: A 1522 GLU cc_start: 0.7302 (tp30) cc_final: 0.6704 (tt0) REVERT: A 1603 MET cc_start: 0.7919 (tpp) cc_final: 0.7120 (tpt) REVERT: A 1611 MET cc_start: 0.7529 (ttp) cc_final: 0.7184 (ttp) REVERT: B 74 PHE cc_start: 0.7231 (m-80) cc_final: 0.6880 (m-80) REVERT: B 184 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8338 (ptpp) REVERT: B 447 SER cc_start: 0.8377 (m) cc_final: 0.8062 (p) REVERT: B 589 ASP cc_start: 0.6939 (m-30) cc_final: 0.6050 (t0) REVERT: B 718 GLN cc_start: 0.7745 (tp40) cc_final: 0.7228 (tp40) REVERT: B 755 ASN cc_start: 0.7923 (m110) cc_final: 0.7255 (m110) REVERT: B 759 ASP cc_start: 0.7742 (m-30) cc_final: 0.7335 (m-30) REVERT: B 916 LYS cc_start: 0.8865 (mttt) cc_final: 0.8638 (mtmt) REVERT: B 919 SER cc_start: 0.9152 (p) cc_final: 0.8530 (t) REVERT: B 921 HIS cc_start: 0.8356 (m-70) cc_final: 0.7613 (m-70) REVERT: B 965 GLU cc_start: 0.8266 (tt0) cc_final: 0.7348 (pt0) REVERT: B 1047 ARG cc_start: 0.6791 (ttp80) cc_final: 0.5476 (ttm-80) REVERT: C 156 LEU cc_start: 0.9169 (mt) cc_final: 0.8826 (tp) REVERT: C 280 LEU cc_start: 0.7501 (mm) cc_final: 0.6560 (tp) REVERT: E 11 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.5789 (ptm160) REVERT: E 37 LEU cc_start: 0.8338 (tp) cc_final: 0.8053 (tp) REVERT: E 146 HIS cc_start: 0.8002 (m-70) cc_final: 0.7766 (m170) REVERT: E 192 ARG cc_start: 0.6799 (mtt90) cc_final: 0.6533 (mtm-85) REVERT: E 203 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6536 (tm-30) REVERT: F 135 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7624 (mtp180) REVERT: H 12 VAL cc_start: 0.7836 (t) cc_final: 0.7409 (m) REVERT: H 53 ASP cc_start: 0.7034 (t0) cc_final: 0.6735 (t0) REVERT: H 93 TYR cc_start: 0.7449 (m-80) cc_final: 0.7225 (m-10) REVERT: H 97 MET cc_start: 0.8050 (ptp) cc_final: 0.7826 (ptp) REVERT: J 49 MET cc_start: 0.7085 (mmm) cc_final: 0.6766 (mmm) REVERT: K 55 SER cc_start: 0.7876 (p) cc_final: 0.7603 (t) REVERT: M 18 GLN cc_start: 0.2136 (OUTLIER) cc_final: 0.1110 (tm-30) REVERT: M 61 GLU cc_start: 0.5997 (mp0) cc_final: 0.4782 (mt-10) REVERT: G 218 VAL cc_start: 0.2100 (OUTLIER) cc_final: 0.1896 (t) outliers start: 117 outliers final: 83 residues processed: 610 average time/residue: 0.1935 time to fit residues: 197.4124 Evaluate side-chains 580 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 491 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1191 GLN Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 65 TYR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 243 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 159 optimal weight: 20.0000 chunk 255 optimal weight: 0.0070 chunk 259 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 274 optimal weight: 0.9990 chunk 324 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 298 optimal weight: 0.8980 overall best weight: 2.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A1026 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN B1045 GLN B1171 ASN B1199 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN K 70 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.178094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147312 restraints weight = 57999.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146061 restraints weight = 74603.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.147830 restraints weight = 64664.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147984 restraints weight = 41268.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148654 restraints weight = 39658.858| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33884 Z= 0.140 Angle : 0.656 29.009 45773 Z= 0.316 Chirality : 0.044 0.254 5115 Planarity : 0.004 0.052 5915 Dihedral : 4.934 49.425 4537 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.35 % Favored : 96.53 % Rotamer: Outliers : 3.66 % Allowed : 16.86 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.15 (0.13), residues: 4122 helix: 0.69 (0.14), residues: 1373 sheet: -0.60 (0.19), residues: 694 loop : -0.35 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 