Starting phenix.real_space_refine on Sat Jun 6 08:23:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10mb_75280/06_2026/10mb_75280.cif Found real_map, /net/cci-nas-00/data/ceres_data/10mb_75280/06_2026/10mb_75280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10mb_75280/06_2026/10mb_75280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10mb_75280/06_2026/10mb_75280.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10mb_75280/06_2026/10mb_75280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10mb_75280/06_2026/10mb_75280.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 62 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16167 2.51 5 N 4610 2.21 5 O 5819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26767 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 608 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} 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: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 208} 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: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1681 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 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} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "K" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "H" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "I" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 310 Classifications: {'water': 310} Link IDs: {None: 309} Chain: "J" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 235 Classifications: {'water': 235} Link IDs: {None: 234} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16109 SG CYS J 70 116.472 66.709 71.207 1.00124.25 S ATOM 16123 SG CYS J 72 117.126 63.284 69.405 1.00128.01 S ATOM 16231 SG CYS J 85 118.280 65.639 67.784 1.00123.61 S ATOM 16255 SG CYS J 88 115.371 66.182 67.432 1.00125.91 S ATOM 21943 SG CYS J 814 87.615 129.086 68.423 1.00 57.13 S ATOM 22508 SG CYS J 888 85.820 125.615 68.705 1.00 37.46 S ATOM 22559 SG CYS J 895 86.993 127.490 71.932 1.00 43.18 S ATOM 22580 SG CYS J 898 84.560 128.001 70.674 1.00 51.97 S Time building chain proxies: 6.50, per 1000 atoms: 0.24 Number of scatterers: 26767 At special positions: 0 Unit cell: (143.312, 168.324, 164.944, 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 106 16.00 P 62 15.00 Mg 1 11.99 O 5819 8.00 N 4610 7.00 C 16167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " 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 898 " Number of angles added : 12 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5848 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 45 sheets defined 39.1% alpha, 17.7% beta 21 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 33 Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 80 Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.735A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.908A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.998A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.616A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.870A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.607A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.050A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.895A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 removed outlier: 3.616A pdb=" N GLN I 276 " --> pdb=" O ARG I 272 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 292 Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 removed outlier: 4.111A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR I 350 " --> pdb=" O TYR I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.247A 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 437 removed outlier: 3.595A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.750A pdb=" N ARG I 473 " --> pdb=" O VAL I 469 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 612 removed outlier: 4.215A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 663 through 668 removed outlier: 3.804A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.945A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 860 through 864 removed outlier: 4.344A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 983 removed outlier: 4.492A pdb=" N ILE I 948 " --> pdb=" O ARG I 944 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU I 949 " --> pdb=" O ALA I 945 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU I 963 " --> pdb=" O ASP I 959 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 990 Processing helix chain 'I' and resid 993 through 1000 Processing helix chain 'I' and resid 1006 through 1038 Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.638A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.628A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.515A pdb=" N THR I1115 " --> pdb=" O GLN I1111 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA I1120 " --> pdb=" O HIS I1116 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.718A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.601A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.638A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.985A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.868A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.501A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.592A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.539A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.572A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 removed outlier: 3.667A pdb=" N MET J 330 " --> pdb=" O LEU J 327 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE J 331 " --> pdb=" O ALA J 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 327 through 331' Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 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 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.735A pdb=" N ALA J 633 " --> pdb=" O PHE J 629 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER J 635 " --> pdb=" O TYR J 631 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.733A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.595A pdb=" N SER J 670 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.634A pdb=" N ARG J 678 " --> pdb=" O THR J 674 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.862A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.092A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.805A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.562A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1037 through 1041 removed outlier: 3.736A pdb=" N ILE J1041 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.936A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 3.505A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1260 removed outlier: 4.360A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.868A 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 1318 through 1324 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.536A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1371 removed outlier: 3.614A pdb=" N HIS J1366 " --> pdb=" O GLY J1362 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 20 removed outlier: 8.608A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 19 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N HIS G 23 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 116 removed outlier: 3.920A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.700A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 20 removed outlier: 6.632A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU H 201 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 105 removed outlier: 3.654A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.875A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.096A pdb=" N ILE I 59 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU I 68 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.640A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.542A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.961A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.709A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.627A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.811A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.023A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.385A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 840 removed outlier: 3.935A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY I 926 " --> pdb=" O VAL I 877 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.834A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD2, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.748A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.642A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.798A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AD6, first strand: chain 'J' and resid 254 through 255 Processing sheet with id=AD7, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'J' and resid 706 through 709 Processing sheet with id=AD9, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.621A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.201A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN J1019 " --> pdb=" O VAL J1002 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 991 through 997 removed outlier: 3.534A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 3.930A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE7, first strand: chain 'J' and resid 1059 through 1060 Processing sheet with id=AE8, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.960A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE J1177 " --> pdb=" O TYR J1186 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.284A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 7.31 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7855 1.33 - 1.45: 3570 1.45 - 1.57: 14879 1.57 - 1.69: 121 1.69 - 1.81: 184 Bond restraints: 26609 Sorted by residual: bond pdb=" P DC B 25 " pdb=" OP2 DC B 25 " ideal model delta sigma weight residual 1.480 1.522 -0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" P DA B 26 " pdb=" OP1 DA B 26 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" P DG B 27 " pdb=" OP1 DG B 27 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.37e+00 bond pdb=" P DA B 26 " pdb=" OP2 DA B 26 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" P DG B 28 " pdb=" OP2 DG B 28 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.27e+00 ... (remaining 26604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 35746 1.61 - 3.21: 400 3.21 - 4.82: 50 4.82 - 6.43: 11 6.43 - 8.03: 5 Bond angle restraints: 36212 Sorted by residual: angle pdb=" O3' G R 10 " pdb=" C3' G R 10 " pdb=" C2' G R 10 " ideal model delta sigma weight residual 113.70 118.36 -4.66 1.50e+00 4.44e-01 9.64e+00 angle pdb=" C3' G R 10 " pdb=" O3' G R 10 " pdb=" P A R 11 " ideal model delta sigma weight residual 120.20 124.24 -4.04 1.50e+00 4.44e-01 7.27e+00 angle pdb=" N PRO H 30 " pdb=" CA PRO H 30 " pdb=" C PRO H 30 " ideal model delta sigma weight residual 112.47 118.01 -5.54 2.06e+00 2.36e-01 7.24e+00 angle pdb=" O3' DT B 24 " pdb=" P DC B 25 " pdb=" OP2 DC B 25 " ideal model delta sigma weight residual 108.00 116.03 -8.03 3.00e+00 1.11e-01 7.17e+00 angle pdb=" C3' DC B 25 " pdb=" C2' DC B 25 " pdb=" C1' DC B 25 " ideal model delta sigma weight residual 101.60 105.38 -3.78 1.50e+00 4.44e-01 6.35e+00 ... (remaining 36207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 