Starting phenix.real_space_refine on Sat Mar 7 01:45:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x2f_22006/03_2026/6x2f_22006.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2f_22006/03_2026/6x2f_22006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x2f_22006/03_2026/6x2f_22006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2f_22006/03_2026/6x2f_22006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x2f_22006/03_2026/6x2f_22006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2f_22006/03_2026/6x2f_22006.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.068 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 114 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 22296 2.51 5 N 6401 2.21 5 O 7099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.04s 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: 36054 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8934 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1088} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 11, 'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "G" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1721 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10368 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 10383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10383 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 201 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 8} Chain: "P" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1112 Classifications: {'DNA': 55} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 54} Chain: "Q" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1011 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23139 SG CYS J 70 27.729 99.970 85.446 1.00139.65 S ATOM 23153 SG CYS J 72 27.808 103.669 84.394 1.00141.32 S ATOM 23261 SG CYS J 85 25.989 100.923 82.417 1.00146.72 S ATOM 23285 SG CYS J 88 29.659 101.045 82.330 1.00134.74 S ATOM 28961 SG CYS J 814 53.224 38.369 92.070 1.00 96.55 S ATOM 29526 SG CYS J 888 54.225 41.984 91.005 1.00 81.59 S ATOM 29598 SG CYS J 898 55.996 38.784 93.474 1.00 76.52 S Time building chain proxies: 8.04, per 1000 atoms: 0.22 Number of scatterers: 36054 At special positions: 0 Unit cell: (139.1, 209.3, 179.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 141 16.00 P 114 15.00 Mg 1 11.99 O 7099 8.00 N 6401 7.00 C 22296 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: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 6 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 55 sheets defined 38.0% alpha, 16.3% beta 51 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.926A pdb=" N THR A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 removed outlier: 5.053A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 removed outlier: 4.392A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.509A pdb=" N PHE A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 307 removed outlier: 4.503A pdb=" N GLU A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 371 through 381 removed outlier: 3.529A pdb=" N THR A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.905A pdb=" N LEU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 564 through 578 removed outlier: 3.561A pdb=" N ASP A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 removed outlier: 3.628A pdb=" N SER A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 618 removed outlier: 4.299A pdb=" N GLN A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 648 removed outlier: 3.631A pdb=" N VAL A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 737 through 746 removed outlier: 4.577A pdb=" N ILE A 742 " --> pdb=" O HIS A 738 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 768 Processing helix chain 'A' and resid 794 through 808 removed outlier: 3.885A pdb=" N GLU A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 833 Processing helix chain 'A' and resid 848 through 859 removed outlier: 3.582A pdb=" N ARG A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 892 through 901 Processing helix chain 'A' and resid 923 through 936 Processing helix chain 'A' and resid 940 through 950 removed outlier: 4.363A pdb=" N ALA A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 988 removed outlier: 3.514A pdb=" N TYR A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 980 " --> pdb=" O MET A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1001 Processing helix chain 'A' and resid 1019 through 1033 Processing helix chain 'A' and resid 1035 through 1051 Processing helix chain 'A' and resid 1054 through 1074 removed outlier: 3.843A pdb=" N ILE A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A1069 " --> pdb=" O ARG A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1127 through 1145 removed outlier: 3.971A pdb=" N GLU A1144 " --> pdb=" O ARG A1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.889A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.794A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 removed outlier: 3.720A pdb=" N ASP G 114 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE G 115 " --> pdb=" O ALA G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 111 through 115' Processing helix chain 'G' and resid 212 through 229 removed outlier: 3.550A pdb=" N THR G 222 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 removed outlier: 3.932A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.956A pdb=" N ILE H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 226 removed outlier: 3.791A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 231 removed outlier: 4.320A pdb=" N ALA H 230 " --> pdb=" O GLN H 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.632A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 242 through 246 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 292 removed outlier: 3.764A pdb=" N TYR I 291 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.680A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 353 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.674A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.710A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL I 471 " --> pdb=" O GLY I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 487 removed outlier: 3.921A pdb=" N THR I 486 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.601A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER I 508 " --> pdb=" O GLU I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 539 through 543 removed outlier: 4.066A pdb=" N ALA I 543 " --> pdb=" O ARG I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 613 removed outlier: 3.739A pdb=" N GLY I 612 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 660 removed outlier: 3.699A pdb=" N GLN I 659 " --> pdb=" O SER I 656 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 656 through 660' Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.720A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 978 Processing helix chain 'I' and resid 993 through 997 Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.791A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR I1037 " --> pdb=" O ARG I1033 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN I1038 " --> pdb=" O ARG I1034 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.732A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.511A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1177 through 1179 No H-bonds generated for 'chain 'I' and resid 1177 through 1179' Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.870A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1293 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.754A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.606A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.820A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.665A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.551A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.524A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 