25 TYR 0.024 0.002 TYR B1032 PHE 0.028 0.001 PHE B 895 TRP 0.015 0.001 TRP B 832 HIS 0.007 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00320 (33871) covalent geometry : angle 0.61051 (45761) hydrogen bonds : bond 0.03866 ( 1289) hydrogen bonds : angle 5.21054 ( 3597) metal coordination : bond 0.00660 ( 13) metal coordination : angle 14.80621 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 525 time to evaluate : 1.362 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: A 183 SER cc_start: 0.7234 (t) cc_final: 0.6956 (m) REVERT: A 345 LEU cc_start: 0.7036 (mt) cc_final: 0.6470 (tp) REVERT: A 447 THR cc_start: 0.5555 (OUTLIER) cc_final: 0.5279 (p) REVERT: A 618 TYR cc_start: 0.8602 (m-80) cc_final: 0.8228 (m-80) REVERT: A 639 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7515 (mm-40) REVERT: A 656 GLN cc_start: 0.7664 (mt0) cc_final: 0.7082 (tp40) REVERT: A 867 ASP cc_start: 0.7889 (t0) cc_final: 0.7561 (t0) REVERT: A 1191 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.6873 (mt0) REVERT: A 1518 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8852 (p) REVERT: A 1522 GLU cc_start: 0.7480 (tp30) cc_final: 0.6853 (tt0) REVERT: A 1603 MET cc_start: 0.7964 (tpp) cc_final: 0.7256 (tpt) REVERT: A 1631 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7487 (ttm110) REVERT: B 150 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: B 184 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8397 (ptpp) REVERT: B 436 MET cc_start: 0.6426 (mmt) cc_final: 0.6116 (mmt) REVERT: B 447 SER cc_start: 0.8392 (m) cc_final: 0.8072 (p) REVERT: B 718 GLN cc_start: 0.7743 (tp40) cc_final: 0.7327 (tp40) REVERT: B 755 ASN cc_start: 0.7944 (m110) cc_final: 0.7234 (m110) REVERT: B 759 ASP cc_start: 0.7652 (m-30) cc_final: 0.7222 (m-30) REVERT: B 916 LYS cc_start: 0.8875 (mttt) cc_final: 0.8646 (mtmt) REVERT: B 919 SER cc_start: 0.9161 (p) cc_final: 0.8490 (t) REVERT: B 921 HIS cc_start: 0.8426 (m-70) cc_final: 0.7816 (m-70) REVERT: B 958 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8123 (mpp) REVERT: B 965 GLU cc_start: 0.8204 (tt0) cc_final: 0.7363 (pt0) REVERT: B 1047 ARG cc_start: 0.6772 (ttp80) cc_final: 0.5542 (ttm-80) REVERT: C 156 LEU cc_start: 0.9180 (mt) cc_final: 0.8796 (tp) REVERT: C 245 ARG cc_start: 0.6797 (mtp180) cc_final: 0.6505 (tpt-90) REVERT: C 280 LEU cc_start: 0.7522 (mm) cc_final: 0.6698 (tp) REVERT: E 11 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.5847 (ptm160) REVERT: E 37 LEU cc_start: 0.8269 (tp) cc_final: 0.8008 (tp) REVERT: E 192 ARG cc_start: 0.6869 (mtt90) cc_final: 0.6584 (mtm-85) REVERT: E 203 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6588 (tm-30) REVERT: F 135 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7511 (mtm110) REVERT: H 12 VAL cc_start: 0.7706 (t) cc_final: 0.7424 (m) REVERT: H 97 MET cc_start: 0.8201 (ptp) cc_final: 0.7818 (ptp) REVERT: J 49 MET cc_start: 0.7188 (mmm) cc_final: 0.6811 (mmm) REVERT: K 55 SER cc_start: 0.7805 (p) cc_final: 0.7578 (t) REVERT: M 18 GLN cc_start: 0.2488 (OUTLIER) cc_final: 0.1431 (tm-30) REVERT: G 140 GLN cc_start: 0.5229 (pm20) cc_final: 0.4999 (pt0) REVERT: G 218 VAL cc_start: 0.2105 (OUTLIER) cc_final: 0.1880 (t) outliers start: 136 outliers final: 102 residues processed: 614 average time/residue: 0.1997 time to fit residues: 204.9244 Evaluate side-chains 585 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 475 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1191 GLN Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 65 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 30 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 201 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 155 optimal weight: 0.0000 chunk 395 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 340 optimal weight: 7.9990 chunk 309 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN K 70 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.179580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148945 restraints weight = 58683.