15703 26.84 - 53.69: 535 53.69 - 80.53: 69 80.53 - 107.38: 6 107.38 - 134.22: 1 Dihedral angle restraints: 16314 sinusoidal: 7223 harmonic: 9091 Sorted by residual: dihedral pdb=" CA GLU H 29 " pdb=" C GLU H 29 " pdb=" N PRO H 30 " pdb=" CA PRO H 30 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA THR I1292 " pdb=" C THR I1292 " pdb=" N VAL I1293 " pdb=" CA VAL I1293 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" C4' G R 10 " pdb=" C3' G R 10 " pdb=" O3' G R 10 " pdb=" P A R 11 " ideal model delta sinusoidal sigma weight residual 220.00 85.78 134.22 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 16311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4093 0.116 - 0.232: 53 0.232 - 0.348: 0 0.348 - 0.464: 0 0.464 - 0.580: 4 Chirality restraints: 4150 Sorted by residual: chirality pdb=" P DC B 25 " pdb=" OP1 DC B 25 " pdb=" OP2 DC B 25 " pdb=" O5' DC B 25 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.42e+00 chirality pdb=" P DG B 27 " pdb=" OP1 DG B 27 " pdb=" OP2 DG B 27 " pdb=" O5' DG B 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" P DA B 26 " pdb=" OP1 DA B 26 " pdb=" OP2 DA B 26 " pdb=" O5' DA B 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.54e+00 ... (remaining 4147 not shown) Planarity restraints: 4517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.20e+00 pdb=" N PRO I 190 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.82e+00 pdb=" N PRO I 590 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 551 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO I 552 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 552 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 552 " 0.023 5.00e-02 4.00e+02 ... (remaining 4514 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 15 2.59 - 3.17: 21127 3.17 - 3.75: 39130 3.75 - 4.32: 55204 4.32 - 4.90: 92920 Nonbonded interactions: 208396 Sorted by model distance: nonbonded pdb=" O3' U R 19 " pdb="MG MG J1501 " model vdw 2.013 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.266 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.268 2.170 nonbonded pdb=" O4 DT B 13 " pdb=" O6 DG A 19 " model vdw 2.273 2.432 nonbonded pdb=" O2 DT B 13 " pdb=" N2 DG A 19 " model vdw 2.291 2.496 ... (remaining 208391 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 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 231)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 231)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.990 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.720 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.002 0.077 26617 Z= 0.111 Angle : 0.570 34.350 36224 Z= 0.263 Chirality : 0.043 0.580 4150 Planarity : 0.004 0.051 4517 Dihedral : 12.872 134.220 10466 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.12 % Allowed : 5.08 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3148 helix: 1.63 (0.16), residues: 1084 sheet: 0.75 (0.26), residues: 404 loop : -0.41 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I1246 TYR 0.009 0.001 TYR G 185 PHE 0.012 0.001 PHE I 514 TRP 0.004 0.001 TRP J 409 HIS 0.003 0.000 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (26609) covalent geometry : angle 0.47306 / 0.26 (36212) hydrogen bonds : bond 0.14434 / 8.44 ( 1122) hydrogen bonds : angle 5.50561 / 3.51 ( 3109) metal coordination : bond 0.04897 / 2.40 ( 8) metal coordination : angle 17.51827 / 11.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 462 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 25 ARG cc_start: 0.7356 (ttt180) cc_final: 0.7153 (ttm170) REVERT: K 59 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7433 (pp) REVERT: G 57 THR cc_start: 0.9094 (m) cc_final: 0.8523 (p) REVERT: G 181 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7962 (mm-30) REVERT: G 219 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.8064 (ttt180) REVERT: H 129 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8872 (t) REVERT: H 135 ASP cc_start: 0.7681 (t0) cc_final: 0.7369 (t0) REVERT: I 74 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7842 (ttt-90) REVERT: I 95 PRO cc_start: 0.7798 (Cg_exo) cc_final: 0.7446 (Cg_endo) REVERT: I 126 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7607 (mm-30) REVERT: I 127 ILE cc_start: 0.8382 (pt) cc_final: 0.8002 (mt) REVERT: I 370 MET cc_start: 0.7361 (mmm) cc_final: 0.6889 (mmp) REVERT: I 445 ILE cc_start: 0.8655 (tt) cc_final: 0.8415 (mm) REVERT: I 473 ARG cc_start: 0.7711 (ttm170) cc_final: 0.7447 (mtp180) REVERT: I 542 ARG cc_start: 0.6568 (ptt90) cc_final: 0.5689 (mmp80) REVERT: I 647 ARG cc_start: 0.8535 (ttt180) cc_final: 0.7548 (ttm170) REVERT: I 694 ARG cc_start: 0.8102 (mtm180) cc_final: 0.7812 (mtt180) REVERT: I 702 THR cc_start: 0.9158 (m) cc_final: 0.8908 (p) REVERT: I 1064 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8166 (p0) REVERT: I 1089 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7173 (mp0) REVERT: J 21 LYS cc_start: 0.8253 (tttm) cc_final: 0.7966 (tptp) REVERT: J 197 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7458 (tp30) REVERT: J 552 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8731 (mt) REVERT: J 649 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6938 (mptt) REVERT: J 797 THR cc_start: 0.9076 (t) cc_final: 0.8424 (m) REVERT: J 802 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7675 (t0) REVERT: J 1289 ASN cc_start: 0.6722 (m-40) cc_final: 0.6466 (t0) outliers start: 84 outliers final: 32 residues processed: 529 average time/residue: 0.7302 time to fit residues: 443.7785 Evaluate side-chains 360 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 322 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN I 620 ASN J 276 ASN J 309 