331 removed outlier: 3.691A pdb=" N ILE J 331 " --> pdb=" O ALA J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.965A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 417 removed outlier: 4.248A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.764A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.550A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.602A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.142A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 removed outlier: 3.544A pdb=" N SER J 728 " --> pdb=" O MET J 724 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.510A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.912A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.794A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.754A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.543A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1242 removed outlier: 3.753A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR J1230 " --> pdb=" O VAL J1226 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN J1235 " --> pdb=" O ARG J1231 " (cutoff:3.500A) Processing helix chain 'J' and resid 1243 through 1245 No H-bonds generated for 'chain 'J' and resid 1243 through 1245' Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.621A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 removed outlier: 3.997A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 removed outlier: 4.134A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.772A pdb=" N ALA J1338 " --> pdb=" O GLU J1334 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 removed outlier: 3.586A pdb=" N VAL J1351 " --> pdb=" O LEU J1347 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.462A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 16 through 32 removed outlier: 4.055A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 78 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.848A pdb=" N MET A 68 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 42 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL A 108 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU A 44 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 43 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N THR A 285 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE A 45 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU A 282 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU A 339 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN A 284 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 18 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 152 removed outlier: 6.240A pdb=" N ARG A 151 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N THR A 164 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A 192 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU A 205 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 194 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 357 removed outlier: 5.493A pdb=" N GLN A 410 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.951A pdb=" N TYR A 493 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR A 512 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY A 495 " --> pdb=" O MET A 510 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N LYS I 115 " --> pdb=" O PRO A 522 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU I 67 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 680 through 683 removed outlier: 6.162A pdb=" N GLU A 681 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A 652 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLY A 709 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 654 " --> pdb=" O GLY A 709 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG A 624 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR A 755 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 626 " --> pdb=" O THR A 755 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP A 623 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 787 through 792 removed outlier: 6.310A pdb=" N LYS A 787 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 914 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE A 789 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 916 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG A 791 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 883 " --> pdb=" O TRP A 913 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU A 915 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE A 885 " --> pdb=" O LEU A 915 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 812 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N CYS A 867 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR A 814 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA A 839 " --> pdb=" O VAL A 866 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1003 through 1005 removed outlier: 5.650A pdb=" N GLU A1003 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A1086 " --> pdb=" O GLU A1079 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 12 through 15 removed outlier: 4.954A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AB2, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.737A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AB4, first strand: chain 'G' and resid 108 through 110 removed outlier: 4.086A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 14 through 18 removed outlier: 6.205A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 14 through 18 removed outlier: 6.205A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 98 through 101 removed outlier: 6.483A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLY H 151 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N MET H 51 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 98 through 101 Processing sheet with id=AB9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AC1, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AC2, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AC3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.201A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AC5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.441A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N SER I 574 " --> pdb=" O CYS I 559 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.526A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.602A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU I 226 " --> pdb=" O PHE I 337 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.017A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.507A pdb=" N VAL I 297 " --> pdb=" O MET I 315 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.692A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.017A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.512A pdb=" N ASP I 654 " --> pdb=" O ALA I 617 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.315A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.975A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.564A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD8, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.362A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.548A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.000A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AE3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.470A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.443A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AE6, first strand: chain 'J' and resid 103 through 112 removed outlier: 9.859A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE8, first strand: chain 'J' and resid 317 through 319 removed outlier: 6.752A pdb=" N ARG J 322 " --> pdb=" O GLY J 318 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AF1, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AF2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AF3, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.602A pdb=" N ILE J 950 " --> pdb=" O ALA J1018 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'J' and resid 991 through 996 removed outlier: 4.198A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 965 through 967 removed outlier: 4.096A pdb=" N ALA J1001 " --> pdb=" O ILE J 975 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 1025 through 1026 Processing sheet with id=AF7, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AF8, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.617A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AG1, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.656A pdb=" N VAL J1280 " --> pdb=" O ALA J1264 " (cutoff:3.500A) 1365 hydrogen bonds defined for protein. 