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147772 restraints weight = 74430.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.149629 restraints weight = 63480.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149927 restraints weight = 40405.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150540 restraints weight = 38733.331| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33884 Z= 0.119 Angle : 0.620 21.388 45773 Z= 0.306 Chirality : 0.043 0.216 5115 Planarity : 0.004 0.053 5915 Dihedral : 4.741 48.861 4537 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 3.26 % Allowed : 17.96 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.00 (0.13), residues: 4122 helix: 0.85 (0.14), residues: 1371 sheet: -0.49 (0.19), residues: 711 loop : -0.29 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 156 TYR 0.023 0.001 TYR B1032 PHE 0.026 0.001 PHE B 895 TRP 0.016 0.001 TRP B 832 HIS 0.006 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00265 (33871) covalent geometry : angle 0.59498 (45761) hydrogen bonds : bond 0.03581 ( 1289) hydrogen bonds : angle 5.06712 ( 3597) metal coordination : bond 0.00527 ( 13) metal coordination : angle 10.76284 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 524 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 SER cc_start: 0.7211 (t) cc_final: 0.6937 (m) REVERT: A 345 LEU cc_start: 0.6991 (mt) cc_final: 0.6479 (tp) REVERT: A 447 THR cc_start: 0.5595 (OUTLIER) cc_final: 0.5336 (p) REVERT: A 601 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7257 (mtt) REVERT: A 618 TYR cc_start: 0.8536 (m-80) cc_final: 0.8262 (m-80) REVERT: A 639 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7416 (mm-40) REVERT: A 656 GLN cc_start: 0.7599 (mt0) cc_final: 0.7012 (tp40) REVERT: A 928 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8221 (mtm) REVERT: A 1518 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8798 (p) REVERT: A 1522 GLU cc_start: 0.7380 (tp30) cc_final: 0.6846 (tt0) REVERT: A 1603 MET cc_start: 0.7937 (tpp) cc_final: 0.7112 (tpt) REVERT: A 1631 ARG cc_start: 0.7784 (ttm110) cc_final: 0.7570 (ttm110) REVERT: B 150 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: B 184 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8361 (ptpp) REVERT: B 436 MET cc_start: 0.6367 (mmt) cc_final: 0.6111 (mmt) REVERT: B 447 SER cc_start: 0.8392 (m) cc_final: 0.8045 (p) REVERT: B 755 ASN cc_start: 0.8005 (m110) cc_final: 0.7292 (m110) REVERT: B 759 ASP cc_start: 0.7570 (m-30) cc_final: 0.7172 (m-30) REVERT: B 916 LYS cc_start: 0.8853 (mttt) cc_final: 0.8640 (mtmt) REVERT: B 921 HIS cc_start: 0.8392 (m-70) cc_final: 0.7739 (m-70) REVERT: B 965 GLU cc_start: 0.8017 (tt0) cc_final: 0.7338 (pt0) REVERT: B 1047 ARG cc_start: 0.6584 (ttp80) cc_final: 0.5469 (ttm-80) REVERT: C 156 LEU cc_start: 0.9036 (mt) cc_final: 0.8519 (tp) REVERT: C 245 ARG cc_start: 0.6766 (mtp180) cc_final: 0.6467 (tpt-90) REVERT: C 280 LEU cc_start: 0.7507 (mm) cc_final: 0.6747 (tp) REVERT: E 37 LEU cc_start: 0.8169 (tp) cc_final: 0.7897 (tp) REVERT: E 192 ARG cc_start: 0.6897 (mtt90) cc_final: 0.6587 (mtm-85) REVERT: E 203 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6467 (tm-30) REVERT: F 135 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7491 (mtm110) REVERT: H 12 VAL cc_start: 0.7660 (t) cc_final: 0.7234 (m) REVERT: H 97 MET cc_start: 0.8276 (ptp) cc_final: 0.7846 (ptp) REVERT: J 49 MET cc_start: 0.7141 (mmm) cc_final: 0.6747 (mmm) REVERT: M 18 GLN cc_start: 0.2567 (OUTLIER) cc_final: 0.1555 (tm-30) REVERT: M 61 GLU cc_start: 0.5719 (mp0) cc_final: 0.4643 (pt0) REVERT: M 104 SER cc_start: 0.5738 (m) cc_final: 0.5289 (t) REVERT: G 140 GLN cc_start: 0.5078 (pm20) cc_final: 0.4859 (pt0) REVERT: G 218 VAL cc_start: 0.2303 (OUTLIER) cc_final: 0.2082 (t) outliers start: 121 outliers final: 86 residues processed: 600 average time/residue: 0.1878 time to fit residues: 190.8028 Evaluate side-chains 568 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 475 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 1013 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 65 TYR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 285 optimal weight: 20.0000 chunk 79 optimal weight: 0.0980 chunk 376 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 86 optimal weight: 0.0770 chunk 144 optimal weight: 9.9990 overall best weight: 5.