Starting phenix.real_space_refine on Tue Sep 15 06:31:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x4y_22044/09_2026/6x4y_22044.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x4y_22044/09_2026/6x4y_22044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6x4y_22044/09_2026/6x4y_22044.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x4y_22044/09_2026/6x4y_22044.cif" model { file = "/net/cci-nas-00/data/ceres_data/6x4y_22044/09_2026/6x4y_22044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x4y_22044/09_2026/6x4y_22044.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x4y_22044/09_2026/6x4y_22044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x4y_22044/09_2026/6x4y_22044.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 1.070 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 2 5.21 5 S 142 5.16 5 C 22317 2.51 5 N 6408 2.21 5 O 7103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36088 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8958 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 55, 'TRANS': 1088} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 129 Chain: "G" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1725 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 10373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10373 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} 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: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 991 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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 23172 SG CYS J 70 25.047 95.205 100.651 1.00112.87 S ATOM 23186 SG CYS J 72 24.543 98.644 99.389 1.00118.54 S ATOM 23294 SG CYS J 85 22.368 95.538 98.439 1.00112.26 S ATOM 23318 SG CYS J 88 26.163 95.835 97.250 1.00111.11 S ATOM 28994 SG CYS J 814 52.409 34.517 103.893 1.00 80.10 S ATOM 29559 SG CYS J 888 53.415 38.006 103.635 1.00 70.16 S ATOM 29610 SG CYS J 895 51.934 36.475 107.150 1.00 70.25 S ATOM 29631 SG CYS J 898 55.384 35.597 105.566 1.00 66.00 S Time building chain proxies: 7.20, per 1000 atoms: 0.20 Number of scatterers: 36088 At special positions: 0 Unit cell: (140.4, 196.3, 192.4, 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 142 16.00 P 114 15.00 Mg 2 11.99 O 7103 8.00 N 6408 7.00 C 22317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 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 56 sheets defined 37.7% alpha, 14.6% beta 54 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 48 through 63 removed outlier: 4.431A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.832A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 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 235 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.749A pdb=" N TYR A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 287 through 307 removed outlier: 4.071A pdb=" N GLU A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.850A pdb=" N LEU A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 371 through 381 removed outlier: 3.620A pdb=" N GLU A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 402 removed outlier: 3.573A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.970A 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 445 through 449 removed outlier: 3.563A pdb=" N LEU A 449 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 474 removed outlier: 3.738A pdb=" N ASN A 473 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' 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 550 through 554 removed outlier: 3.524A pdb=" N ARG A 554 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 removed outlier: 3.632A pdb=" N LYS A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 597 removed outlier: 3.714A pdb=" N PHE A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 618 Processing helix chain 'A' and resid 634 through 648 removed outlier: 3.657A pdb=" N ALA A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 688 through 701 removed outlier: 4.231A pdb=" N GLN A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 768 Processing helix chain 'A' and resid 794 through 809 removed outlier: 3.512A pdb=" N ARG A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 833 removed outlier: 3.860A pdb=" N GLU A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 858 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 removed outlier: 3.706A pdb=" N LEU A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 950 removed outlier: 3.557A pdb=" N ALA A 946 " --> pdb=" O GLY A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 988 Processing helix chain 'A' and resid 993 through 1001 removed outlier: 3.624A pdb=" N SER A 999 " --> pdb=" O GLU A 995 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A1000 " --> pdb=" O ASP A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1033 removed outlier: 3.669A pdb=" N ARG A1023 " --> pdb=" O ASP A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1051 Processing helix chain 'A' and resid 1054 through 1074 removed outlier: 3.860A 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 1146 removed outlier: 4.216A pdb=" N GLU A1144 " --> pdb=" O ARG A1140 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.861A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 35 through 50 removed outlier: 3.859A pdb=" N ASN H 41 " --> pdb=" O HIS H 37 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.552A pdb=" N ASP H 114 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE H 115 " --> pdb=" O ALA H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 115' Processing helix chain 'H' and resid 212 through 226 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.731A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.518A pdb=" N LEU I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.715A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 292 Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 347 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.692A pdb=" N ALA I 381 " --> pdb=" O THR I 377 " (cutoff:3.500A) removed outlier: 3.794A 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 removed outlier: 3.785A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.828A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL I 471 " --> pdb=" O GLY I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 removed outlier: 4.392A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.636A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 613 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 676 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 862 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 987 through 991 Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.451A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.472A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.524A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.717A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.689A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (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 removed outlier: 3.526A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1280 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.516A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 4.031A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.568A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.774A pdb=" N HIS J 80 " --> pdb=" O ARG J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 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 181 through 191 Processing helix chain 'J' and resid 193 through 207 removed outlier: 4.506A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 230 removed outlier: 4.329A pdb=" N LYS J 219 " --> pdb=" O LYS J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.794A 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 327 through 331 removed outlier: 3.539A 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 394 through 404 Processing