ASN J 364 HIS J 430 HIS J 651 HIS J 739 GLN J 777 HIS J1227 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.203288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141751 restraints weight = 28272.084| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.71 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26617 Z= 0.153 Angle : 0.561 11.757 36224 Z= 0.295 Chirality : 0.043 0.233 4150 Planarity : 0.005 0.053 4517 Dihedral : 13.476 131.358 4326 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.90 % Allowed : 12.02 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3148 helix: 1.77 (0.16), residues: 1101 sheet: 0.63 (0.25), residues: 434 loop : -0.42 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 388 TYR 0.017 0.001 TYR I 105 PHE 0.014 0.001 PHE I 514 TRP 0.005 0.001 TRP I1276 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (26609) covalent geometry : angle 0.55041 / 0.29 (36212) hydrogen bonds : bond 0.05615 / 3.36 ( 1122) hydrogen bonds : angle 4.37961 / 2.81 ( 3109) metal coordination : bond 0.00599 / 0.30 ( 8) metal coordination : angle 5.88710 / 3.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 324 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 59 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8259 (pp) REVERT: G 57 THR cc_start: 0.9082 (m) cc_final: 0.8763 (p) REVERT: G 219 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7758 (ttt180) REVERT: H 38 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.7887 (t) REVERT: I 74 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7711 (ttt-90) REVERT: I 542 ARG cc_start: 0.6175 (ptt90) cc_final: 0.5767 (mmp80) REVERT: I 546 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: I 647 ARG cc_start: 0.7775 (ttt180) cc_final: 0.7531 (ttm170) REVERT: I 1064 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7942 (p0) REVERT: I 1079 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8089 (mt) REVERT: I 1089 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6941 (mp0) REVERT: I 1143 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6756 (tm-30) REVERT: J 552 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8884 (mt) REVERT: J 797 THR cc_start: 0.9127 (t) cc_final: 0.8481 (m) REVERT: J 802 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7245 (t0) outliers start: 105 outliers final: 51 residues processed: 390 average time/residue: 0.7420 time to fit residues: 331.9509 Evaluate side-chains 355 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 546 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1287 ILE Chi-restraints excluded: chain J residue 1318 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 292 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 61 ASN G 103 ASN G 147 GLN I 620 ASN J 430 HIS J 651 HIS J 720 ASN J 739 GLN J 777 HIS J 907 HIS J1126 GLN J1249 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.201596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134070 restraints weight = 28287.363| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.85 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26617 Z= 0.164 Angle : 0.565 12.501 36224 Z= 0.299 Chirality : 0.043 0.240 4150 Planarity : 0.005 0.053 4517 Dihedral : 13.500 129.440 4319 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.19 % Allowed : 12.99 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3148 helix: 1.69 (0.16), residues: 1101 sheet: 0.58 (0.25), residues: 424 loop : -0.51 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 388 TYR 0.015 0.002 TYR G 177 PHE 0.025 0.002 PHE I1025 TRP 0.005 0.001 TRP J 409 HIS 0.008 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (26609) covalent geometry : angle 0.55953 / 0.30 (36212) hydrogen bonds : bond 0.05773 / 3.48 ( 1122) hydrogen bonds : angle 4.30716 / 2.77 ( 3109) metal coordination : bond 0.00480 / 0.24 ( 8) metal coordination : angle 4.27614 / 2.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 308 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 57 THR cc_start: 0.9097 (m) cc_final: 0.8796 (p) REVERT: H 38 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8111 (t) REVERT: I 74 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7702 (ttt-90) REVERT: I 518 ASN cc_start: 0.7548 (p0) cc_final: 0.7134 (OUTLIER) REVERT: I 542 ARG cc_start: 0.6210 (ptt90) cc_final: 0.5755 (mmp80) REVERT: I 546 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: I 647 ARG cc_start: 0.7918 (ttt180) cc_final: 0.7683 (mtm180) REVERT: I 1064 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8117 (p0) REVERT: I 1079 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.7886 (mt) REVERT: I 1143 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: I 1316 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: J 534 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7357 (tp30) REVERT: J 797 THR cc_start: 0.9139 (t) cc_final: 0.8496 (m) REVERT: J 802 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7231 (t70) outliers start: 113 outliers final: 64 residues processed: 388 average time/residue: 0.7462 time to fit residues: 332.0686 Evaluate side-chains 361 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 290 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 546 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1200 LYS Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1316 GLU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1318 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 146 optimal weight: 0.0470 chunk 261 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 297 optimal weight: 6.