Starting phenix.real_space_refine on Fri Mar 6 10:39:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kif_22886/03_2026/7kif_22886.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kif_22886/03_2026/7kif_22886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kif_22886/03_2026/7kif_22886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kif_22886/03_2026/7kif_22886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kif_22886/03_2026/7kif_22886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kif_22886/03_2026/7kif_22886.map" } resolution = 2.94 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= 0.001 sd= 1.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 2 6.06 5 P 117 5.49 5 Mg 1 5.21 5 S 107 5.16 5 C 18631 2.51 5 N 5424 2.21 5 O 6036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30322 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8606 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 9914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9914 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1209} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2548 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 313} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 880 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "O" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1282 Classifications: {'DNA': 63} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 62} Chain breaks: 1 Chain: "P" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1129 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain breaks: 1 Chain: "Z" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 581 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 67} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19155 SG CYS D 891 113.650 130.907 105.612 1.00 79.09 S ATOM 19722 SG CYS D 968 110.172 130.253 103.093 1.00 71.53 S ATOM 19764 SG CYS D 975 110.950 128.981 106.323 1.00 65.84 S ATOM 19782 SG CYS D 978 110.976 132.217 106.682 1.00 66.70 S ATOM 12593 SG CYS D 60 80.951 85.376 68.013 1.00100.90 S ATOM 12611 SG CYS D 62 79.111 83.327 65.295 1.00107.61 S ATOM 12720 SG CYS D 75 82.452 83.005 65.614 1.00108.00 S ATOM 12746 SG CYS D 78 80.766 86.097 64.688 1.00105.27 S ATOM 29955 SG CYS Z 43 72.079 57.567 111.092 1.00125.62 S ATOM 29783 SG CYS Z 20 72.796 61.488 109.439 1.00134.03 S ATOM 29974 SG CYS Z 46 69.771 60.995 112.272 1.00131.37 S ATOM 30026 SG CYS Z 52 69.042 60.450 105.889 1.00128.50 S ATOM 29783 SG CYS Z 20 72.796 61.488 109.439 1.00134.03 S ATOM 29955 SG CYS Z 43 72.079 57.567 111.092 1.00125.62 S Time building chain proxies: 6.67, per 1000 atoms: 0.22 Number of scatterers: 30322 At special positions: 0 Unit cell: (136.4, 188.1, 191.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Fe 4 26.01 S 107 16.00 P 117 15.00 Mg 1 11.99 O 6036 8.00 N 5424 7.00 C 18631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 Z 101 " pdb="FE4 SF4 Z 101 " - pdb=" SG CYS Z 20 " pdb="FE3 SF4 Z 101 " - pdb=" SG CYS Z 52 " pdb="FE1 SF4 Z 101 " - pdb=" SG CYS Z 43 " pdb="FE2 SF4 Z 101 " - pdb=" SG CYS Z 46 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " Number of angles added : 12 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6618 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 48 sheets defined 41.3% alpha, 12.8% beta 54 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.467A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.699A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.053A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.623A pdb=" N ASP C 59 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.903A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 4.712A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.828A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.899A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.568A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 631 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 removed outlier: 3.537A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.855A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.411A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.800A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.800A pdb=" N GLN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.743A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 122 through 130 removed outlier: 3.747A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 183 removed outlier: 4.041A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 228 removed outlier: 3.987A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.379A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.847A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.004A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.762A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 492 removed outlier: 3.973A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.602A pdb=" N ASN D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.797A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 763 removed outlier: 3.976A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.896A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.269A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR D 867 " --> pdb=" O THR D 863 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 884 No H-bonds generated for 'chain 'D' and resid 882 through 884' Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1027 through 1036 removed outlier: 3.765A pdb=" N VAL D1031 " --> pdb=" O GLY D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1143 removed outlier: 3.572A pdb=" N LEU D1122 " --> pdb=" O PRO D1118 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.919A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D1135 " --> pdb=" O GLN D1131 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1146 No H-bonds generated for 'chain 'D' and resid 1144 through 1146' Processing helix chain 'D' and resid 1150 through 1153 Processing helix chain 'D' and resid 1154 through 1160 removed outlier: 3.634A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.523A pdb=" N ARG D1192 " --> pdb=" O ALA D1188 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1216 removed outlier: 3.533A pdb=" N LEU D1215 " --> pdb=" O THR D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.671A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.683A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE D1238 " --> pdb=" O THR D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1254 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.965A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1281 Processing helix chain 'E' and resid 33 through 37 removed outlier: 4.019A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 69 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 209 through 221 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.820A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 335 Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.782A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 removed outlier: 3.536A pdb=" N ASP F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 404 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 438 Processing helix chain 'F' and resid 448 through 466 Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 516 Processing helix chain 'F' and resid 516 through 525 removed outlier: 6.203A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 removed outlier: 3.755A pdb=" N LEU J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE J 105 " --> pdb=" O ARG J 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 65 through 75 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 148 through 160 Processing helix chain 'Z' and resid 24 through 30 removed outlier: 3.606A pdb=" N LEU Z 27 " --> pdb=" O ASP Z 24 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP Z 28 " --> pdb=" O PRO Z 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE Z 29 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 43 removed outlier: 3.812A pdb=" N CYS Z 43 " --> pdb=" O ALA Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 46 No