helix chain 'J' and resid 407 through 416 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 453 through 458 Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.828A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 removed outlier: 3.624A pdb=" N ALA J 533 " --> pdb=" O GLY J 529 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.887A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.602A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.512A pdb=" N SER J 670 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.021A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 removed outlier: 3.506A pdb=" N SER J 728 " --> pdb=" O MET J 724 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.508A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 805 removed outlier: 4.058A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.634A 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: 3.606A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN J1235 " --> pdb=" O ARG J1231 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (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: 4.080A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.646A pdb=" N ILE J1287 " --> pdb=" O SER J1283 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU J1293 " --> pdb=" O ASN J1289 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.740A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA J1338 " --> pdb=" O GLU J1334 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1354 Processing helix chain 'J' and resid 1360 through 1373 removed outlier: 4.350A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG J1373 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.814A 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 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 69 removed outlier: 6.927A pdb=" N MET A 68 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 42 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL A 108 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 44 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A 285 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A 282 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU A 339 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN A 284 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.016A 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: 6.104A pdb=" N ARG A 151 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR A 164 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.792A pdb=" N VAL A 194 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.320A pdb=" N VAL A 385 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLN A 410 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 531 removed outlier: 3.507A pdb=" N ARG A 492 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N MET A 510 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET A 496 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR A 508 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 498 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 506 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 521 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU I 67 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 624 through 625 Processing sheet with id=AA8, first strand: chain 'A' and resid 652 through 655 Processing sheet with id=AA9, first strand: chain 'A' and resid 680 through 683 removed outlier: 6.025A pdb=" N GLU A 681 " --> pdb=" O ILE A 708 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 787 through 792 removed outlier: 6.902A pdb=" N LYS A 787 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU A 914 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE A 789 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR A 916 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG A 791 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 812 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N CYS A 867 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N TYR A 814 " --> pdb=" O CYS A 867 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1003 through 1005 removed outlier: 5.758A pdb=" N GLU A1003 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY A1080 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU A1005 " --> pdb=" O GLY A1080 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 12 through 17 removed outlier: 4.980A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AB5, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.685A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AB7, first strand: chain 'G' and resid 108 through 110 removed outlier: 3.541A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 16 through 18 Processing sheet with id=AB9, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.434A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AC2, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AC3, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.510A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AC5, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.445A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AC7, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.472A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 154 through 159 removed outlier: 6.569A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE I 188 " --> pdb=" O TYR I 172 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 284 through 285 removed outlier: 4.190A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.903A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.792A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.284A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AD5, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AD6, first strand: chain 'I' and resid 716 through 717 Processing sheet with id=AD7, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.785A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.511A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.306A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 8.060A pdb=" N ARG I1223 " --> pdb=" O LEU I1212 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU I1212 " --> pdb=" O ARG I1223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.966A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.522A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.528A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.693A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AE7, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AE8, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.433A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL J 244 " --> pdb=" O GLY J 103 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AF1, first strand: chain 'J' and resid 317 through 319 removed outlier: 4.530A pdb=" N SER J 319 " --> pdb=" O ARG J 322 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.558A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AF4, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.711A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 949 through 951 removed outlier: 7.056A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL J1017 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 991 through 996 removed outlier: 6.541A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF8, first strand: chain 'J' and resid 1034 through 1036 Processing sheet with id=AF9, first strand: chain 'J' and resid 1046 through 1047 removed outlier: 3.675A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AG2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.181A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1356 hydrogen bonds defined for protein. 