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN I 620 ASN J 430 HIS J 651 HIS J 739 GLN J 907 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.203809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3376 r_free = 0.3376 target = 0.128197 restraints weight = 28202.471| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.34 r_work: 0.2899 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26617 Z= 0.118 Angle : 0.511 11.040 36224 Z= 0.271 Chirality : 0.041 0.231 4150 Planarity : 0.004 0.060 4517 Dihedral : 13.333 129.139 4317 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.90 % Allowed : 14.36 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3148 helix: 1.88 (0.16), residues: 1096 sheet: 0.49 (0.25), residues: 438 loop : -0.51 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 133 TYR 0.013 0.001 TYR I 123 PHE 0.014 0.001 PHE I1025 TRP 0.004 0.001 TRP I 997 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (26609) covalent geometry : angle 0.50742 / 0.27 (36212) hydrogen bonds : bond 0.04677 / 2.83 ( 1122) hydrogen bonds : angle 4.10367 / 2.64 ( 3109) metal coordination : bond 0.00349 / 0.17 ( 8) metal coordination : angle 3.29341 / 2.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 314 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 57 THR cc_start: 0.9158 (m) cc_final: 0.8559 (p) REVERT: H 38 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7600 (t) REVERT: H 97 GLU cc_start: 0.7757 (tt0) cc_final: 0.7556 (tt0) REVERT: I 74 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7570 (ttt-90) REVERT: I 95 PRO cc_start: 0.8063 (Cg_endo) cc_final: 0.7787 (Cg_exo) REVERT: I 439 LYS cc_start: 0.8013 (mttt) cc_final: 0.7713 (mttm) REVERT: I 473 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6737 (mtm180) REVERT: I 518 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7220 (p0) REVERT: I 542 ARG cc_start: 0.6291 (ptt90) cc_final: 0.5346 (mmp80) REVERT: I 546 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: I 647 ARG cc_start: 0.8539 (ttt180) cc_final: 0.7562 (mtm180) REVERT: I 702 THR cc_start: 0.9154 (m) cc_final: 0.8928 (p) REVERT: I 1064 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8278 (p0) REVERT: I 1079 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8205 (mt) REVERT: I 1143 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: I 1316 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: J 204 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6885 (tm-30) REVERT: J 227 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7389 (t80) REVERT: J 534 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.7999 (tp30) REVERT: J 552 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8857 (mt) REVERT: J 785 ASP cc_start: 0.8147 (t0) cc_final: 0.7722 (m-30) REVERT: J 797 THR cc_start: 0.9093 (t) cc_final: 0.8419 (m) REVERT: J 802 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7846 (t0) REVERT: J 1189 MET cc_start: 0.7250 (tpp) cc_final: 0.6196 (tpp) REVERT: J 1208 ASP cc_start: 0.7579 (m-30) cc_final: 0.7144 (m-30) REVERT: J 1372 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7425 (ttm-80) outliers start: 105 outliers final: 64 residues processed: 385 average time/residue: 0.7484 time to fit residues: 331.0693 Evaluate side-chains 376 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 301 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 546 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1200 LYS Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1316 GLU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1318 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 208 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 259 optimal weight: 0.7980 chunk 258 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 300 optimal weight: 0.0870 chunk 10 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN I 620 ASN J 430 HIS J 651 HIS ** J 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 739 GLN J1126 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.203369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126886 restraints weight = 28127.658| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.21 r_work: 0.2904 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26617 Z= 0.124 Angle : 0.513 11.373 36224 Z= 0.272 Chirality : 0.042 0.231 4150 Planarity : 0.004 0.058 4517 Dihedral : 13.284 128.514 4317 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.38 % Allowed : 14.47 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3148 helix: 1.92 (0.16), residues: 1094 sheet: 0.47 (0.25), residues: 425 loop : -0.52 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 388 TYR 0.014 0.001 TYR I 301 PHE 0.013 0.001 PHE J1319 TRP 0.004 0.001 TRP I 997 HIS 0.004 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (26609) covalent geometry : angle 0.51074 / 0.27 (36212) hydrogen bonds : bond 0.04799 / 2.91 ( 1122) hydrogen bonds : angle 4.07358 / 2.62 ( 3109) metal coordination : bond 0.00317 / 0.16 ( 8) metal coordination : angle 2.90653 / 1.