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1026 GLN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 952 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN G 126 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.174365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.143688 restraints weight = 58472.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142351 restraints weight = 77960.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144111 restraints weight = 68039.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144284 restraints weight = 43285.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144988 restraints weight = 40068.589| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 33884 Z= 0.217 Angle : 0.722 26.665 45773 Z= 0.359 Chirality : 0.046 0.201 5115 Planarity : 0.005 0.058 5915 Dihedral : 5.095 48.191 4537 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 4.01 % Allowed : 17.99 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.37 (0.13), residues: 4122 helix: 0.53 (0.14), residues: 1382 sheet: -0.71 (0.19), residues: 709 loop : -0.51 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 55 TYR 0.028 0.002 TYR B1032 PHE 0.030 0.002 PHE B 895 TRP 0.015 0.002 TRP B 832 HIS 0.009 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00505 (33871) covalent geometry : angle 0.69266 (45761) hydrogen bonds : bond 0.04466 ( 1289) hydrogen bonds : angle 5.32558 ( 3597) metal coordination : bond 0.00895 ( 13) metal coordination : angle 12.63608 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 495 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 SER cc_start: 0.7310 (t) cc_final: 0.7026 (m) REVERT: A 345 LEU cc_start: 0.7099 (mt) cc_final: 0.6475 (tp) REVERT: A 447 THR cc_start: 0.5582 (OUTLIER) cc_final: 0.5290 (p) REVERT: A 618 TYR cc_start: 0.8580 (m-80) cc_final: 0.8207 (m-80) REVERT: A 656 GLN cc_start: 0.7765 (mt0) cc_final: 0.7050 (tp40) REVERT: A 1021 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7418 (ttm170) REVERT: A 1175 MET cc_start: 0.7901 (tmm) cc_final: 0.7606 (tmm) REVERT: A 1191 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7023 (mt0) REVERT: A 1518 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8933 (p) REVERT: A 1522 GLU cc_start: 0.7581 (tp30) cc_final: 0.6997 (tt0) REVERT: A 1603 MET cc_start: 0.7955 (tpp) cc_final: 0.7156 (tpt) REVERT: B 150 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: B 184 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8222 (mtmt) REVERT: B 436 MET cc_start: 0.6362 (mmt) cc_final: 0.6144 (mmt) REVERT: B 447 SER cc_start: 0.8617 (m) cc_final: 0.8303 (p) REVERT: B 628 TYR cc_start: 0.7704 (t80) cc_final: 0.7464 (t80) REVERT: B 755 ASN cc_start: 0.8089 (m110) cc_final: 0.7583 (m-40) REVERT: B 759 ASP cc_start: 0.7672 (m-30) cc_final: 0.7300 (m-30) REVERT: B 921 HIS cc_start: 0.8645 (m-70) cc_final: 0.8373 (m-70) REVERT: B 965 GLU cc_start: 0.8252 (tt0) cc_final: 0.7277 (pt0) REVERT: B 1047 ARG cc_start: 0.6719 (ttp80) cc_final: 0.5437 (ttm-80) REVERT: C 156 LEU cc_start: 0.8996 (mt) cc_final: 0.8604 (tp) REVERT: C 245 ARG cc_start: 0.6777 (mtp180) cc_final: 0.6552 (tpt-90) REVERT: E 11 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.5741 (ptm160) REVERT: E 37 LEU cc_start: 0.8292 (tp) cc_final: 0.7959 (tp) REVERT: E 192 ARG cc_start: 0.6951 (mtt90) cc_final: 0.6672 (mtm-85) REVERT: E 203 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6457 (tm-30) REVERT: F 135 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7543 (mtm110) REVERT: H 53 ASP cc_start: 0.6781 (t0) cc_final: 0.6525 (t0) REVERT: H 97 MET cc_start: 0.8156 (ptp) cc_final: 0.7821 (ptp) REVERT: J 49 MET cc_start: 0.7300 (mmm) cc_final: 0.6907 (mmm) REVERT: M 18 GLN