3762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 10.27 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6061 1.31 - 1.44: 9473 1.44 - 1.57: 20900 1.57 - 1.69: 225 1.69 - 1.82: 249 Bond restraints: 36908 Sorted by residual: bond pdb=" C VAL A 786 " pdb=" O VAL A 786 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.12e-02 7.97e+03 1.76e+01 bond pdb=" C3' DG P 3 " pdb=" C2' DG P 3 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" N ARG A 783 " pdb=" CA ARG A 783 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" C4' DG P 34 " pdb=" C3' DG P 34 " ideal model delta sigma weight residual 1.529 1.496 0.033 1.00e-02 1.00e+04 1.10e+01 bond pdb=" N MET I 488 " pdb=" CA MET I 488 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.04e-02 9.25e+03 1.05e+01 ... (remaining 36903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 49883 3.62 - 7.23: 471 7.23 - 10.85: 37 10.85 - 14.46: 7 14.46 - 18.08: 2 Bond angle restraints: 50400 Sorted by residual: angle pdb=" N SER J 210 " pdb=" CA SER J 210 " pdb=" C SER J 210 " ideal model delta sigma weight residual 112.68 100.70 11.98 1.33e+00 5.65e-01 8.11e+01 angle pdb=" N ILE I 292 " pdb=" CA ILE I 292 " pdb=" C ILE I 292 " ideal model delta sigma weight residual 113.71 106.26 7.45 9.50e-01 1.11e+00 6.15e+01 angle pdb=" N THR J 212 " pdb=" CA THR J 212 " pdb=" C THR J 212 " ideal model delta sigma weight residual 114.64 104.51 10.13 1.52e+00 4.33e-01 4.44e+01 angle pdb=" N VAL J 839 " pdb=" CA VAL J 839 " pdb=" C VAL J 839 " ideal model delta sigma weight residual 111.88 105.29 6.59 1.06e+00 8.90e-01 3.87e+01 angle pdb=" CB MET A 639 " pdb=" CG MET A 639 " pdb=" SD MET A 639 " ideal model delta sigma weight residual 112.70 94.62 18.08 3.00e+00 1.11e-01 3.63e+01 ... (remaining 50395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.31: 20551 25.31 - 50.62: 1484 50.62 - 75.93: 240 75.93 - 101.23: 22 101.23 - 126.54: 2 Dihedral angle restraints: 22299 sinusoidal: 9870 harmonic: 12429 Sorted by residual: dihedral pdb=" O5' C R 11 " pdb=" C5' C R 11 " pdb=" C4' C R 11 " pdb=" C3' C R 11 " ideal model delta sinusoidal sigma weight residual 180.00 136.87 43.13 3 6.40e+00 2.44e-02 4.26e+01 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 62.21 -122.21 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" CA ARG J 47 " pdb=" C ARG J 47 " pdb=" N THR J 48 " pdb=" CA THR J 48 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 22296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5218 0.094 - 0.189: 489 0.189 - 0.283: 33 0.283 - 0.378: 6 0.378 - 0.472: 1 Chirality restraints: 5747 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 2.17 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CB ILE A 444 " pdb=" CA ILE A 444 " pdb=" CG1 ILE A 444 " pdb=" CG2 ILE A 444 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR J 553 " pdb=" CA THR J 553 " pdb=" OG1 THR J 553 " pdb=" CG2 THR J 553 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 5744 not shown) Planarity restraints: 6199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 464 " -0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C THR A 464 " 0.071 2.00e-02 2.50e+03 pdb=" O THR A 464 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE A 465 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 211 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C GLU J 211 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU J 211 " 0.020 2.00e-02 2.50e+03 pdb=" N THR J 212 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 98 " 0.049 5.00e-02 4.00e+02 7.37e-02 8.68e+00 pdb=" N PRO A 99 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.041 5.00e-02 4.00e+02 ... (remaining 6196 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 255 2.51 - 3.11: 25907 3.11 - 3.71: 57185 3.71 - 4.30: 78161 4.30 - 4.90: 129343 Nonbonded interactions: 290851 Sorted by model distance: nonbonded pdb=" OD1 ASP H 15 " pdb=" OG1 THR H 27 " model vdw 1.919 3.040 nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.008 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.042 2.170 nonbonded pdb=" O ARG H 45 " pdb=" OG SER H 49 " model vdw 2.184 3.040 ... (remaining 290846 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 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: 1.780 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 42.330 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.006 0.068 36916 Z= 0.344 Angle : 0.982 18.080 50412 Z= 0.582 Chirality : 0.057 0.472 5747 Planarity : 0.006 0.074 6199 Dihedral : 16.765 126.543 14287 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.06 % Favored : 91.59 % Rotamer: Outliers : 0.28 % Allowed : 0.52 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.60 (0.12), residues: 4294 helix: -0.97 (0.12), residues: 1507 sheet: -1.81 (0.20), residues: 618 loop : -2.25 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 33 TYR 0.037 0.002 TYR G 177 PHE 0.032 0.002 PHE I 186 TRP 0.049 0.003 TRP J 115 HIS 0.013 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.34 (36908) covalent geometry : angle 0.97589 / 0.58 (50400) hydrogen bonds : bond 0.14367 / 10.14 ( 1487) hydrogen bonds : angle 6.65226 / 4.66 ( 4040) metal coordination : bond 0.01352 / 0.69 ( 8) metal coordination : angle 7.28034 / 4.40 ( 12) *********************** 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 484 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 474 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7623 (tmm) cc_final: 0.7015 (tmm) REVERT: A 242 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 629 ASP cc_start: 0.6824 (t0) cc_final: 0.6364 (t0) REVERT: A 800 GLU cc_start: 0.7897 (pp20) cc_final: 0.7696 (pp20) REVERT: A 811 GLN cc_start: 0.8740 (mp10) cc_final: 0.8499 (mp10) REVERT: A 879 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7215 (p) REVERT: H 125 LYS cc_start: 0.7960 (tptm) cc_final: 0.7706 (tttp) REVERT: H 131 CYS cc_start: 0.8813 (m) cc_final: 0.8510 (m) REVERT: I 459 MET cc_start: 0.8915 (mtm) cc_final: 0.8696 (mtp) REVERT: I 488 MET cc_start: 0.8010 (mmm) cc_final: 0.6588 (mmm) REVERT: I 492 MET cc_start: 0.7697 (pmm) cc_final: 0.7411 (pmm) REVERT: I 955 GLN cc_start: 0.7955 (tp-100) cc_final: 0.7207 (tp40) REVERT: I 959 ASP cc_start: 0.7962 (m-30) cc_final: 0.7645 (m-30) REVERT: I 1264 GLN cc_start: 0.8141 (mp-120) cc_final: 0.7905 (mp10) REVERT: J 117 LEU cc_start: 0.9071 (tp) cc_final: 0.8831 (tp) REVERT: J 129 ASP cc_start: 0.7682 (t70) cc_final: 0.7459 (t0) REVERT: J 133 ARG cc_start: 0.7533 (mtt180) cc_final: 0.7305 (mtt180) REVERT: J 698 MET cc_start: 0.9055 (tpt) cc_final: 0.8784 (mmt) REVERT: J 1334 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 10 outliers final: 5 residues processed: 480 average time/residue: 0.2305 time to fit residues: 181.4517 Evaluate side-chains 383 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 377 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain J residue 210 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN A 895 GLN H 227 GLN I 273 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.126198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092581 restraints weight = 70208.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093287 restraints weight = 39610.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093396 restraints weight = 30891.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094471 restraints weight = 27143.