3825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 264 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 10.35 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9695 1.33 - 1.45: 6929 1.45 - 1.57: 19777 1.57 - 1.70: 225 1.70 - 1.82: 247 Bond restraints: 36873 Sorted by residual: bond pdb=" N PRO I 489 " pdb=" CD PRO I 489 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.71e+01 bond pdb=" N PRO I 552 " pdb=" CD PRO I 552 " ideal model delta sigma weight residual 1.473 1.405 0.068 1.40e-02 5.10e+03 2.34e+01 bond pdb=" CA ARG A 837 " pdb=" CB ARG A 837 " ideal model delta sigma weight residual 1.524 1.456 0.069 1.46e-02 4.69e+03 2.22e+01 bond pdb=" CA PHE J 116 " pdb=" C PHE J 116 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.37e-02 5.33e+03 1.63e+01 bond pdb=" CA ILE J 416 " pdb=" CB ILE J 416 " ideal model delta sigma weight residual 1.540 1.487 0.053 1.36e-02 5.41e+03 1.53e+01 ... (remaining 36868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 48040 2.53 - 5.07: 1971 5.07 - 7.60: 266 7.60 - 10.13: 63 10.13 - 12.66: 16 Bond angle restraints: 50356 Sorted by residual: angle pdb=" C LEU A 344 " pdb=" N PRO A 345 " pdb=" CA PRO A 345 " ideal model delta sigma weight residual 119.84 130.93 -11.09 1.25e+00 6.40e-01 7.87e+01 angle pdb=" C CYS A 617 " pdb=" N GLN A 618 " pdb=" CA GLN A 618 " ideal model delta sigma weight residual 120.39 131.36 -10.97 1.39e+00 5.18e-01 6.22e+01 angle pdb=" N VAL A 564 " pdb=" CA VAL A 564 " pdb=" C VAL A 564 " ideal model delta sigma weight residual 113.20 106.43 6.77 9.60e-01 1.09e+00 4.97e+01 angle pdb=" C THR A 346 " pdb=" N LYS A 347 " pdb=" CA LYS A 347 " ideal model delta sigma weight residual 121.80 133.31 -11.51 1.71e+00 3.42e-01 4.53e+01 angle pdb=" N VAL J 839 " pdb=" CA VAL J 839 " pdb=" C VAL J 839 " ideal model delta sigma weight residual 111.88 104.87 7.01 1.06e+00 8.90e-01 4.37e+01 ... (remaining 50351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 21506 35.82 - 71.65: 761 71.65 - 107.47: 35 107.47 - 143.29: 1 143.29 - 179.11: 2 Dihedral angle restraints: 22305 sinusoidal: 9876 harmonic: 12429 Sorted by residual: dihedral pdb=" C5' ADP A2000 " pdb=" O5' ADP A2000 " pdb=" PA ADP A2000 " pdb=" O2A ADP A2000 " ideal model delta sinusoidal sigma weight residual -60.00 118.71 -178.70 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA ASN J 768 " pdb=" C ASN J 768 " pdb=" N VAL J 769 " pdb=" CA VAL J 769 " ideal model delta harmonic sigma weight residual 180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ASN J1249 " pdb=" C ASN J1249 " pdb=" N ASP J1250 " pdb=" CA ASP J1250 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 22302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5125 0.099 - 0.199: 574 0.199 - 0.298: 38 0.298 - 0.398: 5 0.398 - 0.497: 2 Chirality restraints: 5744 Sorted by residual: chirality pdb=" CB ILE I 117 " pdb=" CA ILE I 117 " pdb=" CG1 ILE I 117 " pdb=" CG2 ILE I 117 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CB VAL A 389 " pdb=" CA VAL A 389 " pdb=" CG1 VAL A 389 " pdb=" CG2 VAL A 389 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CG LEU A 402 " pdb=" CB LEU A 402 " pdb=" CD1 LEU A 402 " pdb=" CD2 LEU A 402 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 5741 not shown) Planarity restraints: 6194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 183 " -0.017 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP I 183 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP I 183 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP I 183 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 183 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP I 183 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 183 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 183 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 183 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP I 183 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 10 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C LYS H 10 " -0.059 2.00e-02 2.50e+03 pdb=" O LYS H 10 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO H 11 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 626 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C VAL A 626 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL A 626 " 0.022 2.00e-02 2.50e+03 pdb=" N CYS A 627 " 0.019 2.00e-02 2.50e+03 ... (remaining 6191 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 607 2.62 - 3.19: 31567 3.19 - 3.76: 60369 3.76 - 4.33: 79057 4.33 - 4.90: 124389 Nonbonded interactions: 295989 Sorted by model distance: nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 2.054 2.170 nonbonded pdb=" O SER J 210 " pdb=" CB ARG J 214 " model vdw 2.070 3.440 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.079 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.100 2.170 nonbonded pdb=" CG1 VAL A 786 " pdb=" CB ALA A 910 " model vdw 2.107 3.880 ... (remaining 295984 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 'G' and (resid 5 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 th \ rough 232)) selection = (chain 'H' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 190 or (resid 191 and (name N or name \ CA or name C or name O or name CB )) or resid 192 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 42.370 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.008 0.149 36880 Z= 0.367 Angle : 1.196 12.664 50362 Z= 0.674 Chirality : 0.064 0.497 5744 Planarity : 0.007 0.077 6194 Dihedral : 17.062 179.114 14293 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.76 % Favored : 91.87 % Rotamer: Outliers : 0.25 % Allowed : 0.86 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.11), residues: 4294 helix: -1.64 (0.12), residues: 1474 sheet: -0.99 (0.22), residues: 580 loop : -2.15 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG I 394 TYR 0.049 0.003 TYR A 150 PHE 0.037 0.003 PHE A1138 TRP 0.056 0.004 TRP I 183 HIS 0.012 0.003 HIS A 842 Details of bonding type rmsd covalent geometry : bond 0.00789 (36873) covalent geometry : angle 1.19563 (50356) hydrogen bonds : bond 0.16129 ( 1477) hydrogen bonds : angle 7.29940 ( 4089) metal coordination : bond 0.01597 ( 7) metal coordination : angle 3.57125 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 497 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8612 (mm) cc_final: 0.8379 (tp) REVERT: A 315 LEU cc_start: 0.7371 (pt) cc_final: 0.7032 (pt) REVERT: A 622 MET cc_start: 0.5991 (mpp) cc_final: 0.5239 (mmt) REVERT: A 745 MET cc_start: 0.5189 (ttt) cc_final: 0.4548 (tpp) REVERT: H 84 ASN cc_start: 0.8560 (m110) cc_final: 0.8154 (m110) REVERT: H 185 TYR cc_start: 0.8779 (p90) cc_final: 0.8071 (p90) REVERT: I 524 ILE cc_start: 0.9574 (tp) cc_final: 0.9270 (tp) REVERT: I 1230 MET cc_start: 0.7880 (ttt) cc_final: 0.7430 (ttt) REVERT: I 1285 TYR cc_start: 0.8559 (m-80) cc_final: 0.8281 (m-80) REVERT: J 29 MET cc_start: 0.7971 (tpt) cc_final: 0.7570 (tpp) REVERT: J 180 MET cc_start: 0.7339 (mpp) cc_final: 0.7058 (mpp) REVERT: J 259 ARG cc_start: 0.5433 (mtm180) cc_final: 0.5017 (mtp180) REVERT: J 264 ASP cc_start: 0.7550 (t0) cc_final: 0.7263 (t0) REVERT: J 479 GLU cc_start: 0.7256 (mt-10) cc_final: 0.7038 (mt-10) REVERT: J 505 ASP cc_start: 0.7603 (t0) cc_final: 0.7007 (t0) REVERT: J 512 TYR cc_start: 0.8464 (t80) cc_final: 0.7894 (t80) REVERT: J 582 ILE cc_start: 0.8924 (mm) cc_final: 0.8591 (tt) REVERT: J 698 MET cc_start: 0.9039 (mmm) cc_final: 0.8701 (mmm) REVERT: J 707 ILE cc_start: 0.8261 (pt) cc_final: 0.8031 (tp) REVERT: J 772 TYR cc_start: 0.9006 (t80) cc_final: 0.8511 (t80) REVERT: J 921 GLN cc_start: 0.8808 (mt0) cc_final: 0.8374 (mt0) REVERT: K 31 GLN cc_start: 0.8357 (tt0) cc_final: 0.8136 (tt0) REVERT: K 32 VAL cc_start: 0.7992 (t) cc_final: 0.7744 (p) outliers start: 9 outliers final: 2 residues processed: 504 average time/residue: 0.2098 time to fit residues: 174.8239 Evaluate side-chains 378 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 376 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 1170 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 120 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1021 ASN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 526 HIS I1070 HIS J 232 ASN J 861 ASN J 875 ASN J 962 ASN K 62 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.108117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.090264 restraints weight = 153051.