H-bonds generated for 'chain 'Z' and resid 44 through 46' Processing helix chain 'Z' and resid 48 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 3.633A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.909A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.668A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 128 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.505A pdb=" N SER A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 26 removed outlier: 5.497A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 191 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 100 removed outlier: 3.532A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 134 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.623A pdb=" N THR B 117 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.708A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'B' and resid 171 through 174 removed outlier: 6.981A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.448A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 627 " --> pdb=" O VAL C 972 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.687A pdb=" N GLU C 146 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 147 " --> pdb=" O ARG M 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 110 through 112 removed outlier: 4.642A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 378 removed outlier: 3.675A pdb=" N SER C 456 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 185 removed outlier: 3.512A pdb=" N GLY C 184 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 184 through 185 removed outlier: 3.512A pdb=" N GLY C 184 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 202 " --> pdb=" O PHE C 214 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC3, first strand: chain 'C' and resid 524 through 531 removed outlier: 5.322A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 560 Processing sheet with id=AC5, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.676A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.788A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC8, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.004A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 749 through 760 removed outlier: 3.537A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 868 " --> pdb=" O PHE C 853 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD2, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.707A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD4, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD5, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.471A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.714A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD8, first strand: chain 'D' and resid 93 through 102 removed outlier: 6.677A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.215A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.905A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.174A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 635 through 637 Processing sheet with id=AE3, first strand: chain 'D' and resid 822 through 824 removed outlier: 9.075A pdb=" N VAL D 824 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG D 834 " --> pdb=" O VAL D 824 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.844A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1075 through 1080 removed outlier: 3.855A pdb=" N VAL D1075 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.853A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE8, first strand: chain 'F' and resid 440 through 441 removed outlier: 3.640A pdb=" N GLY J 8 " --> pdb=" O GLU F 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 39 through 45 Processing sheet with id=AF1, first strand: chain 'M' and resid 8 through 10 Processing sheet with id=AF2, first strand: chain 'M' and resid 22 through 23 Processing sheet with id=AF3, first strand: chain 'M' and resid 26 through 27 1201 hydrogen bonds defined for protein. 3417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 7.51 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 12904 1.43 - 1.64: 17987 1.64 - 1.86: 179 1.86 - 2.07: 0 2.07 - 2.29: 12 Bond restraints: 31082 Sorted by residual: bond pdb=" CB CYS D 78 " pdb=" SG CYS D 78 " ideal model delta sigma weight residual 1.808 1.686 0.122 3.30e-02 9.18e+02 1.36e+01 bond pdb=" C VAL C 922 " pdb=" N PRO C 923 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.20e-02 6.94e+03 1.16e+01 bond pdb=" C TYR D 106 " pdb=" N PHE D 107 " ideal model delta sigma weight residual 1.332 1.296 0.036 1.40e-02 5.10e+03 6.79e+00 bond pdb=" C3' DA P 116 " pdb=" O3' DA P 116 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 5.01e+00 bond pdb=" CB VAL D 880 " pdb=" CG2 VAL D 880 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.58e+00 ... (remaining 31077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 42061 2.96 - 5.93: 499 5.93 - 8.89: 34 8.89 - 11.85: 9 11.85 - 14.82: 3 Bond angle restraints: 42606 Sorted by residual: angle pdb=" C ASP M 147 " pdb=" N ALA M 148 " pdb=" CA ALA M 148 " ideal model delta sigma weight residual 121.54 133.47 -11.93 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C ARG D 578 " pdb=" N LEU D 579 " pdb=" CA LEU D 579 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CA PRO D 835 " ideal model delta sigma weight residual 127.00 140.81 -13.81 2.40e+00 1.74e-01 3.31e+01 angle pdb=" CA ARG C 584 " pdb=" CB ARG C 584 " pdb=" CG ARG C 584 " ideal model delta sigma weight residual 114.10 123.50 -9.40 2.00e+00 2.50e-01 2.21e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CD PRO D 835 " ideal model delta sigma weight residual 120.60 110.52 10.08 2.20e+00 2.07e-01 2.10e+01 ... (remaining 42601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 17712 35.53 - 71.06: 953 71.06 - 106.59: 18 106.59 - 142.11: 0 142.11 - 177.64: 4 Dihedral angle restraints: 18687 sinusoidal: 8402 harmonic: 10285 Sorted by residual: dihedral pdb=" CA LEU F 273 " pdb=" C LEU F 273 " pdb=" N PRO F 274 " pdb=" CA PRO F 274 " ideal model delta harmonic sigma weight residual 180.00 149.86 30.14 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA GLU C 962 " pdb=" C GLU C 962 " pdb=" N LEU C 963 " pdb=" CA LEU C 963 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA PRO B 28 " pdb=" C PRO B 28 " pdb=" N GLY B 29 " pdb=" CA GLY B 29 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 18684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4008 0.073 - 0.145: 784 0.145 - 0.218: 51 0.218 - 0.291: 1 0.291 - 0.363: 3 Chirality restraints: 4847 Sorted by residual: chirality pdb=" CB VAL C 224 " pdb=" CA VAL C 224 " pdb=" CG1 VAL C 224 " pdb=" CG2 VAL C 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA GLN D 657 " pdb=" N GLN D 657 " pdb=" C GLN D 657 " pdb=" CB GLN D 657 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB VAL J 5 " pdb=" CA VAL J 5 " pdb=" CG1 VAL J 5 " pdb=" CG2 VAL J 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4844 not shown) Planarity restraints: 5188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 579 " 0.030 2.00e-02 2.50e+03 5.85e-02 3.42e+01 pdb=" C LEU D 579 " -0.101 2.00e-02 2.50e+03 pdb=" O LEU D 579 " 0.037 2.00e-02 2.50e+03 pdb=" N ASP D 580 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 60 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C CYS D 60 " 0.060 2.00e-02 2.50e+03 pdb=" O CYS D 60 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR D 61 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 148 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C ALA M 148 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA M 148 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS M 149 " -0.020 2.00e-02 2.50e+03 ... (remaining 5185 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 5 2.17 - 2.85: 10395 2.85 - 3.54: 39841 3.54 - 4.22: 67690 4.22 - 4.90: 117642 Nonbonded interactions: 235573 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb=" OD2 ASP D 539 " model vdw 1.489 3.040 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 1.953 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.073 2.170 nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D2002 " model vdw 2.134 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.140 2.170 ... (remaining 235568 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 38.650 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 0.229 31094 Z= 0.367 Angle : 1.095 82.253 42630 Z= 0.491 Chirality : 0.055 0.363 4847 Planarity : 0.007 0.074 5188 Dihedral : 18.241 177.642 12069 Min Nonbonded Distance : 1.489 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 6.85 % Allowed : 11.66 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.12), residues: 3570 helix: -1.36 (0.12), residues: 1408 sheet: -1.57 (0.26), residues: 412 loop : -2.34 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 231 TYR 0.022 0.002 TYR A 168 PHE 0.028 0.002 PHE C 906 TRP 0.018 0.002 TRP C 955 HIS 0.008 0.001 HIS D 854 Details of bonding type rmsd covalent geometry : bond 0.00869 (31082) covalent geometry : angle 0.86581 (42606) hydrogen bonds : bond 0.15737 ( 1331) hydrogen bonds : angle 6.28575 ( 3695) metal coordination : bond 0.09790 ( 12) metal coordination : angle 28.24045 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 263 time to evaluate : 0.907 Fit side-chains REVERT: A 184 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6817 (tm-30) REVERT: C 159 MET cc_start: 0.8880 (mmm) cc_final: 0.8653 (mmm) REVERT: C 302 LYS cc_start: 0.8553 (mttt) cc_final: 0.8152 (mmtp) REVERT: C 397 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: C 429 GLU cc_start: 0.7532 (tp30) cc_final: 0.7259 (tp30) REVERT: C 439 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8203 (t80) REVERT: C 441 ASP cc_start: 0.7812 (t70) cc_final: 0.7537 (t0) REVERT: C 463 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8917 (pp) REVERT: C 470 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8520 (tt) REVERT: C 657 TYR cc_start: 0.8208 (p90) cc_final: 0.7944 (p90) REVERT: C 691 ASP cc_start: 0.7652 (m-30) cc_final: 0.7401 (m-30) REVERT: C 753 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7152 (mm-30) REVERT: C 758 ASP cc_start: 0.8499 (p0) cc_final: 0.7701 (p0) REVERT: C 789 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8537 (pp) REVERT: C 818 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7158 (tm-30) REVERT: C 861 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8559 (mm) REVERT: C 883 ASP cc_start: 0.7796 (m-30) cc_final: 0.7545 (m-30) REVERT: D 82 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8379 (m) REVERT: D 304 GLN cc_start: 0.8499 (pp30) cc_final: 0.8281 (pp30) REVERT: D 491 ILE cc_start: 0.8562 (tt) cc_final: 0.8348 (tt) REVERT: D 700 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8118 (mp) REVERT: E 70 GLN cc_start: 0.7339 (tt0) cc_final: 0.7059 (tt0) REVERT: F 287 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8551 (p0) REVERT: F 325 ASN cc_start: 0.8370 (m-40) cc_final: 0.8111 (m110) REVERT: F 341 TYR cc_start: 0.8887 (m-80) cc_final: 0.8394 (m-80) REVERT: F 366 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8707 (pp) REVERT: F 390 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7281 (tt) REVERT: F 438 PHE cc_start: 0.8818 (m-10) cc_final: 0.8606 (m-10) REVERT: F 458 ASP cc_start: 0.8545 (t0) cc_final: 0.8321 (t0) REVERT: F 505 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8534 (mm-40) REVERT: Z 48 ILE cc_start: 0.9133 (pt) cc_final: 0.8900 (pp) outliers start: 205 outliers final: 88 residues processed: 442 average time/residue: 0.5055 time to fit residues: 275.9742 Evaluate side-chains 326 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 226 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 505 GLN Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 32 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS B 152 ASN C 435 GLN D 329 GLN D 540 GLN D 657 GLN D1110 GLN F 277 GLN ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 GLN ** 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 = 0.3838 r_free = 0.3838 target = 0.120878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075152 restraints weight = 54732.623| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.09 r_work: 0.2948 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31094 Z= 0.122 Angle : 0.823 73.471 42630 Z= 0.318 Chirality : 0.042 0.205 4847 Planarity : 0.005 0.059 5188 Dihedral : 18.683 175.678 5371 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.98 % Allowed : 16.68 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 3570 helix: 0.11 (0.14), residues: 1409 sheet: -1.39 (0.26), residues: 426 loop : -2.04 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 211 TYR 0.019 0.001 TYR D1062 PHE 0.022 0.001 PHE M 71 TRP 0.018 0.001 TRP Z 63 HIS 0.003 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00262 (31082) covalent geometry : angle 0.57608 (42606) hydrogen bonds : bond 0.04472 ( 1331) hydrogen bonds : angle 4.71248 ( 3695) metal coordination : bond 0.01510 ( 12) metal coordination : angle 24.77992 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 262 time to evaluate : 1.050 Fit side-chains REVERT: A 184 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6495 (tm-30) REVERT: B 150 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7322 (p) REVERT: B 226 ASN cc_start: 0.8894 (t0) cc_final: 0.8235 (t0) REVERT: C 140 ILE cc_start: 0.8708 (mt) cc_final: 0.8485 (mp) REVERT: C 159 MET cc_start: 0.8589 (mmm) cc_final: 0.8317 (mmm) REVERT: C 302 LYS cc_start: 0.7929 (mttt) cc_final: 0.7551 (mmtp) REVERT: C 397 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: C 439 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8130 (t80) REVERT: C 441 ASP cc_start: 0.8341 (t70) cc_final: 0.7682 (t0) REVERT: C 463 LEU cc_start: 0.8781 (pp) cc_final: 0.8403 (pp) REVERT: C 470 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7274 (tt) REVERT: C 607 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7143 (mtm) REVERT: C 691 ASP cc_start: 0.7852 (m-30) cc_final: 0.7566 (m-30) REVERT: C 753 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7430 (tp30) REVERT: C 789 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7827 (pp) REVERT: C 818 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6982 (tm-30) REVERT: C 830 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7690 (mmm160) REVERT: C 883 ASP cc_start: 0.8021 (m-30) cc_final: 0.7465 (m-30) REVERT: C 1127 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: D 312 MET cc_start: 0.8814 (mtt) cc_final: 0.8483 (mtt) REVERT: D 359 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8024 (p0) REVERT: D 396 ASN cc_start: 0.8883 (m-40) cc_final: 0.8064 (t0) REVERT: D 880 VAL cc_start: 0.7188 (t) cc_final: 0.6982 (p) REVERT: D 981 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.6671 (ptp90) REVERT: E 70 GLN cc_start: 0.6729 (tt0) cc_final: 0.6424 (tt0) REVERT: F 287 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8660 (p0) REVERT: F 325 ASN cc_start: 0.7866 (m-40) cc_final: 0.7546 (m110) REVERT: F 341 TYR cc_start: 0.8718 (m-80) cc_final: 0.8317 (m-80) REVERT: F 366 ILE cc_start: 0.8520 (pt) cc_final: 0.8189 (pp) REVERT: F 390 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6818 (tt) REVERT: F 438 PHE cc_start: 0.8482 (m-10) cc_final: 0.8171 (m-10) REVERT: F 458 ASP cc_start: 0.8979 (t0) cc_final: 0.8723 (t0) REVERT: F 505 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8666 (mm-40) REVERT: J 32 TYR cc_start: 0.8033 (m-80) cc_final: 0.7815 (m-10) REVERT: M 41 GLN cc_start: 0.8952 (pp30) cc_final: 0.8740 (pp30) REVERT: Z 57 LEU cc_start: 0.9334 (mm) cc_final: 0.8989 (pp) outliers start: 119 outliers final: 49 residues processed: 361 average time/residue: 0.5736 time to fit residues: 251.9721 Evaluate side-chains 289 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1127 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 505 GLN Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain Z residue 32 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 35 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 152 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN D 505 HIS D 540 GLN ** J 28 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 = 0.3798 