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094496 restraints weight = 23376.557| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36916 Z= 0.230 Angle : 0.717 14.160 50412 Z= 0.374 Chirality : 0.047 0.427 5747 Planarity : 0.005 0.058 6199 Dihedral : 15.279 124.333 5968 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer: Outliers : 0.75 % Allowed : 8.92 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.11 (0.12), residues: 4294 helix: -0.36 (0.13), residues: 1519 sheet: -1.72 (0.20), residues: 643 loop : -2.08 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 783 TYR 0.019 0.002 TYR A 259 PHE 0.018 0.002 PHE A 857 TRP 0.013 0.001 TRP J 115 HIS 0.010 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (36908) covalent geometry : angle 0.70826 / 0.37 (50400) hydrogen bonds : bond 0.04865 / 3.28 ( 1487) hydrogen bonds : angle 5.30182 / 3.70 ( 4040) metal coordination : bond 0.01402 / 0.71 ( 8) metal coordination : angle 7.17486 / 4.20 ( 12) *********************** 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 434 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 407 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7571 (tm-30) REVERT: A 629 ASP cc_start: 0.6636 (t0) cc_final: 0.6170 (t0) REVERT: A 800 GLU cc_start: 0.8140 (pp20) cc_final: 0.7789 (pp20) REVERT: A 811 GLN cc_start: 0.8880 (mp10) cc_final: 0.8564 (mp10) REVERT: A 879 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7640 (p) REVERT: A 925 ASP cc_start: 0.8106 (t70) cc_final: 0.7887 (t70) REVERT: H 75 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8016 (tm-30) REVERT: H 125 LYS cc_start: 0.7930 (tptm) cc_final: 0.7694 (tttp) REVERT: H 131 CYS cc_start: 0.8823 (m) cc_final: 0.8510 (m) REVERT: I 370 MET cc_start: 0.8920 (mmm) cc_final: 0.8648 (mmm) REVERT: I 396 ASP cc_start: 0.8663 (t0) cc_final: 0.8251 (t0) REVERT: I 488 MET cc_start: 0.7988 (mmm) cc_final: 0.7096 (mmm) REVERT: I 496 LYS cc_start: 0.8764 (tmtt) cc_final: 0.8475 (tptp) REVERT: I 515 MET cc_start: 0.8759 (ttp) cc_final: 0.8558 (ttp) REVERT: I 955 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7341 (tp40) REVERT: I 959 ASP cc_start: 0.7945 (m-30) cc_final: 0.7486 (m-30) REVERT: I 1264 GLN cc_start: 0.8036 (mp-120) cc_final: 0.7704 (mp10) REVERT: J 86 GLU cc_start: 0.8215 (mp0) cc_final: 0.8007 (mp0) REVERT: J 129 ASP cc_start: 0.7770 (t70) cc_final: 0.7485 (t0) REVERT: J 215 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7517 (mmtm) REVERT: J 264 ASP cc_start: 0.8057 (m-30) cc_final: 0.7804 (m-30) REVERT: J 402 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7726 (tm-30) REVERT: J 404 GLU cc_start: 0.7935 (mp0) cc_final: 0.7691 (mp0) REVERT: J 500 ILE cc_start: 0.9084 (mm) cc_final: 0.8718 (pt) REVERT: J 698 MET cc_start: 0.8911 (tpt) cc_final: 0.8594 (mmt) REVERT: J 918 ILE cc_start: 0.8803 (pt) cc_final: 0.8555 (mt) REVERT: J 1284 ARG cc_start: 0.8126 (mmt180) cc_final: 0.7801 (mmt180) REVERT: J 1334 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7501 (tm-30) REVERT: K 71 GLU cc_start: 0.7926 (tt0) cc_final: 0.7378 (tm-30) outliers start: 27 outliers final: 20 residues processed: 421 average time/residue: 0.2212 time to fit residues: 154.4694 Evaluate side-chains 392 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 371 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 1352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 283 optimal weight: 0.8980 chunk 400 optimal weight: 20.0000 chunk 401 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 330 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN I 273 HIS I 618 GLN I 761 GLN I1268 GLN J 424 ASN ** K 31 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 = 0.3750 r_free = 0.3750 target = 0.128358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.094483 restraints weight = 70434.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095153 restraints weight = 40319.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095263 restraints weight = 31311.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097338 restraints weight = 27656.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097205 restraints weight = 21789.650| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 36916 Z= 0.142 Angle : 0.631 12.387 50412 Z= 0.327 Chirality : 0.045 0.389 5747 Planarity : 0.004 0.055 6199 Dihedral : 15.042 121.890 5967 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.08 % Favored : 92.80 % Rotamer: Outliers : 1.32 % Allowed : 11.92 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.73 (0.12), residues: 4294 helix: 0.02 (0.13), residues: 1511 sheet: -1.44 (0.21), residues: 633 loop : -1.93 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1067 TYR 0.016 0.001 TYR A 259 PHE 0.021 0.001 PHE A 377 TRP 0.010 0.001 TRP J 115 HIS 0.011 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (36908) covalent geometry : angle 0.62347 / 0.33 (50400) hydrogen bonds : bond 0.04141 / 2.78 ( 1487) hydrogen bonds : angle 4.88508 / 3.41 ( 4040) metal coordination : bond 0.01117 / 0.55 ( 8) metal coordination : angle 6.28169 / 3.69 ( 12) *********************** 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 479 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 431 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8178 (pmm) cc_final: 0.7858 (pmm) REVERT: A 242 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 629 ASP cc_start: 0.6350 (t0) cc_final: 0.5946 (t0) REVERT: A 710 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9161 (m) REVERT: A 800 GLU cc_start: 0.8131 (pp20) cc_final: 0.7688 (pp20) REVERT: A 805 GLU cc_start: 0.8651 (tp30) cc_final: 0.8442 (tp30) REVERT: A 811 GLN cc_start: 0.8797 (mp10) cc_final: 0.8443 (mp10) REVERT: A 879 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7648 (p) REVERT: A 925 ASP cc_start: 0.8092 (t70) cc_final: 0.7792 (t0) REVERT: H 18 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8368 (mm-40) REVERT: H 75 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7919 (tm-30) REVERT: H 125 LYS cc_start: 0.7741 (tptm) cc_final: 0.7525 (tttp) REVERT: H 131 CYS cc_start: 0.8704 (m) cc_final: 0.8429 (m) REVERT: I 5 TYR cc_start: 0.7680 (t80) cc_final: 0.7234 (t80) REVERT: I 200 ARG cc_start: 0.7912 (mtt-85) cc_final: 0.7472 (mtt-85) REVERT: I 396 ASP cc_start: 0.8639 (t0) cc_final: 0.7513 (p0) REVERT: I 477 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8521 (tm-30) REVERT: I 492 MET cc_start: 0.7447 (pmm) cc_final: 0.7196 (pmm) REVERT: I 496 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8531 (tptt) REVERT: I 515 MET cc_start: 0.8833 (ttp) cc_final: 0.8596 (ttp) REVERT: I 681 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7085 (mtt) REVERT: I 955 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7352 (tp40) REVERT: I 959 ASP cc_start: 0.8024 (m-30) cc_final: 0.7636 (m-30) REVERT: J 129 ASP cc_start: 0.7595 (t70) cc_final: 0.7370 (t0) REVERT: J 215 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7483 (mmtm) REVERT: J 264 ASP cc_start: 0.7926 (m-30) cc_final: 0.7637 (m-30) REVERT: J 372 MET cc_start: 0.8591 (mtp) cc_final: 0.8256 (mtp) REVERT: J 500 ILE cc_start: 0.9068 (mm) cc_final: 0.8755 (pt) REVERT: J 698 MET cc_start: 0.8977 (tpt) cc_final: 0.8635 (mmt) REVERT: J 806 ASP cc_start: 0.8412 (p0) cc_final: 0.8201 (p0) REVERT: J 1284 ARG cc_start: 0.8097 (mmt180) cc_final: 0.7840 (mmt180) REVERT: J 1334 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7416 (tm-30) outliers start: 48 outliers final: 28 residues processed: 454 average time/residue: 0.2172 time to fit residues: 165.5704 Evaluate side-chains 412 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 381 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 123 optimal weight: 6.9990 chunk 253 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 368 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 293 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 301 optimal weight: 8.9990 chunk 419 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN I 273 HIS ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.126886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093224 restraints weight = 69893.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.094558 restraints weight = 40022.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.094606 restraints weight = 29172.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095253 restraints weight = 25609.