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091743 restraints weight = 90781.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092724 restraints weight = 64328.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.093210 restraints weight = 51864.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093636 restraints weight = 45942.158| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36880 Z= 0.164 Angle : 0.713 12.055 50362 Z= 0.375 Chirality : 0.045 0.164 5744 Planarity : 0.005 0.066 6194 Dihedral : 16.343 178.474 5991 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.40 % Favored : 93.50 % Rotamer: Outliers : 1.52 % Allowed : 9.27 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.12), residues: 4294 helix: -0.70 (0.13), residues: 1525 sheet: -0.93 (0.22), residues: 554 loop : -1.94 (0.12), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 6 TYR 0.025 0.002 TYR G 185 PHE 0.023 0.002 PHE A1138 TRP 0.027 0.002 TRP J1193 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00349 (36873) covalent geometry : angle 0.71164 (50356) hydrogen bonds : bond 0.05071 ( 1477) hydrogen bonds : angle 5.68705 ( 4089) metal coordination : bond 0.00965 ( 7) metal coordination : angle 4.43841 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 430 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8434 (mm) cc_final: 0.8116 (tp) REVERT: A 509 LEU cc_start: 0.8048 (mm) cc_final: 0.7486 (mm) REVERT: A 858 HIS cc_start: 0.5572 (OUTLIER) cc_final: 0.5224 (t-90) REVERT: H 185 TYR cc_start: 0.8758 (p90) cc_final: 0.8172 (p90) REVERT: I 386 GLU cc_start: 0.5888 (mp0) cc_final: 0.5586 (mp0) REVERT: I 459 MET cc_start: 0.8571 (mpp) cc_final: 0.8348 (mpp) REVERT: I 524 ILE cc_start: 0.9593 (tp) cc_final: 0.9239 (tp) REVERT: I 671 LEU cc_start: 0.9615 (tp) cc_final: 0.9393 (tp) REVERT: I 800 MET cc_start: 0.7822 (mtp) cc_final: 0.7621 (mtp) REVERT: I 1230 MET cc_start: 0.7873 (ttt) cc_final: 0.7357 (ttt) REVERT: I 1329 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8459 (pm20) REVERT: J 29 MET cc_start: 0.7812 (tpt) cc_final: 0.7348 (tpp) REVERT: J 264 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8024 (t70) REVERT: J 274 ASN cc_start: 0.8724 (m-40) cc_final: 0.8404 (m-40) REVERT: J 298 MET cc_start: 0.8829 (tmm) cc_final: 0.8627 (ppp) REVERT: J 479 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6975 (mt-10) REVERT: J 512 TYR cc_start: 0.8797 (t80) cc_final: 0.8125 (t80) REVERT: J 707 ILE cc_start: 0.8534 (pt) cc_final: 0.8214 (tp) REVERT: J 725 MET cc_start: 0.8854 (mtm) cc_final: 0.8640 (mtm) REVERT: J 781 LYS cc_start: 0.9116 (tppt) cc_final: 0.8797 (tppt) REVERT: J 921 GLN cc_start: 0.8853 (mt0) cc_final: 0.8299 (mt0) REVERT: K 30 MET cc_start: 0.8233 (tmm) cc_final: 0.7649 (tmm) REVERT: K 54 ILE cc_start: 0.8672 (mm) cc_final: 0.8424 (tp) outliers start: 55 outliers final: 35 residues processed: 462 average time/residue: 0.2049 time to fit residues: 158.8841 Evaluate side-chains 404 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 366 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 824 LYS Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 384 optimal weight: 0.5980 chunk 217 optimal weight: 9.9990 chunk 167 optimal weight: 0.0050 chunk 426 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 173 optimal weight: 0.3980 chunk 337 optimal weight: 6.9990 chunk 419 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 517 GLN I 725 GLN ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1017 GLN I1116 HIS ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.108902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.091247 restraints weight = 152873.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093208 restraints weight = 93417.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093818 restraints weight = 59524.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.094014 restraints weight = 49760.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094116 restraints weight = 47635.926| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36880 Z= 0.137 Angle : 0.654 13.450 50362 Z= 0.339 Chirality : 0.043 0.190 5744 Planarity : 0.005 0.060 6194 Dihedral : 16.067 178.046 5986 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.85 % Rotamer: Outliers : 1.74 % Allowed : 13.00 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -1.71 (0.12), residues: 4294 helix: -0.28 (0.13), residues: 1524 sheet: -0.90 (0.22), residues: 555 loop : -1.83 (0.12), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 17 TYR 0.024 0.001 TYR H 177 PHE 0.023 0.001 PHE A1138 TRP 0.034 0.002 TRP J1193 HIS 0.004 0.001 HIS A 842 Details of bonding type rmsd covalent geometry : bond 0.00297 (36873) covalent geometry : angle 0.65291 (50356) hydrogen bonds : bond 0.04357 ( 1477) hydrogen bonds : angle 5.28215 ( 4089) metal coordination : bond 0.00827 ( 7) metal coordination : angle 3.62234 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 409 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7437 (pmm) cc_final: 0.7209 (pmm) REVERT: A 56 HIS cc_start: 0.7201 (t70) cc_final: 0.6616 (t-90) REVERT: A 157 MET cc_start: 0.7437 (mmm) cc_final: 0.7204 (mmm) REVERT: A 382 ASP cc_start: 0.6912 (t0) cc_final: 0.6508 (t0) REVERT: A 622 MET cc_start: 0.5925 (mpp) cc_final: 0.4779 (mmt) REVERT: A 665 HIS cc_start: 0.7845 (m-70) cc_final: 0.7595 (m-70) REVERT: H 177 TYR cc_start: 0.8696 (m-80) cc_final: 0.8407 (m-80) REVERT: I 386 GLU cc_start: 0.5792 (OUTLIER) cc_final: 0.5347 (mp0) REVERT: I 459 MET cc_start: 0.8586 (mpp) cc_final: 0.8331 (mpp) REVERT: I 524 ILE cc_start: 0.9568 (tp) cc_final: 0.9213 (tp) REVERT: I 1114 GLU cc_start: 0.8923 (tt0) cc_final: 0.8360 (tt0) REVERT: I 1230 MET cc_start: 0.7873 (ttt) cc_final: 0.7590 (ttt) REVERT: I 1328 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8720 (mppt) REVERT: J 29 MET cc_start: 0.7828 (tpt) cc_final: 0.7325 (tpp) REVERT: J 264 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7939 (t70) REVERT: J 274 ASN cc_start: 0.8791 (m-40) cc_final: 0.8451 (m-40) REVERT: J 297 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7246 (tmm-80) REVERT: J 479 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6944 (mt-10) REVERT: J 512 TYR cc_start: 0.8759 (t80) cc_final: 0.8016 (t80) REVERT: J 697 MET cc_start: 0.8371 (ttt) cc_final: 0.8125 (ttp) REVERT: J 707 ILE cc_start: 0.8459 (pt) cc_final: 0.8150 (tp) REVERT: J 725 MET cc_start: 0.8848 (mtm) cc_final: 0.8623 (mtp) REVERT: J 747 MET cc_start: 0.7854 (mmt) cc_final: 0.7632 (mmm) REVERT: J 781 LYS cc_start: 0.9154 (tppt) cc_final: 0.8852 (tppt) REVERT: J 921 GLN cc_start: 0.8779 (mt0) cc_final: 0.8236 (mt0) REVERT: K 30 MET cc_start: 0.8484 (tmm) cc_final: 0.7944 (tmm) REVERT: K 31 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8498 (tp40) REVERT: K 65 ASP cc_start: 0.7014 (m-30) cc_final: 0.6608 (m-30) outliers start: 63 outliers final: 35 residues processed: 445 average time/residue: 0.1972 time to fit residues: 147.4528 Evaluate side-chains 401 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 362 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 16 optimal weight: 20.0000 chunk 211 optimal weight: 0.3980 chunk 299 optimal weight: 1.9990 chunk 400 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 428 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1098 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.107849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.090081 restraints weight = 153118.