r_free = 0.3798 target = 0.117699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.072029 restraints weight = 55134.605| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.02 r_work: 0.2872 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 31094 Z= 0.282 Angle : 0.900 79.501 42630 Z= 0.356 Chirality : 0.046 0.224 4847 Planarity : 0.005 0.065 5188 Dihedral : 18.596 176.213 5284 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.98 % Allowed : 17.15 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3570 helix: 0.52 (0.14), residues: 1402 sheet: -1.31 (0.26), residues: 430 loop : -1.97 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 211 TYR 0.024 0.002 TYR F 258 PHE 0.018 0.002 PHE C 906 TRP 0.016 0.002 TRP Z 63 HIS 0.006 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00676 (31082) covalent geometry : angle 0.65890 (42606) hydrogen bonds : bond 0.05419 ( 1331) hydrogen bonds : angle 4.62982 ( 3695) metal coordination : bond 0.02092 ( 12) metal coordination : angle 25.87570 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 235 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6421 (tm-30) REVERT: B 226 ASN cc_start: 0.8917 (t0) cc_final: 0.8202 (t0) REVERT: B 233 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: C 140 ILE cc_start: 0.8684 (mt) cc_final: 0.8464 (mp) REVERT: C 159 MET cc_start: 0.8807 (mmm) cc_final: 0.8513 (mmm) REVERT: C 230 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6993 (mmm160) REVERT: C 302 LYS cc_start: 0.7946 (mttt) cc_final: 0.7591 (mmtp) REVERT: C 308 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6870 (pp) REVERT: C 397 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: C 439 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8282 (t80) REVERT: C 441 ASP cc_start: 0.8473 (t70) cc_final: 0.7752 (t0) REVERT: C 463 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8344 (pp) REVERT: C 560 LEU cc_start: 0.8236 (tp) cc_final: 0.8005 (tm) REVERT: C 607 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7250 (mtm) REVERT: C 661 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7118 (tpt) REVERT: C 691 ASP cc_start: 0.7852 (m-30) cc_final: 0.7528 (m-30) REVERT: C 756 GLU cc_start: 0.8390 (tt0) cc_final: 0.8016 (tt0) REVERT: C 818 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6927 (tm-30) REVERT: C 858 GLU cc_start: 0.8471 (mp0) cc_final: 0.8196 (OUTLIER) REVERT: C 883 ASP cc_start: 0.8103 (m-30) cc_final: 0.7658 (m-30) REVERT: C 897 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7979 (ttmm) REVERT: C 1127 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: D 145 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8581 (t70) REVERT: D 242 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8140 (tpp-160) REVERT: D 359 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8030 (p0) REVERT: D 396 ASN cc_start: 0.8885 (m-40) cc_final: 0.8086 (t0) REVERT: D 427 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7084 (mtt90) REVERT: D 600 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: D 700 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7106 (mp) REVERT: D 834 ARG cc_start: 0.7477 (mmm160) cc_final: 0.6981 (mmm160) REVERT: E 70 GLN cc_start: 0.6643 (tt0) cc_final: 0.6338 (tt0) REVERT: F 287 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8547 (p0) REVERT: F 325 ASN cc_start: 0.7843 (m-40) cc_final: 0.7511 (m110) REVERT: F 341 TYR cc_start: 0.8766 (m-80) cc_final: 0.8440 (m-80) REVERT: F 366 ILE cc_start: 0.8600 (pt) cc_final: 0.8247 (pp) REVERT: F 382 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7856 (mt) REVERT: F 386 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8381 (tt) REVERT: F 438 PHE cc_start: 0.8518 (m-10) cc_final: 0.8308 (m-10) REVERT: F 458 ASP cc_start: 0.8971 (t0) cc_final: 0.8760 (t0) REVERT: F 505 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8615 (mm-40) REVERT: J 16 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.6952 (p90) REVERT: J 28 GLN cc_start: 0.6810 (pp30) cc_final: 0.6199 (pp30) REVERT: M 25 ARG cc_start: 0.9262 (ttt180) cc_final: 0.8767 (ttm110) REVERT: M 41 GLN cc_start: 0.8915 (pp30) cc_final: 0.8714 (pp30) REVERT: Z 57 LEU cc_start: 0.9345 (mm) cc_final: 0.8963 (pp) outliers start: 149 outliers final: 85 residues processed: 350 average time/residue: 0.6077 time to fit residues: 257.1775 Evaluate side-chains 332 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 228 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 897 LYS Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1127 GLU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 600 GLN Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 505 GLN Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 22 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 360 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 208 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN D 505 HIS D 540 GLN ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.118923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072973 restraints weight = 54390.299| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.05 r_work: 0.2924 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31094 Z= 0.138 Angle : 0.805 75.998 42630 Z= 0.306 Chirality : 0.042 0.160 4847 Planarity : 0.004 0.056 5188 Dihedral : 18.431 176.778 5277 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.38 % Allowed : 18.18 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3570 helix: 0.89 (0.14), residues: 1399 sheet: -1.29 (0.26), residues: 444 loop : -1.84 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 830 TYR 0.024 0.001 TYR F 258 PHE 0.009 0.001 PHE C 906 TRP 0.014 0.001 TRP M 112 HIS 0.016 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00315 (31082) covalent geometry : angle 0.56240 (42606) hydrogen bonds : bond 0.04279 ( 1331) hydrogen bonds : angle 4.35712 ( 3695) metal coordination : bond 0.01323 ( 12) metal coordination : angle 24.26753 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 253 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6389 (tm-30) REVERT: A 217 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: B 1 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7181 (mmm) REVERT: B 123 MET cc_start: 0.8621 (ttp) cc_final: 0.8376 (ttt) REVERT: B 188 ASP cc_start: 0.6689 (t70) cc_final: 0.6451 (p0) REVERT: B 226 ASN cc_start: 0.8884 (t0) cc_final: 0.8199 (t0) REVERT: B 233 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: C 140 ILE cc_start: 0.8689 (mt) cc_final: 0.8450 (mp) REVERT: C 159 MET cc_start: 0.8706 (mmm) cc_final: 0.8460 (mmm) REVERT: C 220 ASP cc_start: 0.8506 (m-30) cc_final: 0.8090 (t0) REVERT: C 230 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7139 (mmm160) REVERT: C 302 LYS cc_start: 0.7803 (mttt) cc_final: 0.7418 (mmtp) REVERT: C 308 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6775 (pp) REVERT: C 439 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8150 (t80) REVERT: C 441 ASP cc_start: 0.8403 (t70) cc_final: 0.7714 (t0) REVERT: C 463 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8488 (pp) REVERT: C 549 ASP cc_start: 0.7997 (t0) cc_final: 0.7775 (p0) REVERT: C 607 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7286 (mtt) REVERT: C 691 ASP cc_start: 0.7857 (m-30) cc_final: 0.7579 (m-30) REVERT: C 789 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7906 (pp) REVERT: C 818 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6910 (tm-30) REVERT: C 858 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8175 (OUTLIER) REVERT: C 883 ASP cc_start: 0.8052 (m-30) cc_final: 0.7457 (m-30) REVERT: C 915 ILE cc_start: 0.8955 (pt) cc_final: 0.8671 (tt) REVERT: D 242 ARG cc_start: 0.8452 (tpp-160) cc_final: 0.8052 (mmt180) REVERT: D 359 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7999 (p0) REVERT: D 396 ASN cc_start: 0.8875 (m-40) cc_final: 0.8081 (t0) REVERT: D 600 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7991 (pt0) REVERT: D 880 VAL cc_start: 0.7249 (OUTLIER) cc_final: 0.6972 (p) REVERT: E 70 GLN cc_start: 0.6607 (tt0) cc_final: 0.6292 (tt0) REVERT: F 273 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7794 (tm) REVERT: F 287 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8530 (p0) REVERT: F 325 ASN cc_start: 0.7803 (m-40) cc_final: 0.7480 (m110) REVERT: F 366 ILE cc_start: 0.8571 (pt) cc_final: 0.8210 (pp) REVERT: F 386 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8415 (tt) REVERT: F 438 PHE cc_start: 0.8544 (m-10) cc_final: 0.8279 (m-10) REVERT: J 28 GLN cc_start: 0.6772 (pp30) cc_final: 0.6074 (pp30) REVERT: M 25 ARG cc_start: 0.9259 (ttt180) cc_final: 0.8746 (ttm110) REVERT: M 41 GLN cc_start: 0.8928 (pp30) cc_final: 0.8682 (pp30) REVERT: Z 57 LEU cc_start: 0.9334 (mm) cc_final: 0.8983 (pp) REVERT: Z 72 ASP cc_start: 0.7801 (t0) cc_final: 0.7381 (t0) outliers start: 131 outliers final: 62 residues processed: 357 average time/residue: 0.5589 time to fit residues: 243.0267 Evaluate side-chains 318 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 241 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 858 GLU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 600 GLN Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain Z residue 32 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 245 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 160 optimal weight: 0.0070 chunk 135 optimal weight: 3.9990 chunk 340 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 349 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 152 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS D 540 GLN ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.118897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072845 restraints weight = 54320.933| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.07 r_work: 0.2921 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31094 Z= 0.152 Angle : 0.804 76.839 42630 Z= 0.306 Chirality : 0.042 0.209 4847 Planarity : 0.004 0.061 5188 Dihedral : 18.320 177.574 5262 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.88 % Allowed : 18.55 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3570 helix: 1.05 (0.14), residues: 1401 sheet: -1.19 (0.26), residues: 440 loop : -1.74 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 182 TYR 0.024 0.001 TYR F 258 PHE 0.010 0.001 PHE C 906 TRP 0.019 0.001 TRP M 112 HIS 0.004 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00354 (31082) covalent geometry : angle 0.56782 (42606) hydrogen bonds : bond 0.04259 ( 1331) hydrogen bonds : angle 4.26733 ( 3695) metal coordination : bond 0.01371 ( 12) metal coordination : angle 23.99847 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 251 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6472 (tm-30) REVERT: A 217 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: B 1 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7151 (mmm) REVERT: B 188 ASP cc_start: 0.6641 (t70) cc_final: 0.6377 (p0) REVERT: B 226 ASN cc_start: 0.8883 (t0) cc_final: 0.8181 (t0) REVERT: B 233 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8176 (pm20) REVERT: C 140 ILE cc_start: 0.8676 (mt) cc_final: 0.8448 (mp) REVERT: C 159 MET cc_start: 0.8729 (mmm) cc_final: 0.8417 (mmm) REVERT: C 220 ASP cc_start: 0.8515 (m-30) cc_final: 0.8109 (t0) REVERT: C 230 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7220 (mmm160) REVERT: C 302 LYS cc_start: 0.7743 (mttt) cc_final: 0.7362 (mmtp) REVERT: C 308 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6673 (pp) REVERT: C 439 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8178 (t80) REVERT: C 441 ASP cc_start: 0.8378 (t70) cc_final: 0.7751 (t0) REVERT: C 463 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8387 (pp) REVERT: C 549 ASP cc_start: 0.8042 (t0) cc_final: 0.7799 (p0) REVERT: C 607 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7284 (mtt) REVERT: C 691 ASP cc_start: 0.7851 (m-30) cc_final: 0.7459 (m-30) REVERT: C 702 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7891 (mm) REVERT: C 704 ASP cc_start: 0.8093 (m-30) cc_final: 0.7878 (m-30) REVERT: C 789 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7846 (pp) REVERT: C 818 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6893 (tm-30) REVERT: C 858 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8186 (OUTLIER) REVERT: C 883 ASP cc_start: 0.8059 (m-30) cc_final: 0.7472 (m-30) REVERT: C 915 ILE cc_start: 0.8978 (pt) cc_final: 0.8694 (tt) REVERT: D 74 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7887 (mp) REVERT: D 145 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8593 (t70) REVERT: D 242 ARG cc_start: 0.8561 (tpp-160) cc_final: 0.8339 (mmp80) REVERT: D 359 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7999 (p0) REVERT: D 396 ASN cc_start: 0.8870 (m-40) cc_final: 0.8083 (t0) REVERT: D 541 MET cc_start: 0.9060 (ttm) cc_final: 0.8608 (mmm) REVERT: D 600 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7992 (pt0) REVERT: D 880 VAL cc_start: 0.7071 (t) cc_final: 0.6797 (p) REVERT: E 70 GLN cc_start: 0.6551 (tt0) cc_final: 0.6241 (tt0) REVERT: F 325 ASN cc_start: 0.7759 (m-40) cc_final: 0.7430 (m110) REVERT: F 366 ILE cc_start: 0.8566 (pt) cc_final: 0.8190 (pp) REVERT: F 382 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7853 (mt) REVERT: F 386 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8449 (tt) REVERT: F 438 PHE cc_start: 0.8626 (m-10) cc_final: 0.8390 (m-10) REVERT: J 28 GLN cc_start: 0.6769 (pp30) cc_final: 0.6116 (pp30) REVERT: J 84 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.5814 (mpp) REVERT: M 25 ARG cc_start: 0.9260 (ttt180) cc_final: 0.8708 (ttm110) REVERT: M 41 GLN cc_start: 0.8900 (pp30) cc_final: 0.8638 (pp30) REVERT: Z 27 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8448 (tm) REVERT: Z 57 LEU cc_start: 0.9327 (mm) cc_final: 0.8979 (pp) REVERT: Z 72 ASP cc_start: 0.7650 (t0) cc_final: 0.7333 (t0) outliers start: 146 outliers final: 78 residues processed: 368 average time/residue: 0.5628 time to fit residues: 253.0980 Evaluate side-chains 336 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 240 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 858 GLU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 600 GLN Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 204 optimal weight: 0.3980 chunk 292 optimal weight: 8.9990 chunk 301 optimal weight: 0.5980 chunk 345 optimal weight: 6.9990 chunk 309 optimal weight: 0.0980 chunk 346 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 352 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 152 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS D1110 GLN ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 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 = 0.3828 r_free = 0.3828 target = 0.119830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073881 restraints weight = 54891.488| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.08 r_work: 0.2900 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31094 Z= 0.178 Angle : 0.820 77.598 42630 Z= 0.315 Chirality : 0.043 0.250 4847 Planarity : 0.004 0.057 5188 Dihedral : 18.288 178.366 5259 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.81 % Allowed : 19.32 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3570 helix: 1.08 (0.14), residues: 1402 sheet: -1.10 (0.26), residues: 444 loop : -1.72 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1231 TYR 0.013 0.001 TYR D 915 PHE 0.013 0.001 PHE D 107 TRP 0.022 0.001 TRP M 112 HIS 0.004 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00421 (31082) covalent geometry : angle 0.58854 (42606) hydrogen bonds : bond 0.04437 ( 1331) hydrogen bonds : angle 4.27591 ( 3695) metal coordination : bond 0.01470 ( 12) metal coordination : angle 24.08983 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 248 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8292 (tptt) REVERT: A 184 GLU cc_start: 0.6838 (tm-30) cc_final: 0.6521 (tm-30) REVERT: A 217 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: B 1 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7194 (mmm) REVERT: B 226 ASN cc_start: 0.8865 (t0) cc_final: 0.8156 (t0) REVERT: B 233 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: C 140 ILE cc_start: 0.8652 (mt) cc_final: 0.8430 (mp) REVERT: C 159 MET cc_start: 0.8723 (mmm) cc_final: 0.8410 (mmm) REVERT: C 220 ASP cc_start: 0.8547 (m-30) cc_final: 0.8074 (t0) REVERT: C 230 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7270 (mmm160) REVERT: C 250 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8508 (pp20) REVERT: C 302 LYS cc_start: 0.7660 (mttt) cc_final: 0.7303 (mmtp) REVERT: C 308 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6611 (pp) REVERT: C 397 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: C 439 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8194 (t80) REVERT: C 441 ASP cc_start: 0.8350 (t70) cc_final: 0.7705 (t0) REVERT: C 463 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8396 (pp) REVERT: C 549 ASP cc_start: 0.8018 (t0) cc_final: 0.7811 (p0) REVERT: C 691 ASP cc_start: 0.7876 (m-30) cc_final: 0.7597 (m-30) REVERT: C 704 ASP cc_start: 0.8073 (m-30) cc_final: 0.7864 (m-30) REVERT: C 758 ASP cc_start: 0.8671 (p0) cc_final: 0.8232 (p0) REVERT: C 789 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7873 (pp) REVERT: C 818 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6857 (tm-30) REVERT: C 858 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8222 (OUTLIER) REVERT: C 883 ASP cc_start: 0.8041 (m-30) cc_final: 0.7468 (m-30) REVERT: C 1039 ASP cc_start: 0.8069 (m-30) cc_final: 0.7814 (m-30) REVERT: D 74 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7891 (mt) REVERT: D 242 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.8002 (mmt180) REVERT: D 359 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7969 (p0) REVERT: D 396 ASN cc_start: 0.8834 (m-40) cc_final: 0.8064 (t0) REVERT: D 600 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: D 880 VAL cc_start: 0.7256 (OUTLIER) cc_final: 0.6986 (p) REVERT: E 70 GLN cc_start: 0.6490 (tt0) cc_final: 0.6159 (tt0) REVERT: F 325 ASN cc_start: 0.7736 (m-40) cc_final: 0.7397 (m110) REVERT: F 366 ILE cc_start: 0.8556 (pt) cc_final: 0.8177 (pp) REVERT: F 382 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7834 (mt) REVERT: F 386 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8462 (tt) REVERT: F 438 PHE cc_start: 0.8616 (m-10) cc_final: 0.8328 (m-10) REVERT: J 28 GLN cc_start: 0.6709 (pp30) cc_final: 0.6117 (pp30) REVERT: J 84 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.5787 (mpp) REVERT: M 25 ARG cc_start: 0.9235 (ttt180) cc_final: 0.8720 (ttm110) REVERT: M 41 GLN cc_start: 0.8878 (pp30) cc_final: 0.8652 (pp30) REVERT: Z 27 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8421 (tm) REVERT: Z 57 LEU cc_start: 0.9376 (mm) cc_final: 0.9008 (pp) REVERT: Z 72 ASP cc_start: 0.7622 (t0) cc_final: 0.7316 (t0) outliers start: 144 outliers final: 86 residues processed: 362 average time/residue: 0.5790 time to fit residues: 255.6370 Evaluate side-chains 345 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 241 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 858 GLU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 600 GLN Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 70 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 201 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 287 optimal weight: 5.9990 chunk 132 optimal weight: 0.3980 chunk 329 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 177 optimal weight: 20.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.118686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.072474 restraints weight = 54548.782| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.07 r_work: 0.2911 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31094 Z= 0.170 Angle : 0.811 77.682 42630 Z= 0.311 Chirality : 0.042 0.158 4847 Planarity : 0.004 0.058 5188 Dihedral : 18.258 178.924 5256 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.81 % Allowed : 19.62 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3570 helix: 1.16 (0.14), residues: 1400 sheet: -1.03 (0.26), residues: 442 loop : -1.70 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 506 TYR 0.013 0.001 TYR D 915 PHE 0.014 0.001 PHE D 107 TRP 0.027 0.001 TRP M 112 HIS 0.016 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00401 (31082) covalent geometry : angle 0.58170 (42606) hydrogen bonds : bond 0.04350 ( 1331) hydrogen bonds : angle 4.25180 ( 3695) metal coordination : bond 0.01411 ( 12) metal coordination : angle 23.84427 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 249 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8281 (tptt) REVERT: A 182 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7836 (mmt-90) REVERT: A 184 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6521 (tm-30) REVERT: A 217 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 226 ASN cc_start: 0.8871 (t0) cc_final: 0.8161 (t0) REVERT: B 233 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: C 140 ILE cc_start: 0.8641 (mt) cc_final: 0.8436 (mp) REVERT: C 159 MET cc_start: 0.8746 (mmm) cc_final: 0.8234 (mmm) REVERT: C 220 ASP cc_start: 0.8546 (m-30) cc_final: 0.8061 (t0) REVERT: C 224 VAL cc_start: 0.8341 (p) cc_final: 0.8131 (p) REVERT: C 230 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7286 (mmm160) REVERT: C 250 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8503 (pp20) REVERT: C 302 LYS cc_start: 0.7682 (mttt) cc_final: 0.7325 (mmtp) REVERT: C 308 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6662 (pp) REVERT: C 370 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8551 (pp) REVERT: C 439 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8149 (t80) REVERT: C 441 ASP cc_start: 0.8359 (t70) cc_final: 0.7719 (t0) REVERT: C 463 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8412 (pp) REVERT: C 691 ASP cc_start: 0.7913 (m-30) cc_final: 0.7608 (m-30) REVERT: C 704 ASP cc_start: 0.8092 (m-30) cc_final: 0.7884 (m-30) REVERT: C 758 ASP cc_start: 0.8651 (p0) cc_final: 0.8262 (p0) REVERT: C 789 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7864 (pp) REVERT: C 818 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6843 (tm-30) REVERT: C 858 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8213 (OUTLIER) REVERT: C 883 ASP cc_start: 0.8066 (m-30) cc_final: 0.7496 (m-30) REVERT: C 897 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8024 (ttmm) REVERT: C 1039 ASP cc_start: 0.8064 (m-30) cc_final: 0.7803 (m-30) REVERT: D 73 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8342 (mm) REVERT: D 74 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7939 (OUTLIER) REVERT: D 242 ARG cc_start: 0.8568 (tpp-160) cc_final: 0.8026 (mmt180) REVERT: D 359 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7968 (p0) REVERT: D 396 ASN cc_start: 0.8849 (m-40) cc_final: 0.8076 (t0) REVERT: D 600 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: D 880 VAL cc_start: 0.7254 (OUTLIER) cc_final: 0.6975 (p) REVERT: E 70 GLN cc_start: 0.6481 (tt0) cc_final: 0.6154 (tt0) REVERT: F 273 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7894 (tm) REVERT: F 325 ASN cc_start: 0.7748 (m-40) cc_final: 0.7411 (m110) REVERT: F 366 ILE cc_start: 0.8567 (pt) cc_final: 0.8193 (pp) REVERT: F 382 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7827 (mt) REVERT: F 390 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7338 (tt) REVERT: J 28 GLN cc_start: 0.6758 (pp30) cc_final: 0.6175 (pp30) REVERT: J 84 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.5736 (mpp) REVERT: M 41 GLN cc_start: 0.8891 (pp30) cc_final: 0.8663 (pp30) REVERT: Z 27 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8420 (tm) REVERT: Z 57 LEU cc_start: 0.9385 (mm) cc_final: 0.9037 (pp) REVERT: Z 72 ASP cc_start: 0.7615 (t0) cc_final: 0.7320 (t0) outliers start: 144 outliers final: 95 residues processed: 364 average time/residue: 0.5551 time to fit residues: 246.0545 Evaluate side-chains 352 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 238 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 858 GLU Chi-restraints excluded: chain C residue 897 LYS Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 600 GLN Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 70 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 87 optimal weight: 3.9990 chunk 274 optimal weight: 0.2980 chunk 153 