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095318 restraints weight = 23170.551| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36916 Z= 0.187 Angle : 0.644 12.814 50412 Z= 0.331 Chirality : 0.045 0.388 5747 Planarity : 0.004 0.051 6199 Dihedral : 14.988 122.696 5963 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.69 % Favored : 92.22 % Rotamer: Outliers : 1.82 % Allowed : 14.68 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.61 (0.13), residues: 4294 helix: 0.18 (0.13), residues: 1509 sheet: -1.46 (0.21), residues: 635 loop : -1.88 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 166 TYR 0.017 0.001 TYR A 259 PHE 0.019 0.001 PHE A 377 TRP 0.008 0.001 TRP J1193 HIS 0.007 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (36908) covalent geometry : angle 0.63674 / 0.33 (50400) hydrogen bonds : bond 0.04083 / 2.74 ( 1487) hydrogen bonds : angle 4.78925 / 3.34 ( 4040) metal coordination : bond 0.01138 / 0.58 ( 8) metal coordination : angle 6.26226 / 3.63 ( 12) *********************** 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 457 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 391 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 622 MET cc_start: 0.7338 (tpp) cc_final: 0.7106 (tpp) REVERT: A 629 ASP cc_start: 0.6388 (t0) cc_final: 0.5983 (t0) REVERT: A 800 GLU cc_start: 0.8164 (pp20) cc_final: 0.7704 (pp20) REVERT: A 925 ASP cc_start: 0.8165 (t70) cc_final: 0.7852 (t0) REVERT: A 1067 ARG cc_start: 0.7653 (ptm160) cc_final: 0.7434 (ptm160) REVERT: H 18 GLN cc_start: 0.8855 (tp-100) cc_final: 0.8527 (mm-40) REVERT: H 66 HIS cc_start: 0.7705 (t-90) cc_final: 0.7190 (t-90) REVERT: H 75 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7919 (tm-30) REVERT: I 5 TYR cc_start: 0.7431 (t80) cc_final: 0.6967 (t80) REVERT: I 396 ASP cc_start: 0.8654 (t0) cc_final: 0.7543 (p0) REVERT: I 477 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8485 (tm-30) REVERT: I 496 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8536 (tptt) REVERT: I 955 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7355 (tp40) REVERT: I 959 ASP cc_start: 0.7970 (m-30) cc_final: 0.7624 (m-30) REVERT: J 42 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7184 (pm20) REVERT: J 129 ASP cc_start: 0.7609 (t70) cc_final: 0.7326 (t0) REVERT: J 264 ASP cc_start: 0.7986 (m-30) cc_final: 0.7625 (m-30) REVERT: J 372 MET cc_start: 0.8720 (mtp) cc_final: 0.8385 (mtp) REVERT: J 478 LEU cc_start: 0.9270 (mt) cc_final: 0.9064 (mt) REVERT: J 500 ILE cc_start: 0.9073 (mm) cc_final: 0.8759 (pt) REVERT: J 698 MET cc_start: 0.8987 (tpt) cc_final: 0.8621 (mmt) REVERT: J 788 LEU cc_start: 0.8471 (mp) cc_final: 0.8196 (mp) REVERT: J 806 ASP cc_start: 0.8489 (p0) cc_final: 0.8266 (p0) REVERT: J 1284 ARG cc_start: 0.8109 (mmt180) cc_final: 0.7760 (mmt90) REVERT: J 1334 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7443 (tm-30) outliers start: 66 outliers final: 47 residues processed: 433 average time/residue: 0.2202 time to fit residues: 160.5820 Evaluate side-chains 422 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 374 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 200 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 HIS I 618 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093680 restraints weight = 70206.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094974 restraints weight = 40168.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095174 restraints weight = 29624.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095446 restraints weight = 25756.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.095621 restraints weight = 23943.265| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36916 Z= 0.178 Angle : 0.633 12.579 50412 Z= 0.325 Chirality : 0.044 0.388 5747 Planarity : 0.004 0.050 6199 Dihedral : 14.920 122.314 5959 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.27 % Favored : 92.64 % Rotamer: Outliers : 2.13 % Allowed : 15.46 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.13), residues: 4294 helix: 0.25 (0.13), residues: 1519 sheet: -1.38 (0.21), residues: 647 loop : -1.87 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 782 TYR 0.017 0.001 TYR J 679 PHE 0.020 0.001 PHE A 377 TRP 0.008 0.001 TRP J1193 HIS 0.007 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (36908) covalent geometry : angle 0.62609 / 0.32 (50400) hydrogen bonds : bond 0.03971 / 2.65 ( 1487) hydrogen bonds : angle 4.70052 / 3.28 ( 4040) metal coordination : bond 0.01102 / 0.56 ( 8) metal coordination : angle 6.03694 / 3.51 ( 12) *********************** 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 469 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 392 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8132 (tmm) cc_final: 0.7787 (tmm) REVERT: A 242 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 622 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.7038 (tpp) REVERT: A 629 ASP cc_start: 0.6517 (t0) cc_final: 0.6190 (t0) REVERT: A 710 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9176 (m) REVERT: A 800 GLU cc_start: 0.8172 (pp20) cc_final: 0.7803 (pp20) REVERT: A 827 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: A 925 ASP cc_start: 0.8180 (t70) cc_final: 0.7812 (t0) REVERT: A 1067 ARG cc_start: 0.7780 (ptm160) cc_final: 0.7503 (ptm160) REVERT: H 18 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8584 (mm-40) REVERT: H 66 HIS cc_start: 0.7897 (t-90) cc_final: 0.7334 (t-90) REVERT: H 75 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7909 (tm-30) REVERT: I 5 TYR cc_start: 0.7371 (t80) cc_final: 0.6908 (t80) REVERT: I 315 MET cc_start: 0.7374 (tpp) cc_final: 0.7081 (tpp) REVERT: I 396 ASP cc_start: 0.8635 (t0) cc_final: 0.7550 (p0) REVERT: I 477 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8427 (tm-30) REVERT: I 492 MET cc_start: 0.7347 (pmm) cc_final: 0.6955 (pmm) REVERT: I 496 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8535 (tptt) REVERT: I 704 MET cc_start: 0.8602 (tpt) cc_final: 0.8286 (tpp) REVERT: I 955 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7433 (tp40) REVERT: I 959 ASP cc_start: 0.7980 (m-30) cc_final: 0.7634 (m-30) REVERT: I 962 GLU cc_start: 0.4375 (tp30) cc_final: 0.4053 (tp30) REVERT: I 1290 MET cc_start: 0.8907 (mmm) cc_final: 0.8322 (mmt) REVERT: J 42 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: J 129 ASP cc_start: 0.7507 (t70) cc_final: 0.7217 (t0) REVERT: J 180 MET cc_start: 0.7990 (ttm) cc_final: 0.7734 (ttm) REVERT: J 264 ASP cc_start: 0.7925 (m-30) cc_final: 0.7525 (m-30) REVERT: J 372 MET cc_start: 0.8733 (mtp) cc_final: 0.8370 (mtp) REVERT: J 500 ILE cc_start: 0.9068 (mm) cc_final: 0.8739 (pt) REVERT: J 625 MET cc_start: 0.8587 (ttp) cc_final: 0.8194 (ttp) REVERT: J 698 MET cc_start: 0.8963 (tpt) cc_final: 0.8583 (mmt) REVERT: J 806 ASP cc_start: 0.8490 (p0) cc_final: 0.8265 (p0) REVERT: J 1259 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8794 (mm-40) REVERT: K 61 ASN cc_start: 0.8075 (t0) cc_final: 0.7843 (t0) outliers start: 77 outliers final: 55 residues processed: 445 average time/residue: 0.2122 time to fit residues: 159.4304 Evaluate side-chains 432 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 373 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 50 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 427 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 290 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN A 895 GLN I 31 GLN J1289 ASN ** K 31 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 = 0.3741 r_free = 0.3741 target = 0.127663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.093428 restraints weight = 69840.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.093207 restraints weight = 40649.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093979 restraints weight = 28926.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094308 restraints weight = 24398.