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.091884 restraints weight = 96531.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.092689 restraints weight = 61671.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.092880 restraints weight = 52640.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092968 restraints weight = 48398.793| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36880 Z= 0.155 Angle : 0.645 12.983 50362 Z= 0.333 Chirality : 0.043 0.173 5744 Planarity : 0.004 0.058 6194 Dihedral : 15.972 177.249 5986 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.67 % Rotamer: Outliers : 1.94 % Allowed : 15.33 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -1.54 (0.12), residues: 4294 helix: -0.10 (0.13), residues: 1545 sheet: -0.87 (0.22), residues: 571 loop : -1.75 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 69 TYR 0.016 0.001 TYR J 165 PHE 0.024 0.001 PHE A1138 TRP 0.032 0.002 TRP J1193 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00340 (36873) covalent geometry : angle 0.64384 (50356) hydrogen bonds : bond 0.04183 ( 1477) hydrogen bonds : angle 5.15170 ( 4089) metal coordination : bond 0.00906 ( 7) metal coordination : angle 3.39142 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 383 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ASP cc_start: 0.7183 (t0) cc_final: 0.6866 (t0) REVERT: A 571 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7286 (mm) REVERT: H 177 TYR cc_start: 0.8596 (m-80) cc_final: 0.8243 (m-80) REVERT: I 386 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.4919 (mp0) REVERT: I 524 ILE cc_start: 0.9598 (tp) cc_final: 0.9227 (tp) REVERT: I 1060 ILE cc_start: 0.7942 (tp) cc_final: 0.7580 (tp) REVERT: I 1230 MET cc_start: 0.7860 (ttt) cc_final: 0.7301 (ttt) REVERT: I 1328 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8652 (mppt) REVERT: J 29 MET cc_start: 0.7773 (tpt) cc_final: 0.7213 (tpp) REVERT: J 264 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7939 (t70) REVERT: J 274 ASN cc_start: 0.8817 (m-40) cc_final: 0.8481 (m-40) REVERT: J 297 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7294 (tmm-80) REVERT: J 347 VAL cc_start: 0.9354 (t) cc_final: 0.9066 (m) REVERT: J 479 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6864 (mt-10) REVERT: J 512 TYR cc_start: 0.8789 (t80) cc_final: 0.7993 (t80) REVERT: J 697 MET cc_start: 0.8421 (ttt) cc_final: 0.8023 (ttp) REVERT: J 725 MET cc_start: 0.8926 (mtm) cc_final: 0.8704 (mtp) REVERT: J 747 MET cc_start: 0.7924 (mmt) cc_final: 0.7639 (mmm) REVERT: J 781 LYS cc_start: 0.9178 (tppt) cc_final: 0.8874 (tppt) REVERT: J 1020 TRP cc_start: 0.5378 (p90) cc_final: 0.4803 (p90) REVERT: J 1236 GLU cc_start: 0.7701 (tp30) cc_final: 0.7498 (tp30) REVERT: K 30 MET cc_start: 0.8413 (tmm) cc_final: 0.8161 (tmm) outliers start: 70 outliers final: 46 residues processed: 422 average time/residue: 0.1947 time to fit residues: 138.9917 Evaluate side-chains 399 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 349 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 176 optimal weight: 20.0000 chunk 278 optimal weight: 0.9990 chunk 420 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 303 optimal weight: 7.9990 chunk 413 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 85 GLN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 859 HIS ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 69 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** J 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1238 GLN J1367 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.100612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.083546 restraints weight = 155739.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.084271 restraints weight = 104227.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.084433 restraints weight = 72117.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.084606 restraints weight = 72493.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.084658 restraints weight = 66585.956| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 36880 Z= 0.335 Angle : 0.822 12.892 50362 Z= 0.427 Chirality : 0.047 0.238 5744 Planarity : 0.006 0.086 6194 Dihedral : 16.231 177.245 5986 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.03 % Favored : 91.92 % Rotamer: Outliers : 3.51 % Allowed : 17.35 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -1.83 (0.12), residues: 4294 helix: -0.33 (0.13), residues: 1519 sheet: -1.18 (0.21), residues: 580 loop : -1.87 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 232 TYR 0.034 0.003 TYR I1305 PHE 0.036 0.003 PHE A1138 TRP 0.022 0.003 TRP J 868 HIS 0.013 0.002 HIS A 948 Details of bonding type rmsd covalent geometry : bond 0.00726 (36873) covalent geometry : angle 0.81984 (50356) hydrogen bonds : bond 0.05494 ( 1477) hydrogen bonds : angle 5.57906 ( 4089) metal coordination : bond 0.01900 ( 7) metal coordination : angle 5.15995 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 361 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.8103 (tpp) cc_final: 0.7853 (tpp) REVERT: A 423 ARG cc_start: 0.7382 (mmt-90) cc_final: 0.7174 (mmp80) REVERT: A 571 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7640 (mm) REVERT: A 858 HIS cc_start: 0.6003 (OUTLIER) cc_final: 0.5580 (t-90) REVERT: A 959 LEU cc_start: 0.6776 (tp) cc_final: 0.6502 (tp) REVERT: G 193 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: H 193 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: I 130 MET cc_start: 0.9197 (ttm) cc_final: 0.8714 (ttm) REVERT: I 386 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5124 (mp0) REVERT: I 524 ILE cc_start: 0.9586 (tp) cc_final: 0.9240 (tp) REVERT: I 1230 MET cc_start: 0.7902 (ttt) cc_final: 0.7209 (ttt) REVERT: I 1243 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7754 (tmm) REVERT: I 1328 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8812 (mppt) REVERT: I 1329 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8516 (pm20) REVERT: J 29 MET cc_start: 0.7961 (tpt) cc_final: 0.7399 (tpp) REVERT: J 151 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.6033 (tmm) REVERT: J 180 MET cc_start: 0.6501 (mpp) cc_final: 0.6088 (mpp) REVERT: J 264 ASP cc_start: 0.8288 (t0) cc_final: 0.7797 (t70) REVERT: J 274 ASN cc_start: 0.8822 (m-40) cc_final: 0.8494 (m-40) REVERT: J 297 ARG cc_start: 0.8306 (ttp80) cc_final: 0.8033 (ptm-80) REVERT: J 304 ASP cc_start: 0.8402 (t70) cc_final: 0.8200 (t70) REVERT: J 330 MET cc_start: 0.8533 (mtm) cc_final: 0.7900 (mtm) REVERT: J 400 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8279 (ttm) REVERT: J 418 GLU cc_start: 0.7672 (mp0) cc_final: 0.7142 (mp0) REVERT: J 512 TYR cc_start: 0.8962 (t80) cc_final: 0.8409 (t80) REVERT: J 725 MET cc_start: 0.9023 (mtm) cc_final: 0.8731 (mtp) REVERT: J 781 LYS cc_start: 0.9096 (tppt) cc_final: 0.8878 (tppt) REVERT: J 1238 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8420 (tp-100) REVERT: J 1327 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: K 30 MET cc_start: 0.8509 (tmm) cc_final: 0.7982 (tmm) REVERT: K 44 ASP cc_start: 0.6851 (p0) cc_final: 0.6474 (p0) REVERT: K 65 ASP cc_start: 0.7157 (m-30) cc_final: 0.6717 (m-30) REVERT: K 69 ARG cc_start: 0.7307 (mtm110) cc_final: 0.6909 (mtm110) outliers start: 127 outliers final: 75 residues processed: 448 average time/residue: 0.2025 time to fit residues: 153.5523 Evaluate side-chains 429 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 342 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 931 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1217 THR Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1243 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 699 ASP Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1238 GLN Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 315 optimal weight: 6.9990 chunk 379 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 339 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 408 optimal weight: 0.8980 chunk 389 optimal weight: 9.9990 chunk 412 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 111 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS ** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN I1116 HIS J 424 ASN J 489 ASN J1238 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.105693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.087723 restraints weight = 152057.