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 247 optimal weight: 0.0470 chunk 250 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN D 505 HIS ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN ** Z 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.121221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075190 restraints weight = 54399.831| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.09 r_work: 0.2958 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31094 Z= 0.114 Angle : 0.770 73.736 42630 Z= 0.298 Chirality : 0.041 0.156 4847 Planarity : 0.004 0.058 5188 Dihedral : 18.151 179.580 5253 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.44 % Allowed : 21.09 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3570 helix: 1.30 (0.14), residues: 1403 sheet: -0.85 (0.27), residues: 403 loop : -1.60 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1143 TYR 0.011 0.001 TYR J 32 PHE 0.034 0.001 PHE D 107 TRP 0.032 0.001 TRP M 112 HIS 0.003 0.001 HIS C 941 Details of bonding type rmsd covalent geometry : bond 0.00253 (31082) covalent geometry : angle 0.55763 (42606) hydrogen bonds : bond 0.03703 ( 1331) hydrogen bonds : angle 4.13515 ( 3695) metal coordination : bond 0.01021 ( 12) metal coordination : angle 22.38292 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 270 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8289 (tptt) REVERT: A 182 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7762 (mmt-90) REVERT: A 184 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6266 (tm-30) REVERT: A 217 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: B 188 ASP cc_start: 0.6567 (t70) cc_final: 0.6305 (p0) REVERT: B 226 ASN cc_start: 0.8859 (t0) cc_final: 0.8169 (t0) REVERT: B 233 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8217 (pm20) REVERT: C 140 ILE cc_start: 0.8668 (mt) cc_final: 0.8463 (mp) REVERT: C 159 MET cc_start: 0.8827 (mmm) cc_final: 0.8306 (mmm) REVERT: C 220 ASP cc_start: 0.8521 (m-30) cc_final: 0.7902 (t0) REVERT: C 230 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7093 (mmm-85) REVERT: C 302 LYS cc_start: 0.7680 (mttt) cc_final: 0.7367 (mmtp) REVERT: C 370 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8469 (pp) REVERT: C 396 MET cc_start: 0.6974 (ttp) cc_final: 0.6723 (ttp) REVERT: C 439 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8108 (t80) REVERT: C 441 ASP cc_start: 0.8249 (t70) cc_final: 0.7655 (t0) REVERT: C 463 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8427 (pp) REVERT: C 691 ASP cc_start: 0.7878 (m-30) cc_final: 0.7611 (m-30) REVERT: C 758 ASP cc_start: 0.8619 (p0) cc_final: 0.8275 (p0) REVERT: C 789 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7834 (pp) REVERT: C 795 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 818 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6845 (tm-30) REVERT: C 858 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8209 (OUTLIER) REVERT: C 881 ASP cc_start: 0.8850 (p0) cc_final: 0.8348 (p0) REVERT: C 883 ASP cc_start: 0.8019 (m-30) cc_final: 0.7433 (m-30) REVERT: C 1039 ASP cc_start: 0.8026 (m-30) cc_final: 0.7761 (m-30) REVERT: D 73 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8413 (mm) REVERT: D 242 ARG cc_start: 0.8544 (tpp-160) cc_final: 0.8010 (mmt180) REVERT: D 359 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7962 (p0) REVERT: D 396 ASN cc_start: 0.8834 (m-40) cc_final: 0.8056 (t0) REVERT: D 541 MET cc_start: 0.9040 (ttm) cc_final: 0.8727 (mmm) REVERT: D 600 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: D 888 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8270 (mt-10) REVERT: D 981 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.6622 (ptp90) REVERT: E 70 GLN cc_start: 0.6555 (tt0) cc_final: 0.6259 (tt0) REVERT: F 273 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7902 (tm) REVERT: F 325 ASN cc_start: 0.7720 (m-40) cc_final: 0.7400 (m110) REVERT: F 349 TRP cc_start: 0.7991 (m100) cc_final: 0.7640 (m100) REVERT: F 366 ILE cc_start: 0.8510 (pt) cc_final: 0.8129 (pp) REVERT: J 28 GLN cc_start: 0.6695 (pp30) cc_final: 0.6124 (pp30) REVERT: M 25 ARG cc_start: 0.9216 (ttt180) cc_final: 0.8785 (ttm110) REVERT: Z 27 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8454 (tm) REVERT: Z 57 LEU cc_start: 0.9348 (mm) cc_final: 0.9017 (pp) REVERT: Z 72 ASP cc_start: 0.7497 (t0) cc_final: 0.7271 (t0) outliers start: 103 outliers final: 60 residues processed: 352 average time/residue: 0.5819 time to fit residues: 249.0532 Evaluate side-chains 325 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 251 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 858 GLU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 600 GLN Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain Z residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 137 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 271 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 350 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.118712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.072342 restraints weight = 54379.190| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.08 r_work: 0.2909 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 31094 Z= 0.199 Angle : 0.829 77.699 42630 Z= 0.325 Chirality : 0.044 0.294 4847 Planarity : 0.004 0.057 5188 Dihedral : 18.193 179.825 5250 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.81 % Allowed : 21.09 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3570 helix: 1.24 (0.14), residues: 1402 sheet: -0.89 (0.26), residues: 437 loop : -1.63 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 830 TYR 0.012 0.001 TYR D 915 PHE 0.021 0.001 PHE F 438 TRP 0.031 0.001 TRP M 112 HIS 0.005 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00474 (31082) covalent geometry : angle 0.61229 (42606) hydrogen bonds : bond 0.04430 ( 1331) hydrogen bonds : angle 4.24113 ( 3695) metal coordination : bond 0.01481 ( 12) metal coordination : angle 23.56430 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 249 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8150 (tptt) REVERT: A 153 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8285 (mtt180) REVERT: A 182 ARG cc_start: 0.8202 (mmt90) cc_final: 0.7874 (mmt-90) REVERT: A 184 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6594 (tm-30) REVERT: A 217 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: B 97 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7936 (pt) REVERT: B 188 ASP cc_start: 0.6594 (t70) cc_final: 0.6300 (p0) REVERT: B 226 ASN cc_start: 0.8860 (t0) cc_final: 0.8139 (t0) REVERT: B 233 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: C 140 ILE cc_start: 0.8653 (mt) cc_final: 0.8446 (mp) REVERT: C 159 MET cc_start: 0.8853 (mmm) cc_final: 0.8303 (mmm) REVERT: C 220 ASP cc_start: 0.8560 (m-30) cc_final: 0.8067 (t0) REVERT: C 230 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7061 (mmm-85) REVERT: C 250 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8510 (pp20) REVERT: C 302 LYS cc_start: 0.7704 (mttt) cc_final: 0.7387 (mmtp) REVERT: C 370 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8490 (pp) REVERT: C 439 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8189 (t80) REVERT: C 441 ASP cc_start: 0.8352 (t70) cc_final: 0.7721 (t0) REVERT: C 463 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8403 (pp) REVERT: C 560 LEU cc_start: 0.8268 (tp) cc_final: 0.8051 (tm) REVERT: C 691 ASP cc_start: 0.7859 (m-30) cc_final: 0.7599 (m-30) REVERT: C 758 ASP cc_start: 0.8638 (p0) cc_final: 0.8281 (p0) REVERT: C 789 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7839 (pp) REVERT: C 818 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6828 (tm-30) REVERT: C 858 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8225 (OUTLIER) REVERT: C 883 ASP cc_start: 0.8013 (m-30) cc_final: 0.7419 (m-30) REVERT: C 897 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7983 (ttmm) REVERT: C 1039 ASP cc_start: 0.8121 (m-30) cc_final: 0.7870 (m-30) REVERT: D 73 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8340 (mm) REVERT: D 74 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7875 (mt) REVERT: D 359 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7971 (p0) REVERT: D 396 ASN cc_start: 0.8842 (m-40) cc_final: 0.8079 (t0) REVERT: D 600 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: D 880 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6886 (p) REVERT: E 70 GLN cc_start: 0.6554 (tt0) cc_final: 0.6232 (tt0) REVERT: F 273 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7963 (tm) REVERT: F 299 ASN cc_start: 0.8049 (m-40) cc_final: 0.7727 (m110) REVERT: F 325 ASN cc_start: 0.7793 (m-40) cc_final: 0.7464 (m110) REVERT: F 366 ILE cc_start: 0.8520 (pt) cc_final: 0.8152 (pp) REVERT: F 382 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7946 (mt) REVERT: J 28 GLN cc_start: 0.6723 (pp30) cc_final: 0.6227 (pp30) REVERT: J 84 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.5843 (mpp) REVERT: Z 27 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8418 (tm) REVERT: Z 57 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9035 (pp) REVERT: Z 72 ASP cc_start: 0.7555 (t0) cc_final: 0.7304 (t0) outliers start: 114 outliers final: 73 residues processed: 341 average time/residue: 0.5505 time to fit residues: 227.7029 Evaluate side-chains 337 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 243 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 858 GLU Chi-restraints excluded: chain C residue 897 LYS Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 600 GLN Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 355 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 345 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 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 = 0.3858 r_free = 0.3858 target = 0.120829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.074674 restraints weight = 53942.870| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.09 r_work: 0.2951 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31094 Z= 0.127 Angle : 0.796 74.454 42630 Z= 0.312 Chirality : 0.042 0.285 4847 Planarity : 0.004 0.056 5188 Dihedral : 18.101 179.397 5250 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.21 % Allowed : 21.79 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3570 helix: 1.38 (0.15), residues: 1400 sheet: -0.75 (0.27), residues: 410 loop : -1.55 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 830 TYR 0.011 0.001 TYR J 32 PHE 0.022 0.001 PHE F 438 TRP 0.031 0.001 TRP M 112 HIS 0.002 0.001 HIS D 854 Details of bonding type rmsd covalent geometry : bond 0.00287 (31082) covalent geometry : angle 0.58879 (42606) hydrogen bonds : bond 0.03847 ( 1331) hydrogen bonds : angle 4.16843 ( 3695) metal coordination : bond 0.01019 ( 12) metal coordination : angle 22.60417 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 258 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8853 (m) cc_final: 0.8564 (t) REVERT: A 131 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8247 (tptt) REVERT: A 153 ARG cc_start: 0.8508 (tpp-160) cc_final: 0.8264 (mtt180) REVERT: A 182 ARG cc_start: 0.8128 (mmt90) cc_final: 0.7879 (mmt-90) REVERT: A 184 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6441 (tm-30) REVERT: A 217 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: B 97 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7901 (pt) REVERT: B 188 ASP cc_start: 0.6495 (t70) cc_final: 0.6248 (p0) REVERT: B 226 ASN cc_start: 0.8836 (t0) cc_final: 0.8130 (t0) REVERT: B 233 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: C 140 ILE cc_start: 0.8664 (mt) cc_final: 0.8461 (mp) REVERT: C 159 MET cc_start: 0.8850 (mmm) cc_final: 0.8331 (mmm) REVERT: C 220 ASP cc_start: 0.8542 (m-30) cc_final: 0.7906 (t0) REVERT: C 230 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7346 (mmm160) REVERT: C 250 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8569 (pp20) REVERT: C 302 LYS cc_start: 0.7664 (mttt) cc_final: 0.7351 (mmtp) REVERT: C 370 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8463 (pp) REVERT: C 396 MET cc_start: 0.7133 (ttp) cc_final: 0.6915 (ttp) REVERT: C 439 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8149 (t80) REVERT: C 441 ASP cc_start: 0.8258 (t70) cc_final: 0.7674 (t0) REVERT: C 463 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8418 (pp) REVERT: C 691 ASP cc_start: 0.7856 (m-30) cc_final: 0.7491 (m-30) REVERT: C 756 GLU cc_start: 0.8242 (tt0) cc_final: 0.7783 (tt0) REVERT: C 758 ASP cc_start: 0.8605 (p0) cc_final: 0.8246 (p0) REVERT: C 789 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7830 (pp) REVERT: C 818 GLU cc_start: 0.7451 (tm-30) cc_final: 0.6829 (tm-30) REVERT: C 858 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8226 (OUTLIER) REVERT: C 881 ASP cc_start: 0.8833 (p0) cc_final: 0.8337 (p0) REVERT: C 883 ASP cc_start: 0.7995 (m-30) cc_final: 0.7383 (m-30) REVERT: D 73 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8389 (mm) REVERT: D 74 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7763 (mt) REVERT: D 359 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7971 (p0) REVERT: D 396 ASN cc_start: 0.8813 (m-40) cc_final: 0.8049 (t0) REVERT: D 541 MET cc_start: 0.9013 (ttm) cc_final: 0.8706 (mmm) REVERT: D 600 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: D 888 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8260 (mt-10) REVERT: D 892 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8243 (mm-40) REVERT: D 981 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.6599 (ptp90) REVERT: E 70 GLN cc_start: 0.6569 (tt0) cc_final: 0.6271 (tt0) REVERT: F 273 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.8005 (tm) REVERT: F 299 ASN cc_start: 0.8029 (m-40) cc_final: 0.7692 (m-40) REVERT: F 325 ASN cc_start: 0.7710 (m-40) cc_final: 0.7406 (m110) REVERT: F 349 TRP cc_start: 0.7981 (m100) cc_final: 0.7626 (m100) REVERT: F 366 ILE cc_start: 0.8494 (pt) cc_final: 0.8111 (pp) REVERT: F 382 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7874 (tt) REVERT: J 28 GLN cc_start: 0.6641 (pp30) cc_final: 0.6147 (pp30) REVERT: J 83 ASP cc_start: 0.8885 (m-30) cc_final: 0.8654 (p0) REVERT: M 25 ARG cc_start: 0.9195 (ttt180) cc_final: 0.8779 (ttm110) REVERT: Z 27 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8426 (tm) REVERT: Z 72 ASP cc_start: 0.7484 (t0) cc_final: 0.7216 (t0) outliers start: 96 outliers final: 67 residues processed: 338 average time/residue: 0.6051 time to fit residues: 247.9218 Evaluate side-chains 332 residues out of total 3030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 246 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 858 GLU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 600 GLN Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 892 GLN Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain Z residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 255 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 283 optimal weight: 7.9990 chunk 319 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 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 = 0.3856 r_free = 0.3856 target = 0.120776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.074522 restraints weight = 54451.389| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.10 r_work: 0.2945 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31094 Z= 0.132 Angle : 0.789 74.736 42630 Z= 0.308 Chirality : 0.042 0.287 4847 Planarity : 0.004 0.056 5188 Dihedral : 18.053 179.071 5249 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.28 % Allowed : 21.79 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3570 helix: 1.41 (0.14), residues: 1405 sheet: -0.70 (0.27), residues: 410 loop : -1.53 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 830 TYR 0.035 0.001 TYR D 915 PHE 0.028 0.001 PHE D 107 TRP 0.030 0.001 TRP M 112 HIS 0.003 0.001 HIS C1042 Details of bonding type rmsd covalent geometry : bond 0.00303 (31082) covalent geometry : angle 0.58054 (42606) hydrogen bonds : bond 0.03860 ( 1331) hydrogen bonds : angle 4.14548 ( 3695) metal coordination : bond 0.01008 ( 12) metal coordination : angle 22.51754 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10901.13 seconds wall clock time: 186 minutes 0.32 seconds (11160.32 seconds total)