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094431 restraints weight = 22837.143| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36916 Z= 0.146 Angle : 0.614 12.504 50412 Z= 0.314 Chirality : 0.044 0.392 5747 Planarity : 0.004 0.051 6199 Dihedral : 14.812 121.896 5959 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.92 % Favored : 92.99 % Rotamer: Outliers : 2.32 % Allowed : 16.20 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.41 (0.13), residues: 4294 helix: 0.38 (0.13), residues: 1521 sheet: -1.33 (0.21), residues: 648 loop : -1.79 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 47 TYR 0.017 0.001 TYR J 679 PHE 0.022 0.001 PHE A 377 TRP 0.010 0.001 TRP J1193 HIS 0.007 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (36908) covalent geometry : angle 0.60823 / 0.31 (50400) hydrogen bonds : bond 0.03778 / 2.53 ( 1487) hydrogen bonds : angle 4.58557 / 3.20 ( 4040) metal coordination : bond 0.01003 / 0.50 ( 8) metal coordination : angle 5.65820 / 3.28 ( 12) *********************** 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 471 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 387 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.8312 (tmm) cc_final: 0.7993 (tmm) REVERT: A 157 MET cc_start: 0.6023 (ptt) cc_final: 0.5703 (ppp) REVERT: A 242 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 311 MET cc_start: 0.7770 (tpp) cc_final: 0.7554 (tpp) REVERT: A 629 ASP cc_start: 0.6601 (t0) cc_final: 0.6273 (t0) REVERT: A 708 ILE cc_start: 0.8998 (mp) cc_final: 0.8754 (mt) REVERT: A 710 THR cc_start: 0.9390 (OUTLIER) cc_final: 0.9167 (m) REVERT: A 800 GLU cc_start: 0.8244 (pp20) cc_final: 0.7839 (pp20) REVERT: A 827 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: A 925 ASP cc_start: 0.8248 (t70) cc_final: 0.7859 (t0) REVERT: A 1067 ARG cc_start: 0.7965 (ptm160) cc_final: 0.7665 (ptm160) REVERT: H 18 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8593 (mm-40) REVERT: H 66 HIS cc_start: 0.7866 (t-90) cc_final: 0.7224 (t-90) REVERT: H 75 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7863 (tm-30) REVERT: I 5 TYR cc_start: 0.7441 (t80) cc_final: 0.6985 (t80) REVERT: I 183 TRP cc_start: 0.8229 (m-10) cc_final: 0.7553 (m-10) REVERT: I 200 ARG cc_start: 0.7777 (mtt-85) cc_final: 0.7548 (mtt-85) REVERT: I 315 MET cc_start: 0.7457 (tpp) cc_final: 0.7152 (tpp) REVERT: I 396 ASP cc_start: 0.8670 (t0) cc_final: 0.7537 (p0) REVERT: I 477 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8370 (tm-30) REVERT: I 492 MET cc_start: 0.7583 (pmm) cc_final: 0.7353 (pmm) REVERT: I 496 LYS cc_start: 0.8716 (tmtt) cc_final: 0.8418 (tptp) REVERT: I 704 MET cc_start: 0.8577 (tpt) cc_final: 0.8215 (tpp) REVERT: I 949 GLU cc_start: 0.8331 (mp0) cc_final: 0.7862 (pm20) REVERT: I 955 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7470 (tp40) REVERT: I 959 ASP cc_start: 0.8057 (m-30) cc_final: 0.7607 (m-30) REVERT: J 42 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: J 117 LEU cc_start: 0.9040 (tp) cc_final: 0.8815 (tp) REVERT: J 129 ASP cc_start: 0.7648 (t70) cc_final: 0.7311 (t0) REVERT: J 225 GLU cc_start: 0.8398 (tp30) cc_final: 0.8188 (tp30) REVERT: J 229 GLN cc_start: 0.8007 (mm110) cc_final: 0.7762 (mm110) REVERT: J 372 MET cc_start: 0.8695 (mtp) cc_final: 0.8328 (mtp) REVERT: J 500 ILE cc_start: 0.9041 (mm) cc_final: 0.8740 (pt) REVERT: J 625 MET cc_start: 0.8593 (ttp) cc_final: 0.8226 (ttp) REVERT: J 667 GLN cc_start: 0.8213 (mt0) cc_final: 0.7871 (mm110) REVERT: J 698 MET cc_start: 0.8991 (tpt) cc_final: 0.8753 (mmt) REVERT: J 806 ASP cc_start: 0.8503 (p0) cc_final: 0.8249 (p0) REVERT: J 1259 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8821 (mm-40) REVERT: K 61 ASN cc_start: 0.8009 (t0) cc_final: 0.7767 (t0) outliers start: 84 outliers final: 61 residues processed: 446 average time/residue: 0.2153 time to fit residues: 161.5679 Evaluate side-chains 433 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 369 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 127 optimal weight: 0.8980 chunk 312 optimal weight: 0.0070 chunk 194 optimal weight: 7.9990 chunk 319 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 426 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 376 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN J 865 HIS ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.094139 restraints weight = 70579.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093999 restraints weight = 43818.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094615 restraints weight = 31744.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095064 restraints weight = 25886.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095229 restraints weight = 23860.795| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36916 Z= 0.154 Angle : 0.617 13.005 50412 Z= 0.315 Chirality : 0.044 0.393 5747 Planarity : 0.004 0.051 6199 Dihedral : 14.713 122.172 5957 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.96 % Favored : 92.94 % Rotamer: Outliers : 2.57 % Allowed : 16.42 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.31 (0.13), residues: 4294 helix: 0.49 (0.13), residues: 1515 sheet: -1.29 (0.21), residues: 641 loop : -1.76 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 47 TYR 0.018 0.001 TYR J 679 PHE 0.022 0.001 PHE A 377 TRP 0.011 0.001 TRP J1193 HIS 0.006 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (36908) covalent geometry : angle 0.61047 / 0.32 (50400) hydrogen bonds : bond 0.03738 / 2.50 ( 1487) hydrogen bonds : angle 4.52914 / 3.16 ( 4040) metal coordination : bond 0.01015 / 0.51 ( 8) metal coordination : angle 5.62447 / 3.25 ( 12) *********************** 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 476 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 383 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8672 (mm) REVERT: A 242 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 311 MET cc_start: 0.7733 (tpp) cc_final: 0.7526 (tpp) REVERT: A 622 MET cc_start: 0.7346 (tpp) cc_final: 0.7111 (tpp) REVERT: A 629 ASP cc_start: 0.6563 (t0) cc_final: 0.6270 (t0) REVERT: A 708 ILE cc_start: 0.8981 (mp) cc_final: 0.8756 (mt) REVERT: A 710 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9160 (m) REVERT: A 786 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9167 (p) REVERT: A 800 GLU cc_start: 0.8217 (pp20) cc_final: 0.7790 (pp20) REVERT: A 827 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: A 925 ASP cc_start: 0.8200 (t70) cc_final: 0.7805 (t0) REVERT: A 1067 ARG cc_start: 0.7796 (ptm160) cc_final: 0.7522 (ptm160) REVERT: G 62 ASP cc_start: 0.7276 (p0) cc_final: 0.7010 (p0) REVERT: H 18 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8682 (mm-40) REVERT: H 66 HIS cc_start: 0.7763 (t-90) cc_final: 0.7205 (t-90) REVERT: H 75 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7868 (tm-30) REVERT: I 5 TYR cc_start: 0.7447 (t80) cc_final: 0.7075 (t80) REVERT: I 183 TRP cc_start: 0.8273 (m-10) cc_final: 0.7571 (m-10) REVERT: I 369 MET cc_start: 0.8717 (ppp) cc_final: 0.8495 (ppp) REVERT: I 396 ASP cc_start: 0.8628 (t0) cc_final: 0.7619 (p0) REVERT: I 477 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8356 (tm-30) REVERT: I 488 MET cc_start: 0.7779 (mmm) cc_final: 0.7202 (tpp) REVERT: I 492 MET cc_start: 0.7567 (pmm) cc_final: 0.7313 (pmm) REVERT: I 496 LYS cc_start: 0.8713 (tmtt) cc_final: 0.8416 (tptp) REVERT: I 704 MET cc_start: 0.8581 (tpt) cc_final: 0.8257 (tpp) REVERT: I 949 GLU cc_start: 0.8363 (mp0) cc_final: 0.7926 (pm20) REVERT: I 955 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7379 (tp40) REVERT: I 959 ASP cc_start: 0.7976 (m-30) cc_final: 0.7519 (m-30) REVERT: J 42 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: J 129 ASP cc_start: 0.7523 (t70) cc_final: 0.7198 (t0) REVERT: J 180 MET cc_start: 0.7681 (ttm) cc_final: 0.7142 (ttm) REVERT: J 225 GLU cc_start: 0.8379 (tp30) cc_final: 0.8111 (tp30) REVERT: J 372 MET cc_start: 0.8706 (mtp) cc_final: 0.8328 (mtp) REVERT: J 500 ILE cc_start: 0.9060 (mm) cc_final: 0.8747 (pt) REVERT: J 625 MET cc_start: 0.8574 (ttp) cc_final: 0.8204 (ttp) REVERT: J 667 GLN cc_start: 0.8162 (mt0) cc_final: 0.7887 (mm110) REVERT: J 698 MET cc_start: 0.9027 (tpt) cc_final: 0.8771 (mmt) REVERT: J 777 HIS cc_start: 0.6742 (t-90) cc_final: 0.6310 (t-90) REVERT: J 788 LEU cc_start: 0.8511 (mp) cc_final: 0.8178 (mp) REVERT: J 806 ASP cc_start: 0.8436 (p0) cc_final: 0.8202 (p0) REVERT: J 1259 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8865 (mm-40) REVERT: K 3 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7920 (mmm-85) REVERT: K 11 GLU cc_start: 0.8249 (pt0) cc_final: 0.8019 (pt0) REVERT: K 61 ASN cc_start: 0.8074 (t0) cc_final: 0.7824 (t0) outliers start: 93 outliers final: 72 residues processed: 450 average time/residue: 0.2146 time to fit residues: 161.9870 Evaluate side-chains 447 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 370 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 208 optimal weight: 0.7980 chunk 305 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 227 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 253 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 386 optimal weight: 0.0170 chunk 340 optimal weight: 0.0770 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS I 760 ASN J 365 GLN J 951 GLN ** K 31 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 = 0.3777 r_free = 0.3777 target = 0.130291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096152 restraints weight = 69766.