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 303 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 57 THR cc_start: 0.9192 (m) cc_final: 0.8608 (p) REVERT: G 157 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8049 (p) REVERT: H 38 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.7787 (t) REVERT: H 97 GLU cc_start: 0.7733 (tt0) cc_final: 0.7515 (tt0) REVERT: H 226 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: I 74 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7575 (ttt-90) REVERT: I 95 PRO cc_start: 0.7984 (Cg_endo) cc_final: 0.7728 (Cg_exo) REVERT: I 370 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7299 (mmp) REVERT: I 439 LYS cc_start: 0.7928 (mttt) cc_final: 0.7689 (mttm) REVERT: I 518 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7325 (OUTLIER) REVERT: I 542 ARG cc_start: 0.6306 (ptt90) cc_final: 0.5351 (mmp80) REVERT: I 546 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: I 647 ARG cc_start: 0.8495 (ttt180) cc_final: 0.7566 (mtm180) REVERT: I 660 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.8810 (m) REVERT: I 702 THR cc_start: 0.9152 (m) cc_final: 0.8951 (p) REVERT: I 1064 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8279 (p0) REVERT: I 1079 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8194 (mt) REVERT: I 1143 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: I 1316 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: J 151 MET cc_start: 0.4836 (OUTLIER) cc_final: 0.4607 (ppp) REVERT: J 227 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7386 (t80) REVERT: J 237 MET cc_start: 0.8963 (mtm) cc_final: 0.8659 (mtm) REVERT: J 395 LYS cc_start: 0.7661 (mmmm) cc_final: 0.7346 (tppp) REVERT: J 534 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8010 (tp30) REVERT: J 552 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8906 (mt) REVERT: J 785 ASP cc_start: 0.8203 (t0) cc_final: 0.7771 (m-30) REVERT: J 797 THR cc_start: 0.9118 (t) cc_final: 0.8446 (m) REVERT: J 802 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7874 (t0) REVERT: J 1208 ASP cc_start: 0.7584 (m-30) cc_final: 0.7156 (m-30) REVERT: J 1372 ARG cc_start: 0.7833 (tpp-160) cc_final: 0.7455 (ttp80) outliers start: 118 outliers final: 70 residues processed: 384 average time/residue: 0.7303 time to fit residues: 323.6788 Evaluate side-chains 380 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 295 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 226 GLU Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 546 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1200 LYS Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1316 GLU Chi-restraints excluded: chain I residue 1333 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 792 ASN Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1318 SER Chi-restraints excluded: chain J residue 1329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 275 optimal weight: 0.3980 chunk 232 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN I 620 ASN I1134 GLN J 430 HIS J 651 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.200315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3304 r_free = 0.3304 target = 0.122810 restraints weight = 28153.226| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.26 r_work: 0.2843 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26617 Z= 0.178 Angle : 0.586 13.641 36224 Z= 0.309 Chirality : 0.044 0.232 4150 Planarity : 0.005 0.054 4517 Dihedral : 13.454 127.957 4316 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.42 % Allowed : 15.03 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.15), residues: 3148 helix: 1.64 (0.16), residues: 1107 sheet: 0.33 (0.24), residues: 434 loop : -0.63 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 388 TYR 0.015 0.002 TYR G 177 PHE 0.013 0.002 PHE J1319 TRP 0.012 0.001 TRP I 997 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (26609) covalent geometry : angle 0.58357 / 0.31 (36212) hydrogen bonds : bond 0.06076 / 3.67 ( 1122) hydrogen bonds : angle 4.23003 / 2.73 ( 3109) metal coordination : bond 0.00335 / 0.16 ( 8) metal coordination : angle 2.82358 / 1.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 299 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 57 THR cc_start: 0.9256 (m) cc_final: 0.8695 (p) REVERT: G 157 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8017 (m) REVERT: H 38 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8063 (t) REVERT: H 97 GLU cc_start: 0.7807 (tt0) cc_final: 0.7585 (tt0) REVERT: H 214 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: H 226 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: I 74 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7601 (ttt-90) REVERT: I 124 MET cc_start: 0.7768 (ptm) cc_final: 0.7454 (ptm) REVERT: I 370 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7333 (mmp) REVERT: I 439 LYS cc_start: 0.7965 (mttt) cc_final: 0.7725 (mttm) REVERT: I 484 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8054 (tt) REVERT: I 518 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7569 (p0) REVERT: I 542 ARG cc_start: 0.6280 (ptt90) cc_final: 0.5329 (mmp80) REVERT: I 546 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: I 647 ARG cc_start: 0.8501 (ttt180) cc_final: 0.7545 (mtm180) REVERT: I 660 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.8795 (m) REVERT: I 1064 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8265 (p0) REVERT: I 1079 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8203 (mt) REVERT: I 1143 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: I 1316 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: J 66 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7463 (mmtp) REVERT: J 151 MET cc_start: 0.5057 (OUTLIER) cc_final: 0.4840 (ppp) REVERT: J 237 MET cc_start: 0.9027 (mtm) cc_final: 0.8657 (mtm) REVERT: J 325 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7470 (mtmt) REVERT: J 534 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: J 785 ASP cc_start: 0.8249 (t0) cc_final: 0.7793 (m-30) REVERT: J 802 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7943 (t70) REVERT: J 1189 MET cc_start: 0.7223 (tpp) cc_final: 0.6625 (tpp) REVERT: J 1208 ASP cc_start: 0.7574 (m-30) cc_final: 0.7145 (m-30) REVERT: J 1372 ARG cc_start: 0.7758 (tpp-160) cc_final: 0.7423 (ttp80) outliers start: 119 outliers final: 70 residues processed: 382 average time/residue: 0.7377 time to fit residues: 323.4418 Evaluate side-chains 383 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 296 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 