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.089270 restraints weight = 90689.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.090140 restraints weight = 64033.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.090638 restraints weight = 51434.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091030 restraints weight = 45558.741| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36880 Z= 0.150 Angle : 0.675 13.941 50362 Z= 0.344 Chirality : 0.044 0.233 5744 Planarity : 0.004 0.059 6194 Dihedral : 16.062 177.330 5986 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.43 % Favored : 93.55 % Rotamer: Outliers : 2.63 % Allowed : 19.06 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -1.50 (0.13), residues: 4294 helix: -0.05 (0.13), residues: 1537 sheet: -0.95 (0.22), residues: 573 loop : -1.71 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1231 TYR 0.017 0.001 TYR J 165 PHE 0.024 0.001 PHE A1138 TRP 0.040 0.002 TRP J1020 HIS 0.004 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00331 (36873) covalent geometry : angle 0.67294 (50356) hydrogen bonds : bond 0.04139 ( 1477) hydrogen bonds : angle 5.16545 ( 4089) metal coordination : bond 0.00870 ( 7) metal coordination : angle 4.36578 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 382 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8118 (t0) cc_final: 0.7757 (p0) REVERT: A 157 MET cc_start: 0.7582 (mmm) cc_final: 0.7002 (mmm) REVERT: A 571 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7476 (mm) REVERT: A 858 HIS cc_start: 0.5563 (OUTLIER) cc_final: 0.5251 (t-90) REVERT: H 177 TYR cc_start: 0.8690 (m-80) cc_final: 0.7926 (m-80) REVERT: H 186 ASN cc_start: 0.8013 (t0) cc_final: 0.7794 (t0) REVERT: H 193 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: I 130 MET cc_start: 0.9304 (ttm) cc_final: 0.8728 (ttm) REVERT: I 386 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.4708 (mp0) REVERT: I 524 ILE cc_start: 0.9628 (tp) cc_final: 0.9202 (tp) REVERT: I 699 LEU cc_start: 0.9302 (mt) cc_final: 0.9078 (mp) REVERT: I 813 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6565 (pp20) REVERT: I 1230 MET cc_start: 0.7805 (ttt) cc_final: 0.7025 (ttt) REVERT: I 1328 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8680 (mppt) REVERT: J 29 MET cc_start: 0.7880 (tpt) cc_final: 0.7248 (tpp) REVERT: J 151 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.5841 (tmm) REVERT: J 180 MET cc_start: 0.5958 (mpp) cc_final: 0.5472 (mpp) REVERT: J 264 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7654 (t70) REVERT: J 297 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7912 (ptm-80) REVERT: J 330 MET cc_start: 0.8640 (mtm) cc_final: 0.7768 (mtm) REVERT: J 347 VAL cc_start: 0.9322 (t) cc_final: 0.9064 (m) REVERT: J 418 GLU cc_start: 0.7571 (mp0) cc_final: 0.7300 (mp0) REVERT: J 512 TYR cc_start: 0.8807 (t80) cc_final: 0.8097 (t80) REVERT: J 697 MET cc_start: 0.8451 (ttp) cc_final: 0.8052 (ttp) REVERT: J 725 MET cc_start: 0.8987 (mtm) cc_final: 0.8758 (mtm) REVERT: J 747 MET cc_start: 0.7997 (mmt) cc_final: 0.7749 (mmm) REVERT: J 781 LYS cc_start: 0.9183 (tppt) cc_final: 0.8929 (tppt) REVERT: K 30 MET cc_start: 0.8369 (tmm) cc_final: 0.8020 (tmm) outliers start: 95 outliers final: 56 residues processed: 450 average time/residue: 0.1979 time to fit residues: 151.1294 Evaluate side-chains 419 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 355 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 931 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 24 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 323 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 chunk 246 optimal weight: 0.5980 chunk 87 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 359 optimal weight: 6.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN I1116 HIS J 335 GLN J 489 ASN ** J 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.086154 restraints weight = 153597.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.087589 restraints weight = 91557.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088409 restraints weight = 65089.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089008 restraints weight = 52835.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089316 restraints weight = 46112.150| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36880 Z= 0.197 Angle : 0.693 13.130 50362 Z= 0.354 Chirality : 0.044 0.211 5744 Planarity : 0.005 0.064 6194 Dihedral : 16.029 178.783 5986 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.08 % Favored : 92.90 % Rotamer: Outliers : 3.02 % Allowed : 19.54 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -1.48 (0.13), residues: 4294 helix: 0.01 (0.13), residues: 1528 sheet: -0.97 (0.22), residues: 576 loop : -1.72 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 423 TYR 0.016 0.002 TYR I1305 PHE 0.038 0.002 PHE A 972 TRP 0.023 0.002 TRP J 868 HIS 0.006 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00436 (36873) covalent geometry : angle 0.69146 (50356) hydrogen bonds : bond 0.04330 ( 1477) hydrogen bonds : angle 5.17513 ( 4089) metal coordination : bond 0.01141 ( 7) metal coordination : angle 4.18435 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 366 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.3815 (mmt) cc_final: 0.3013 (mpp) REVERT: A 571 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7604 (mm) REVERT: A 858 HIS cc_start: 0.5687 (OUTLIER) cc_final: 0.5346 (t-90) REVERT: H 186 ASN cc_start: 0.8032 (t0) cc_final: 0.7775 (t0) REVERT: H 193 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: I 130 MET cc_start: 0.9313 (ttm) cc_final: 0.8753 (ttm) REVERT: I 386 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.4744 (mp0) REVERT: I 524 ILE cc_start: 0.9614 (tp) cc_final: 0.9192 (tp) REVERT: I 1060 ILE cc_start: 0.8084 (tp) cc_final: 0.7701 (tp) REVERT: I 1230 MET cc_start: 0.7850 (ttt) cc_final: 0.7026 (ttt) REVERT: I 1328 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8689 (mppt) REVERT: J 29 MET cc_start: 0.7917 (tpt) cc_final: 0.7272 (tpp) REVERT: J 264 ASP cc_start: 0.8183 (t0) cc_final: 0.7698 (t70) REVERT: J 297 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7245 (tmm-80) REVERT: J 330 MET cc_start: 0.8583 (mtm) cc_final: 0.7634 (mtm) REVERT: J 347 VAL cc_start: 0.9428 (t) cc_final: 0.9190 (m) REVERT: J 400 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8056 (ttm) REVERT: J 418 GLU cc_start: 0.7596 (mp0) cc_final: 0.7339 (mp0) REVERT: J 479 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7449 (mt-10) REVERT: J 512 TYR cc_start: 0.8951 (t80) cc_final: 0.8221 (t80) REVERT: J 697 MET cc_start: 0.8465 (ttp) cc_final: 0.8138 (ttp) REVERT: J 725 MET cc_start: 0.9025 (mtm) cc_final: 0.8798 (mtm) REVERT: J 747 MET cc_start: 0.7990 (mmt) cc_final: 0.7734 (mmm) REVERT: J 781 LYS cc_start: 0.9166 (tppt) cc_final: 0.8918 (tppt) REVERT: J 1048 ARG cc_start: 0.6745 (tpt170) cc_final: 0.6007 (tpt90) REVERT: J 1327 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: K 30 MET cc_start: 0.8269 (tmm) cc_final: 0.7927 (tmm) REVERT: K 69 ARG cc_start: 0.7551 (mtm110) cc_final: 0.7151 (mtm110) outliers start: 109 outliers final: 81 residues processed: 441 average time/residue: 0.2012 time to fit residues: 149.5721 Evaluate side-chains 441 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 353 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 931 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 699 ASP Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1331 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 362 optimal weight: 10.0000 chunk 348 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 351 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 350 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 245 optimal weight: 0.0000 chunk 431 optimal weight: 10.0000 chunk 384 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN I1116 HIS ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1313 HIS J 489 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.106756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089161 restraints weight = 152042.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090924 restraints weight = 93645.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.091365 restraints weight = 64660.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.091866 restraints weight = 53756.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.091938 restraints weight = 50999.847| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36880 Z= 0.134 Angle : 0.668 13.708 50362 Z= 0.337 Chirality : 0.044 0.289 5744 Planarity : 0.004 0.056 6194 Dihedral : 15.886 175.834 5986 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 2.46 % Allowed : 20.39 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -1.37 (0.13), residues: 4294 helix: 0.12 (0.13), residues: 1544 sheet: -1.00 (0.22), residues: 581 loop : -1.65 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 423 TYR 0.017 0.001 TYR H 177 PHE 0.020 0.001 PHE A1138 TRP 0.019 0.002 TRP J1020 HIS 0.005 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00298 (36873) covalent geometry : angle 0.66736 (50356) hydrogen bonds : bond 0.03843 ( 1477) hydrogen bonds : angle 5.00127 ( 4089) metal coordination : bond 0.00687 ( 7) metal coordination : angle 3.49769 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 399 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7449 (mmm) cc_final: 0.6771 (mmm) REVERT: A 382 ASP cc_start: 0.7133 (t0) cc_final: 0.6827 (t0) REVERT: A 410 GLN cc_start: 0.6244 (mm110) cc_final: 0.5830 (mm-40) REVERT: A 571 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7585 (mm) REVERT: A 745 MET cc_start: 0.5795 (mtt) cc_final: 0.5442 (mmt) REVERT: A 802 ILE cc_start: 0.8294 (mt) cc_final: 0.8041 (mm) REVERT: A 858 HIS cc_start: 0.5518 (OUTLIER) cc_final: 0.5221 (t-90) REVERT: G 204 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: H 177 TYR cc_start: 0.8376 (m-80) cc_final: 0.8083 (m-80) REVERT: H 185 TYR cc_start: 0.8631 (p90) cc_final: 0.8264 (p90) REVERT: H 186 ASN cc_start: 0.7953 (t0) cc_final: 0.7673 (t0) REVERT: H 193 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: I 130 MET cc_start: 0.9264 (ttm) cc_final: 0.8672 (ttm) REVERT: I 386 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5624 (mp0) REVERT: I 524 ILE cc_start: 0.9613 (tp) cc_final: 0.9166 (tp) REVERT: I 588 GLU cc_start: 0.8589 (pt0) cc_final: 0.8364 (pt0) REVERT: I 653 MET cc_start: 0.6215 (ttp) cc_final: 0.5647 (ptm) REVERT: I 1328 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8754 (mppt) REVERT: J 29 MET cc_start: 0.7833 (tpt) cc_final: 0.7177 (tpp) REVERT: J 264 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7560 (t70) REVERT: J 297 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7206 (tmm-80) REVERT: J 330 MET cc_start: 0.8578 (mtm) cc_final: 0.7740 (mtm) REVERT: J 347 VAL cc_start: 0.9297 (t) cc_final: 0.8990 (m) REVERT: J 418 GLU cc_start: 0.7441 (mp0) cc_final: 0.7167 (mp0) REVERT: J 479 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7344 (mt-10) REVERT: J 512 TYR cc_start: 0.8828 (t80) cc_final: 0.8026 (t80) REVERT: J 544 LEU cc_start: 0.9241 (tp) cc_final: 0.8855 (tp) REVERT: J 697 MET cc_start: 0.8463 (ttp) cc_final: 0.8108 (ttp) REVERT: J 747 MET cc_start: 0.7968 (mmt) cc_final: 0.7660 (mmm) REVERT: J 781 LYS cc_start: 0.9162 (tppt) cc_final: 0.8946 (tppt) REVERT: K 30 MET cc_start: 0.8296 (tmm) cc_final: 0.7997 (tmm) REVERT: K 52 ARG cc_start: 0.7420 (ptp90) cc_final: 0.7049 (ptp-170) outliers start: 89 outliers final: 61 residues processed: 454 average time/residue: 0.1988 time to fit residues: 152.5672 Evaluate side-chains 429 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 361 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 931 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 256 optimal weight: 8.9990 chunk 326 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 410 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 347 optimal weight: 5.9990 chunk 418 optimal weight: 0.0370 chunk 378 optimal weight: 7.9990 overall best weight: 4.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 ASN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS J 489 ASN ** J 771 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 = 0.3838 r_free = 0.3838 target = 0.103272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085514 restraints weight = 153870.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.087109 restraints weight = 99240.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.087672 restraints weight = 65221.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.088089 restraints weight = 53941.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.088064 restraints weight = 50960.512| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36880 Z= 0.234 Angle : 0.740 12.473 50362 Z= 0.374 Chirality : 0.045 0.270 5744 Planarity : 0.005 0.055 6194 Dihedral : 15.941 174.924 5986 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.76 % Rotamer: Outliers : 2.82 % Allowed : 20.75 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -1.44 (0.13), residues: 4294 helix: 0.08 (0.13), residues: 1524 sheet: -0.98 (0.22), residues: 599 loop : -1.72 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 67 TYR 0.018 0.002 TYR I1305 PHE 0.034 0.002 PHE A 972 TRP 0.052 0.002 TRP J1193 HIS 0.013 0.002 HIS A 948 Details of bonding type rmsd covalent geometry : bond 0.00520 (36873) covalent geometry : angle 0.73840 (50356) hydrogen bonds : bond 0.04417 ( 1477) hydrogen bonds : angle 5.19922 ( 4089) metal coordination : bond 0.01329 ( 7) metal coordination : angle 3.99377 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 359 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ASP cc_start: 0.7551 (t0) cc_final: 0.7253 (t0) REVERT: A 410 GLN cc_start: 0.6481 (mm110) cc_final: 0.6049 (mm-40) REVERT: A 426 MET cc_start: 0.5473 (tpt) cc_final: 0.5251 (tpp) REVERT: A 496 MET cc_start: 0.8284 (tpp) cc_final: 0.8060 (tpp) REVERT: A 571 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7729 (mm) REVERT: A 858 HIS cc_start: 0.5950 (OUTLIER) cc_final: 0.5544 (t-90) REVERT: A 1008 MET cc_start: 0.6016 (mmp) cc_final: 0.5813 (mmp) REVERT: G 193 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6992 (pm20) REVERT: G 204 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: H 193 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: I 130 MET cc_start: 0.9305 (ttm) cc_final: 0.8745 (ttm) REVERT: I 386 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.4928 (mp0) REVERT: I 524 ILE cc_start: 0.9614 (tp) cc_final: 0.9204 (tp) REVERT: I 1328 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8808 (mppt) REVERT: J 29 MET cc_start: 0.8070 (tpt) cc_final: 0.7383 (tpp) REVERT: J 155 GLU cc_start: 0.6583 (pp20) cc_final: 0.6207 (pp20) REVERT: J 264 ASP cc_start: 0.8194 (t0) cc_final: 0.7726 (t70) REVERT: J 297 ARG cc_start: 0.8408 (ttp80) cc_final: 0.7373 (tmm-80) REVERT: J 330 MET cc_start: 0.8586 (mtm) cc_final: 0.7651 (mtm) REVERT: J 347 VAL cc_start: 0.9384 (t) cc_final: 0.9128 (m) REVERT: J 418 GLU cc_start: 0.7653 (mp0) cc_final: 0.7094 (mp0) REVERT: J 479 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7427 (mt-10) REVERT: J 512 TYR cc_start: 0.8994 (t80) cc_final: 0.8333 (t80) REVERT: J 697 MET cc_start: 0.8551 (ttp) cc_final: 0.8211 (ttp) REVERT: J 725 MET cc_start: 0.8444 (mtm) cc_final: 0.8034 (mtp) REVERT: J 781 LYS cc_start: 0.9177 (tppt) cc_final: 0.8928 (tppt) REVERT: J 1048 ARG cc_start: 0.6698 (tpt170) cc_final: 0.6167 (tpt90) REVERT: J 1327 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: K 8 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6978 (p0) REVERT: K 30 MET cc_start: 0.8382 (tmm) cc_final: 0.8050 (tmm) REVERT: K 52 ARG cc_start: 0.7551 (ptp90) cc_final: 0.7167 (ptp-170) outliers start: 102 outliers final: 80 residues processed: 428 average time/residue: 0.2015 time to fit residues: 145.5463 Evaluate side-chains 433 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 344 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 931 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 669 GLN Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 54 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 409 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 363 optimal weight: 0.8980 chunk 178 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 391 optimal weight: 7.9990 chunk 340 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 235 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS I1257 GLN J 489 ASN ** J 771 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 = 0.3887 r_free = 0.3887 target = 0.106396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.088382 restraints weight = 151645.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.089904 restraints weight = 90936.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.090843 restraints weight = 64684.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091126 restraints weight = 51989.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.091508 restraints weight = 47000.373| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36880 Z= 0.140 Angle : 0.693 13.148 50362 Z= 0.347 Chirality : 0.044 0.338 5744 Planarity : 0.004 0.054 6194 Dihedral : 15.830 175.433 5986 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.24 % Favored : 93.74 % Rotamer: Outliers : 2.19 % Allowed : 21.36 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -1.34 (0.13), residues: 4294 helix: 0.17 (0.13), residues: 1537 sheet: -0.99 (0.22), residues: 591 loop : -1.65 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 69 TYR 0.018 0.001 TYR J 772 PHE 0.039 0.001 PHE A 972 TRP 0.038 0.002 TRP J1193 HIS 0.009 0.001 HIS A 948 Details of bonding type rmsd covalent geometry : bond 0.00314 (36873) covalent geometry : angle 0.69194 (50356) hydrogen bonds : bond 0.03884 ( 1477) hydrogen bonds : angle 4.99800 ( 4089) metal coordination : bond 0.00721 ( 7) metal coordination : angle 3.44376 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 371 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.4271 (mmt) cc_final: 0.3735 (mpp) REVERT: A 382 ASP cc_start: 0.7219 (t0) cc_final: 0.6859 (t0) REVERT: A 410 GLN cc_start: 0.6105 (mm110) cc_final: 0.5878 (mm-40) REVERT: A 426 MET cc_start: 0.5071 (tpt) cc_final: 0.4860 (tpp) REVERT: A 496 MET cc_start: 0.8275 (tpp) cc_final: 0.8043 (tpp) REVERT: A 571 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7497 (mm) REVERT: A 802 ILE cc_start: 0.8304 (mt) cc_final: 0.8042 (mm) REVERT: A 858 HIS cc_start: 0.5574 (OUTLIER) cc_final: 0.5197 (t-90) REVERT: G 204 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: H 177 TYR cc_start: 0.8489 (m-80) cc_final: 0.7933 (m-80) REVERT: H 185 TYR cc_start: 0.8592 (p90) cc_final: 0.8284 (p90) REVERT: H 186 ASN cc_start: 0.7990 (t0) cc_final: 0.7725 (t0) REVERT: H 193 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: I 130 MET cc_start: 0.9276 (ttm) cc_final: 0.8752 (ttm) REVERT: I 386 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5639 (mp0) REVERT: I 459 MET cc_start: 0.8441 (mpp) cc_final: 0.8129 (mpp) REVERT: I 524 ILE cc_start: 0.9616 (tp) cc_final: 0.9184 (tp) REVERT: I 653 MET cc_start: 0.6240 (ttp) cc_final: 0.5680 (ptm) REVERT: I 1064 ASP cc_start: 0.8323 (m-30) cc_final: 0.8045 (m-30) REVERT: I 1114 GLU cc_start: 0.9020 (tt0) cc_final: 0.8774 (tt0) REVERT: I 1328 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8776 (mppt) REVERT: J 29 MET cc_start: 0.7768 (tpt) cc_final: 0.7136 (tpp) REVERT: J 155 GLU cc_start: 0.6523 (pp20) cc_final: 0.6252 (pp20) REVERT: J 264 ASP cc_start: 0.7988 (t0) cc_final: 0.7550 (t70) REVERT: J 297 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7330 (tmm-80) REVERT: J 330 MET cc_start: 0.8580 (mtm) cc_final: 0.7735 (mtm) REVERT: J 347 VAL cc_start: 0.9263 (t) cc_final: 0.9009 (m) REVERT: J 418 GLU cc_start: 0.7458 (mp0) cc_final: 0.6947 (mp0) REVERT: J 479 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7364 (mt-10) REVERT: J 697 MET cc_start: 0.8453 (ttp) cc_final: 0.8152 (ttp) REVERT: J 725 MET cc_start: 0.8241 (mtm) cc_final: 0.7963 (mtp) REVERT: J 1048 ARG cc_start: 0.6727 (tpt170) cc_final: 0.6175 (tpt90) REVERT: K 8 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6832 (p0) REVERT: K 30 MET cc_start: 0.8287 (tmm) cc_final: 0.8075 (tmm) REVERT: K 52 ARG cc_start: 0.7379 (ptp90) cc_final: 0.6995 (ptp-170) outliers start: 79 outliers final: 69 residues processed: 423 average time/residue: 0.2002 time to fit residues: 143.5766 Evaluate side-chains 436 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 360 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 931 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 669 GLN Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1080 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 43 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 366 optimal weight: 1.9990 chunk 413 optimal weight: 9.9990 chunk 403 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 chunk 418 optimal weight: 10.0000 chunk 183 optimal weight: 0.0030 chunk 334 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 965 GLN I1116 HIS ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN J 489 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.107069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089569 restraints weight = 151905.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.091330 restraints weight = 91016.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.092446 restraints weight = 58460.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092391 restraints weight = 48487.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.092464 restraints weight = 46667.405| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36880 Z= 0.133 Angle : 0.696 15.481 50362 Z= 0.346 Chirality : 0.044 0.342 5744 Planarity : 0.004 0.055 6194 Dihedral : 15.724 175.014 5986 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.19 % Favored : 93.78 % Rotamer: Outliers : 2.32 % Allowed : 21.47 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.72 % 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: -1.25 (0.13), residues: 4294 helix: 0.24 (0.13), residues: 1547 sheet: -0.93 (0.22), residues: 580 loop : -1.60 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG K 69 TYR 0.016 0.001 TYR H 177 PHE 0.037 0.001 PHE A 972 TRP 0.036 0.002 TRP J1193 HIS 0.008 0.001 HIS A 948 Details of bonding type rmsd covalent geometry : bond 0.00299 (36873) covalent geometry : angle 0.69508 (50356) hydrogen bonds : bond 0.03779 ( 1477) hydrogen bonds : angle 4.89703 ( 4089) metal coordination : bond 0.00633 ( 7) metal coordination : angle 2.95208 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6009.00 seconds wall clock time: 104 minutes 40.31 seconds (6280.31 seconds total)