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097699 restraints weight = 39307.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097908 restraints weight = 26787.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098256 restraints weight = 24032.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.098411 restraints weight = 22339.339| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36916 Z= 0.113 Angle : 0.598 12.639 50412 Z= 0.307 Chirality : 0.043 0.403 5747 Planarity : 0.004 0.072 6199 Dihedral : 14.525 120.935 5957 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 2.26 % Allowed : 17.39 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.09 (0.13), residues: 4294 helix: 0.67 (0.14), residues: 1518 sheet: -1.13 (0.21), residues: 615 loop : -1.65 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 200 TYR 0.019 0.001 TYR J 679 PHE 0.026 0.001 PHE A 377 TRP 0.025 0.001 TRP I 183 HIS 0.006 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (36908) covalent geometry : angle 0.59352 / 0.31 (50400) hydrogen bonds : bond 0.03400 / 2.27 ( 1487) hydrogen bonds : angle 4.37137 / 3.06 ( 4040) metal coordination : bond 0.00854 / 0.39 ( 8) metal coordination : angle 4.80525 / 2.78 ( 12) *********************** 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 496 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 414 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8660 (mm) REVERT: A 242 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 629 ASP cc_start: 0.6593 (t0) cc_final: 0.6284 (t0) REVERT: A 710 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9135 (m) REVERT: A 800 GLU cc_start: 0.8185 (pp20) cc_final: 0.7765 (pp20) REVERT: A 805 GLU cc_start: 0.8631 (tp30) cc_final: 0.8179 (tp30) REVERT: A 827 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: A 925 ASP cc_start: 0.8142 (t70) cc_final: 0.7752 (t0) REVERT: H 66 HIS cc_start: 0.7657 (t-90) cc_final: 0.7162 (t-90) REVERT: H 75 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7911 (tm-30) REVERT: H 131 CYS cc_start: 0.8582 (m) cc_final: 0.8300 (m) REVERT: H 227 GLN cc_start: 0.8992 (mm110) cc_final: 0.8678 (mm110) REVERT: I 5 TYR cc_start: 0.7394 (t80) cc_final: 0.7027 (t80) REVERT: I 70 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7377 (t80) REVERT: I 183 TRP cc_start: 0.7717 (m-10) cc_final: 0.7422 (m-10) REVERT: I 396 ASP cc_start: 0.8492 (t0) cc_final: 0.7910 (p0) REVERT: I 496 LYS cc_start: 0.8662 (tmtt) cc_final: 0.8276 (tptp) REVERT: I 704 MET cc_start: 0.8499 (tpt) cc_final: 0.8185 (tpp) REVERT: I 955 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7444 (tp40) REVERT: I 959 ASP cc_start: 0.7911 (m-30) cc_final: 0.7493 (m-30) REVERT: I 1066 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8399 (ptm) REVERT: I 1296 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.7755 (t70) REVERT: J 42 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7145 (pm20) REVERT: J 117 LEU cc_start: 0.8825 (tp) cc_final: 0.8559 (tp) REVERT: J 129 ASP cc_start: 0.7570 (t70) cc_final: 0.7218 (t0) REVERT: J 180 MET cc_start: 0.7810 (ttm) cc_final: 0.7412 (ttm) REVERT: J 356 THR cc_start: 0.9394 (p) cc_final: 0.9093 (p) REVERT: J 500 ILE cc_start: 0.9124 (mm) cc_final: 0.8764 (pt) REVERT: J 562 GLU cc_start: 0.7774 (tt0) cc_final: 0.7548 (pt0) REVERT: J 625 MET cc_start: 0.8498 (ttp) cc_final: 0.8090 (ttp) REVERT: J 667 GLN cc_start: 0.8155 (mt0) cc_final: 0.7932 (mm110) REVERT: J 785 ASP cc_start: 0.8577 (t70) cc_final: 0.7987 (t70) REVERT: J 806 ASP cc_start: 0.8331 (p0) cc_final: 0.8123 (p0) REVERT: J 1313 SER cc_start: 0.9293 (m) cc_final: 0.9025 (p) REVERT: K 3 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7594 (mmm-85) REVERT: K 11 GLU cc_start: 0.8224 (pt0) cc_final: 0.7998 (pt0) REVERT: K 16 ARG cc_start: 0.8226 (ttt90) cc_final: 0.7954 (ttm170) REVERT: K 61 ASN cc_start: 0.8022 (t0) cc_final: 0.7769 (t0) outliers start: 82 outliers final: 58 residues processed: 472 average time/residue: 0.2191 time to fit residues: 172.9433 Evaluate side-chains 443 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 378 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 296 optimal weight: 0.2980 chunk 142 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 105 optimal weight: 0.0770 chunk 371 optimal weight: 3.9990 chunk 414 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 428 optimal weight: 5.9990 overall best weight: 1.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN I 139 ASN I 339 ASN J 232 ASN J 365 GLN ** K 31 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 = 0.3760 r_free = 0.3760 target = 0.129203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095145 restraints weight = 70626.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.096004 restraints weight = 41195.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.096303 restraints weight = 30732.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096796 restraints weight = 26429.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096921 restraints weight = 24243.689| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36916 Z= 0.154 Angle : 0.619 12.529 50412 Z= 0.316 Chirality : 0.044 0.393 5747 Planarity : 0.004 0.050 6199 Dihedral : 14.518 122.165 5957 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.32 % Rotamer: Outliers : 2.15 % Allowed : 18.11 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.06 (0.13), residues: 4294 helix: 0.68 (0.14), residues: 1519 sheet: -1.12 (0.21), residues: 635 loop : -1.61 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 47 TYR 0.020 0.001 TYR J 679 PHE 0.022 0.001 PHE A 377 TRP 0.036 0.001 TRP J1193 HIS 0.011 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (36908) covalent geometry : angle 0.61390 / 0.32 (50400) hydrogen bonds : bond 0.03540 / 2.37 ( 1487) hydrogen bonds : angle 4.37816 / 3.06 ( 4040) metal coordination : bond 0.00907 / 0.45 ( 8) metal coordination : angle 5.20116 / 2.95 ( 12) *********************** 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: 78 poor density : 383 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8683 (mm) REVERT: A 174 MET cc_start: 0.8471 (mmt) cc_final: 0.8214 (tpp) REVERT: A 242 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7648 (tm-30) REVERT: A 629 ASP cc_start: 0.6620 (t0) cc_final: 0.6338 (t0) REVERT: A 710 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9156 (m) REVERT: A 794 ASP cc_start: 0.7958 (t70) cc_final: 0.7535 (t0) REVERT: A 800 GLU cc_start: 0.8171 (pp20) cc_final: 0.7744 (pp20) REVERT: A 827 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: A 925 ASP cc_start: 0.8197 (t70) cc_final: 0.7798 (t0) REVERT: A 1040 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: H 66 HIS cc_start: 0.7700 (t-90) cc_final: 0.7184 (t-90) REVERT: H 75 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7822 (tm-30) REVERT: H 131 CYS cc_start: 0.8623 (m) cc_final: 0.8387 (m) REVERT: H 227 GLN cc_start: 