cc_start: 0.2762 (OUTLIER) cc_final: 0.2174 (tt0) REVERT: M 104 SER cc_start: 0.5007 (m) cc_final: 0.4787 (t) REVERT: G 140 GLN cc_start: 0.5100 (pm20) cc_final: 0.4862 (pt0) outliers start: 149 outliers final: 121 residues processed: 598 average time/residue: 0.1953 time to fit residues: 197.0497 Evaluate side-chains 586 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 459 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1191 GLN Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 65 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 126 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 34 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 226 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 chunk 389 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 385 optimal weight: 8.9990 chunk 271 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 257 optimal weight: 9.9990 chunk 401 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN A1500 GLN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 251 HIS ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN K 70 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.173514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142590 restraints weight = 58462.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140975 restraints weight = 75051.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143040 restraints weight = 64897.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143052 restraints weight = 40339.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.143833 restraints weight = 38099.103| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 33884 Z= 0.212 Angle : 0.720 25.786 45773 Z= 0.359 Chirality : 0.046 0.272 5115 Planarity : 0.005 0.064 5915 Dihedral : 5.159 48.262 4537 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.37 % Favored : 95.51 % Rotamer: Outliers : 3.72 % Allowed : 18.82 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.45 (0.13), residues: 4122 helix: 0.50 (0.14), residues: 1369 sheet: -0.80 (0.19), residues: 693 loop : -0.58 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 156 TYR 0.032 0.002 TYR A 514 PHE 0.031 0.002 PHE B 895 TRP 0.018 0.002 TRP B 832 HIS 0.007 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00496 (33871) covalent geometry : angle 0.69091 (45761) hydrogen bonds : bond 0.04378 ( 1289) hydrogen bonds : angle 5.34712 ( 3597) metal coordination : bond 0.00892 ( 13) metal coordination : angle 12.57005 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 475 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 SER cc_start: 0.7305 (t) cc_final: 0.7024 (m) REVERT: A 447 THR cc_start: 0.5393 (OUTLIER) cc_final: 0.5018 (p) REVERT: A 618 TYR cc_start: 0.8432 (m-80) cc_final: 0.8187 (m-80) REVERT: A 656 GLN cc_start: 0.7790 (mt0) cc_final: 0.7103 (tp40) REVERT: A 962 SER cc_start: 0.9011 (p) cc_final: 0.8811 (t) REVERT: A 977 MET cc_start: 0.9108 (tpp) cc_final: 0.8819 (tpp) REVERT: A 1021 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7449 (ttm170) REVERT: A 1191 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6969 (mt0) REVERT: A 1518 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8980 (p) REVERT: A 1522 GLU cc_start: 0.7644 (tp30) cc_final: 0.7062 (tt0) REVERT: A 1603 MET cc_start: 0.7761 (tpp) cc_final: 0.6980 (tpt) REVERT: A 1631 ARG cc_start: 0.7615 (ttm110) cc_final: 0.7384 (ttm110) REVERT: B 150 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6919 (mm-30) REVERT: B 184 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8322 (mtmt) REVERT: B 436 MET cc_start: 0.6296 (mmt) cc_final: 0.6067 (mmp) REVERT: B 440 PHE cc_start: 0.7782 (m-10) cc_final: 0.7488 (m-80) REVERT: B 447 SER cc_start: 0.8652 (m) cc_final: 0.8303 (p) REVERT: B 628 TYR cc_start: 0.7756 (t80) cc_final: 0.7472 (t80) REVERT: B 755 ASN cc_start: 0.8158 (m110) cc_final: 0.7679 (m-40) REVERT: B 759 ASP cc_start: 0.7659 (m-30) cc_final: 0.7304 (m-30) REVERT: B 851 TYR cc_start: 0.7739 (t80) cc_final: 0.7412 (t80) REVERT: B 921 HIS cc_start: 0.8675 (m-70) cc_final: 0.8212 (m-70) REVERT: B 965 GLU cc_start: 0.8273 (tt0) cc_final: 0.7276 (pt0) REVERT: B 1180 PHE cc_start: 0.8143 (t80) cc_final: 0.7691 (t80) REVERT: B 1192 MET cc_start: 0.6863 (tpp) cc_final: 0.6258 (tpt) REVERT: C 156 LEU cc_start: 0.8975 (mt) cc_final: 0.8621 (tp) REVERT: C 280 LEU cc_start: 0.7860 (mm) cc_final: 0.7025 (tp) REVERT: E 37 LEU cc_start: 0.8341 (tp) cc_final: 0.8057 (tp) REVERT: E 81 GLU cc_start: 0.6100 (tp30) cc_final: 0.5827 (tp30) REVERT: E 192 ARG cc_start: 0.6935 (mtt90) cc_final: 0.6619 (mtm-85) REVERT: E 203 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6490 (tm-30) REVERT: E 208 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7408 (t80) REVERT: F 135 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7471 (mtm110) REVERT: H 53 ASP cc_start: 0.7076 (t0) cc_final: 0.6831 (t0) REVERT: H 97 MET cc_start: 0.8202 (ptp) cc_final: 0.7879 (ptp) REVERT: J 49 MET cc_start: 0.7338 (mmm) cc_final: 0.6937 (mmm) REVERT: M 18 GLN cc_start: 0.3440 (OUTLIER) cc_final: 0.2692 (tt0) REVERT: M 68 SER cc_start: 0.5273 (p) cc_final: 0.4798 (m) REVERT: M 104 SER cc_start: 0.5821 (m) cc_final: 0.5588 (t) REVERT: G 140 GLN cc_start: 0.5133 (pm20) cc_final: 0.4856 (pt0) outliers start: 138 outliers final: 114 residues processed: 571 average time/residue: 0.1898 time to fit residues: 183.3216 Evaluate side-chains 571 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 451 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1191 GLN Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 208 TYR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 65 TYR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 9 optimal weight: 0.6980 chunk 241 optimal weight: 10.0000 chunk 286 optimal weight: 0.9980 chunk 5 optimal weight: 30.0000 chunk 160 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 406 optimal weight: 0.3980 chunk 376 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 435 ASN A 649 ASN A1026 GLN A1293 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 735 HIS C 93 GLN K 70 HIS ** L 53 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 = 0.4140 r_free = 0.4140 target = 0.178157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147488 restraints weight = 58647.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146082 restraints weight = 76298.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147747 restraints weight = 60700.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.148881 restraints weight = 37847.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.149174 restraints weight = 34966.110| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33884 Z= 0.117 Angle : 0.646 18.511 45773 Z= 0.323 Chirality : 0.044 0.285 5115 Planarity : 0.004 0.055 5915 Dihedral : 4.804 44.128 4537 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.49 % Favored : 96.39 % Rotamer: Outliers : 2.21 % Allowed : 20.60 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.15 (0.13), residues: 4122 helix: 0.77 (0.14), residues: 1383 sheet: -0.66 (0.19), residues: 715 loop : -0.38 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 156 TYR 0.026 0.001 TYR A 514 PHE 0.025 0.001 PHE B 895 TRP 0.018 0.001 TRP B 832 HIS 0.006 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00260 (33871) covalent geometry : angle 0.62964 (45761) hydrogen bonds : bond 0.03640 ( 1289) hydrogen bonds : angle 5.12283 ( 3597) metal coordination : bond 0.00527 ( 13) metal coordination : angle 8.92395 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 496 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 SER cc_start: 0.7214 (t) cc_final: 0.6910 (m) REVERT: A 447 THR cc_start: 0.5349 (OUTLIER) cc_final: 0.4984 (p) REVERT: A 589 MET cc_start: 0.8180 (tpp) cc_final: 0.7770 (tpp) REVERT: A 656 GLN cc_start: 0.7608 (mt0) cc_final: 0.7007 (tp40) REVERT: A 977 MET cc_start: 0.9097 (tpp) cc_final: 0.8860 (tpp) REVERT: A 1021 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7369 (ttm170) REVERT: A 1191 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.6962 (mt0) REVERT: A 1518 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8832 (p) REVERT: A 1522 GLU cc_start: 0.7451 (tp30) cc_final: 0.6943 (tt0) REVERT: A 1603 MET cc_start: 0.7709 (tpp) cc_final: 0.6886 (tpt) REVERT: A 1647 ASN cc_start: 0.6775 (t0) cc_final: 0.6555 (m110) REVERT: B 90 TYR cc_start: 0.6956 (t80) cc_final: 0.5775 (m-10) REVERT: B 436 MET cc_start: 0.6195 (mmt) cc_final: 0.5969 (mmp) REVERT: B 447 SER cc_start: 0.8614 (m) cc_final: 0.8245 (p) REVERT: B 561 ILE cc_start: 0.9052 (mt) cc_final: 0.8260 (mm) REVERT: B 742 TYR cc_start: 0.8296 (m-80) cc_final: 0.8061 (m-80) REVERT: B 755 ASN cc_start: 0.8047 (m110) cc_final: 0.7607 (m-40) REVERT: B 759 ASP cc_start: 0.7517 (m-30) cc_final: 0.7142 (m-30) REVERT: B 921 HIS cc_start: 0.8478 (m-70) cc_final: 0.7779 (m-70) REVERT: B 965 GLU cc_start: 0.8268 (tt0) cc_final: 0.7372 (pt0) REVERT: B 1044 PHE cc_start: 0.7228 (p90) cc_final: 0.7015 (p90) REVERT: B 1180 PHE cc_start: 0.7960 (t80) cc_final: 0.7462 (t80) REVERT: B 1192 MET cc_start: 0.6645 (tpp) cc_final: 0.6017 (tpt) REVERT: C 71 MET cc_start: 0.6292 (mtt) cc_final: 0.5980 (mtt) REVERT: C 156 LEU cc_start: 0.8961 (mt) cc_final: 0.8573 (tp) REVERT: C 280 LEU cc_start: 0.7704 (mm) cc_final: 0.6989 (tp) REVERT: E 37 LEU cc_start: 0.8298 (tp) cc_final: 0.8020 (tp) REVERT: E 79 TRP cc_start: 0.6294 (t-100) cc_final: 0.6032 (t-100) REVERT: E 203 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6208 (tm-30) REVERT: F 135 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7444 (mtm110) REVERT: H 97 MET cc_start: 0.8083 (ptp) cc_final: 0.7743 (ptp) REVERT: J 49 MET cc_start: 0.7439 (mmm) cc_final: 0.7103 (mmm) REVERT: M 18 GLN cc_start: 0.3348 (OUTLIER) cc_final: 0.2649 (tt0) REVERT: M 68 SER cc_start: 0.5147 (p) cc_final: 0.4585 (m) REVERT: G 140 GLN cc_start: 0.5166 (pm20) cc_final: 0.4889 (pt0) outliers start: 82 outliers final: 73 residues processed: 554 average time/residue: 0.1904 time to fit residues: 178.3801 Evaluate side-chains 540 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 463 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1191 GLN Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 65 TYR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 395 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 371 optimal weight: 20.0000 chunk 326 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 380 optimal weight: 30.0000 chunk 250 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 385 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS I 32 GLN K 70 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.177449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147580 restraints weight = 58061.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145934 restraints weight = 75951.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147451 restraints weight = 64439.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148320 restraints weight = 39767.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148698 restraints weight = 36880.976| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.319 33884 Z= 0.233 Angle : 0.763 59.197 45773 Z= 0.408 Chirality : 0.046 0.560 5115 Planarity : 0.005 0.060 5915 Dihedral : 4.792 44.111 4537 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 2.48 % Allowed : 20.81 % Favored : 76.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.18 (0.13), residues: 4122 helix: 0.72 (0.14), residues: 1389 sheet: -0.64 (0.19), residues: 715 loop : -0.41 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 156 TYR 0.044 0.002 TYR A 618 PHE 0.058 0.002 PHE B 440 TRP 0.151 0.003 TRP E 79 HIS 0.005 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00518 (33871) covalent geometry : angle 0.74957 (45761) hydrogen bonds : bond 0.03708 ( 1289) hydrogen bonds : angle 5.11775 ( 3597) metal coordination : bond 0.00632 ( 13) metal coordination : angle 8.91239 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5565.91 seconds wall clock time: 97 minutes 26.29 seconds (5846.29 seconds total)