226 GLU Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 546 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1200 LYS Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1316 GLU Chi-restraints excluded: chain I residue 1333 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 325 LYS Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1318 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 13 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN I 620 ASN J 430 HIS J 651 HIS J 907 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.200776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136021 restraints weight = 28024.038| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.76 r_work: 0.3120 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26617 Z= 0.172 Angle : 0.578 13.178 36224 Z= 0.306 Chirality : 0.044 0.233 4150 Planarity : 0.005 0.053 4517 Dihedral : 13.447 127.949 4316 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.30 % Allowed : 15.55 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3148 helix: 1.60 (0.16), residues: 1108 sheet: 0.38 (0.25), residues: 420 loop : -0.69 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 388 TYR 0.015 0.002 TYR G 177 PHE 0.014 0.001 PHE J1319 TRP 0.007 0.001 TRP I 997 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (26609) covalent geometry : angle 0.57553 / 0.31 (36212) hydrogen bonds : bond 0.05783 / 3.50 ( 1122) hydrogen bonds : angle 4.19936 / 2.71 ( 3109) metal coordination : bond 0.00322 / 0.16 ( 8) metal coordination : angle 2.72393 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 301 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 57 THR cc_start: 0.9238 (m) cc_final: 0.8686 (p) REVERT: G 157 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7921 (m) REVERT: G 229 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7660 (mt-10) REVERT: H 38 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8235 (t) REVERT: I 74 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7945 (ttt-90) REVERT: I 124 MET cc_start: 0.8164 (ptm) cc_final: 0.7952 (ptm) REVERT: I 370 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7856 (mmp) REVERT: I 542 ARG cc_start: 0.6496 (ptt90) cc_final: 0.5706 (mmp80) REVERT: I 546 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8772 (mp0) REVERT: I 647 ARG cc_start: 0.8329 (ttt180) cc_final: 0.7758 (mtm180) REVERT: I 660 VAL cc_start: 0.9301 (OUTLIER) cc_final: 0.8802 (m) REVERT: I 1064 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8274 (p0) REVERT: I 1079 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8205 (mt) REVERT: I 1143 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: J 151 MET cc_start: 0.4292 (OUTLIER) cc_final: 0.4033 (ppp) REVERT: J 227 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7863 (t80) REVERT: J 237 MET cc_start: 0.8967 (mtm) cc_final: 0.8697 (mtm) REVERT: J 325 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7548 (mtmt) REVERT: J 534 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: J 785 ASP cc_start: 0.8384 (t0) cc_final: 0.8039 (m-30) REVERT: J 797 THR cc_start: 0.9169 (t) cc_final: 0.8537 (m) REVERT: J 802 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8041 (t70) outliers start: 116 outliers final: 75 residues processed: 381 average time/residue: 0.7475 time to fit residues: 327.8497 Evaluate side-chains 375 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 287 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 546 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1200 LYS Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1333 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 325 LYS Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1318 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 124 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 252 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 275 optimal weight: 0.0040 chunk 157 optimal weight: 3.9990 chunk 314 optimal weight: 0.9990 chunk 293 optimal weight: 0.2980 chunk 107 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN I 620 ASN I1070 HIS I1134 GLN J 430 HIS J 651 HIS J 907 HIS J1197 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.205720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138563 restraints weight = 28551.246| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.91 r_work: 0.3084 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26617 Z= 0.098 Angle : 0.497 10.866 36224 Z= 0.261 Chirality : 0.040 0.226 4150 Planarity : 0.004 0.053 4517 Dihedral : 13.162 128.640 4316 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.01 % Allowed : 17.07 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3148 helix: 2.01 (0.16), residues: 1097 sheet: 0.60 (0.25), residues: 431 loop : -0.54 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 403 TYR 0.011 0.001 TYR J 511 PHE 0.015 0.001 PHE J1319 TRP 0.007 0.001 TRP J 33 HIS 0.006 0.000 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (26609) covalent geometry : angle 0.49511 / 0.26 (36212) hydrogen bonds : bond 0.03623 / 2.20 ( 1122) hydrogen bonds : angle 3.97041 / 2.56 ( 3109) metal coordination : bond 0.00229 / 0.11 ( 8) metal coordination : angle 2.13288 / 1.