0.9010 (mm110) cc_final: 0.8717 (mm110) REVERT: I 5 TYR cc_start: 0.7435 (t80) cc_final: 0.7060 (t80) REVERT: I 70 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7436 (t80) REVERT: I 396 ASP cc_start: 0.8536 (t0) cc_final: 0.7934 (p0) REVERT: I 477 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8373 (tm-30) REVERT: I 492 MET cc_start: 0.7594 (pmm) cc_final: 0.7067 (pmm) REVERT: I 496 LYS cc_start: 0.8685 (tmtt) cc_final: 0.8307 (tptp) REVERT: I 704 MET cc_start: 0.8546 (tpt) cc_final: 0.8236 (tpp) REVERT: I 949 GLU cc_start: 0.8401 (mp0) cc_final: 0.7708 (pm20) REVERT: I 955 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7718 (tp40) REVERT: I 1296 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.7851 (t70) REVERT: J 42 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: J 117 LEU cc_start: 0.8777 (tp) cc_final: 0.8457 (tp) REVERT: J 129 ASP cc_start: 0.7624 (t70) cc_final: 0.7251 (t0) REVERT: J 372 MET cc_start: 0.8690 (mtp) cc_final: 0.8325 (mtp) REVERT: J 500 ILE cc_start: 0.9181 (mm) cc_final: 0.8818 (pt) REVERT: J 562 GLU cc_start: 0.7790 (tt0) cc_final: 0.7454 (pt0) REVERT: J 667 GLN cc_start: 0.8246 (mt0) cc_final: 0.7988 (mm110) REVERT: J 785 ASP cc_start: 0.8631 (t70) cc_final: 0.8062 (t70) REVERT: J 806 ASP cc_start: 0.8364 (p0) cc_final: 0.8103 (p0) REVERT: J 1313 SER cc_start: 0.9278 (m) cc_final: 0.8987 (p) REVERT: K 3 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7609 (mmm-85) REVERT: K 11 GLU cc_start: 0.8245 (pt0) cc_final: 0.8021 (pt0) REVERT: K 61 ASN cc_start: 0.8083 (t0) cc_final: 0.7819 (t0) outliers start: 78 outliers final: 63 residues processed: 443 average time/residue: 0.2210 time to fit residues: 164.6717 Evaluate side-chains 442 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 372 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 268 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 269 optimal weight: 0.0470 chunk 145 optimal weight: 8.9990 chunk 246 optimal weight: 0.2980 chunk 155 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 402 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 overall best weight: 2.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN K 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094744 restraints weight = 69875.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095820 restraints weight = 38772.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.095884 restraints weight = 29045.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096940 restraints weight = 26370.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096943 restraints weight = 23187.568| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 36916 Z= 0.188 Angle : 0.704 59.196 50412 Z= 0.379 Chirality : 0.045 0.649 5747 Planarity : 0.004 0.050 6199 Dihedral : 14.523 122.154 5957 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 2.07 % Allowed : 18.30 % Favored : 79.63 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 4294 helix: 0.68 (0.14), residues: 1519 sheet: -1.11 (0.21), residues: 645 loop : -1.62 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 47 TYR 0.020 0.001 TYR J 144 PHE 0.021 0.001 PHE A 377 TRP 0.068 0.002 TRP I 183 HIS 0.008 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (36908) covalent geometry : angle 0.69914 / 0.38 (50400) hydrogen bonds : bond 0.03553 / 2.38 ( 1487) hydrogen bonds : angle 4.37940 / 3.06 ( 4040) metal coordination : bond 0.00901 / 0.45 ( 8) metal coordination : angle 5.20774 / 2.96 ( 12) ********************** 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 447 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 372 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8677 (mm) REVERT: A 174 MET cc_start: 0.8504 (mmt) cc_final: 0.8240 (tpp) REVERT: A 242 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 629 ASP cc_start: 0.6604 (t0) cc_final: 0.6291 (t0) REVERT: A 710 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9153 (m) REVERT: A 800 GLU cc_start: 0.8171 (pp20) cc_final: 0.7745 (pp20) REVERT: A 827 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: A 925 ASP cc_start: 0.8158 (t70) cc_final: 0.7762 (t0) REVERT: A 1040 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: H 66 HIS cc_start: 0.7667 (t-90) cc_final: 0.7184 (t-90) REVERT: H 75 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7826 (tm-30) REVERT: H 131 CYS cc_start: 0.8585 (m) cc_final: 0.8342 (m) REVERT: H 227 GLN cc_start: 0.9008 (mm110) cc_final: 0.8716 (mm110) REVERT: I 5 TYR cc_start: 0.7431 (t80) cc_final: 0.7099 (t80) REVERT: I 70 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7434 (t80) REVERT: I 396 ASP cc_start: 0.8516 (t0) cc_final: 0.7932 (p0) REVERT: I 477 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8377 (tm-30) REVERT: I 492 MET cc_start: 0.7570 (pmm) cc_final: 0.7055 (pmm) REVERT: I 496 LYS cc_start: 0.8672 (tmtt) cc_final: 0.8297 (tptp) REVERT: I 704 MET cc_start: 0.8542 (tpt) cc_final: 0.8237 (tpp) REVERT: I 949 GLU cc_start: 0.8382 (mp0) cc_final: 0.7697 (pm20) REVERT: I 955 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7432 (tp40) REVERT: I 959 ASP cc_start: 0.7915 (m-30) cc_final: 0.7454 (m-30) REVERT: I 1296 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.7852 (t70) REVERT: J 42 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7145 (pm20) REVERT: J 117 LEU cc_start: 0.8782 (tp) cc_final: 0.8458 (tp) REVERT: J 129 ASP cc_start: 0.7579 (t70) cc_final: 0.7208 (t0) REVERT: J 372 MET cc_start: 0.8683 (mtp) cc_final: 0.8317 (mtp) REVERT: J 500 ILE cc_start: 0.9177 (mm) cc_final: 0.8811 (pt) REVERT: J 562 GLU cc_start: 0.7751 (tt0) cc_final: 0.7451 (pt0) REVERT: J 667 GLN cc_start: 0.8235 (mt0) cc_final: 0.7986 (mm110) REVERT: J 785 ASP cc_start: 0.8617 (t70) cc_final: 0.8004 (t70) REVERT: J 806 ASP cc_start: 0.8347 (p0) cc_final: 0.8111 (p0) REVERT: J 1313 SER cc_start: 0.9263 (m) cc_final: 0.8991 (p) REVERT: K 3 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7605 (mmm-85) REVERT: K 11 GLU cc_start: 0.8240 (pt0) cc_final: 0.8021 (pt0) REVERT: K 61 ASN cc_start: 0.8092 (t0) cc_final: 0.7829 (t0) outliers start: 75 outliers final: 68 residues processed: 430 average time/residue: 0.2162 time to fit residues: 157.1837 Evaluate side-chains 447 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 372 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 12 optimal weight: 2.9990 chunk 215 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 173 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN J 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.128909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095325 restraints weight = 70189.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096798 restraints weight = 39220.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096942 restraints weight = 29131.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097201 restraints weight = 25509.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097374 restraints weight = 23826.194| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 36916 Z= 0.188 Angle : 0.704 59.196 50412 Z= 0.379 Chirality : 0.045 0.649 5747 Planarity : 0.004 0.050 6199 Dihedral : 14.523 122.154 5957 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 2.10 % Allowed : 18.30 % Favored : 79.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 4294 helix: 0.68 (0.14), residues: 1519 sheet: -1.11 (0.21), residues: 645 loop : -1.62 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 47 TYR 0.020 0.001 TYR J 144 PHE 0.021 0.001 PHE A 377 TRP 0.068 0.002 TRP I 183 HIS 0.008 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (36908) covalent geometry : angle 0.69914 / 0.38 (50400) hydrogen bonds : bond 0.03553 / 2.38 ( 1487) hydrogen bonds : angle 4.37940 / 3.06 ( 4040) metal coordination : bond 0.00901 / 0.45 ( 8) metal coordination : angle 5.20774 / 2.96 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5865.14 seconds wall clock time: 102 minutes 25.05 seconds (6145.05 seconds total)