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 308 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.8839 (tpp80) cc_final: 0.8496 (mmp80) REVERT: G 57 THR cc_start: 0.9122 (m) cc_final: 0.8457 (p) REVERT: G 157 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8082 (p) REVERT: G 199 ASP cc_start: 0.7686 (m-30) cc_final: 0.7426 (m-30) REVERT: G 229 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7433 (mt-10) REVERT: I 74 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7871 (ttt-90) REVERT: I 370 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7578 (mmp) REVERT: I 518 ASN cc_start: 0.7452 (OUTLIER) cc_final: 0.6997 (OUTLIER) REVERT: I 542 ARG cc_start: 0.6486 (ptt90) cc_final: 0.5362 (mmp80) REVERT: I 647 ARG cc_start: 0.8534 (ttt180) cc_final: 0.7627 (mtm180) REVERT: I 660 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8835 (m) REVERT: I 1064 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8249 (p0) REVERT: I 1079 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8124 (mt) REVERT: I 1119 MET cc_start: 0.8364 (ttm) cc_final: 0.8055 (ttm) REVERT: I 1143 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: J 151 MET cc_start: 0.4657 (OUTLIER) cc_final: 0.4389 (ppp) REVERT: J 227 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7657 (t80) REVERT: J 237 MET cc_start: 0.8974 (mtm) cc_final: 0.8674 (mtm) REVERT: J 534 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8165 (tp30) REVERT: J 552 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8938 (mt) REVERT: J 572 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8505 (t) REVERT: J 797 THR cc_start: 0.9095 (t) cc_final: 0.8406 (m) REVERT: J 802 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7658 (t0) REVERT: J 1189 MET cc_start: 0.6952 (tpp) cc_final: 0.6709 (tpp) outliers start: 81 outliers final: 45 residues processed: 364 average time/residue: 0.7415 time to fit residues: 309.8985 Evaluate side-chains 345 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 89 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 284 optimal weight: 30.0000 chunk 197 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 620 ASN J 430 HIS J 651 HIS J 777 HIS J 817 HIS J1197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.201483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.137789 restraints weight = 28262.139| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.68 r_work: 0.3072 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26617 Z= 0.163 Angle : 0.583 13.175 36224 Z= 0.304 Chirality : 0.043 0.233 4150 Planarity : 0.005 0.082 4517 Dihedral : 13.259 127.370 4311 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.86 % Allowed : 17.63 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3148 helix: 1.85 (0.16), residues: 1099 sheet: 0.45 (0.25), residues: 443 loop : -0.58 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG J 133 TYR 0.014 0.001 TYR G 177 PHE 0.013 0.001 PHE J1319 TRP 0.004 0.001 TRP J 580 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (26609) covalent geometry : angle 0.58096 / 0.30 (36212) hydrogen bonds : bond 0.05401 / 3.28 ( 1122) hydrogen bonds : angle 4.11080 / 2.65 ( 3109) metal coordination : bond 0.00292 / 0.14 ( 8) metal coordination : angle 2.47597 / 1.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 293 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.8660 (tpp80) cc_final: 0.8431 (mmp80) REVERT: G 57 THR cc_start: 0.9197 (m) cc_final: 0.8675 (p) REVERT: G 157 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7959 (m) REVERT: G 229 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7710 (mt-10) REVERT: H 38 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8194 (p) REVERT: I 74 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7977 (ttt-90) REVERT: I 370 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7828 (mmp) REVERT: I 518 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7241 (OUTLIER) REVERT: I 542 ARG cc_start: 0.6549 (ptt90) cc_final: 0.5629 (mmp80) REVERT: I 647 ARG cc_start: 0.8357 (ttt180) cc_final: 0.7721 (mtm180) REVERT: I 660 VAL cc_start: 0.9308 (OUTLIER) cc_final: 0.8802 (m) REVERT: I 876 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: I 1064 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8176 (p0) REVERT: I 1079 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8183 (mt) REVERT: I 1143 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: J 151 MET cc_start: 0.4434 (OUTLIER) cc_final: 0.4149 (ppp) REVERT: J 186 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: J 227 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7854 (t80) REVERT: J 237 MET cc_start: 0.8993 (mtm) cc_final: 0.8722 (mtm) REVERT: J 534 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8281 (tp30) REVERT: J 552 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8965 (mt) REVERT: J 785 ASP cc_start: 0.8343 (t0) cc_final: 0.7962 (m-30) REVERT: J 797 THR cc_start: 0.9141 (t) cc_final: 0.8482 (m) REVERT: J 802 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7758 (t70) REVERT: J 1189 MET cc_start: 0.6716 (tpp) cc_final: 0.6502 (tpp) outliers start: 77 outliers final: 49 residues processed: 347 average time/residue: 0.7663 time to fit residues: 303.8363 Evaluate side-chains 348 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 285 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 876 GLU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 95 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 251 optimal weight: 0.3980 chunk 166 optimal weight: 0.0040 chunk 230 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 618 GLN I 620 ASN J 430 HIS J 651 HIS J 792 ASN J1197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.204303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131028 restraints weight = 28498.382| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.38 r_work: 0.2937 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26617 Z= 0.103 Angle : 0.518 11.639 36224 Z= 0.270 Chirality : 0.041 0.227 4150 Planarity : 0.004 0.080 4517 Dihedral : 13.093 128.806 4311 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.41 % Allowed : 18.00 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3148 helix: 2.02 (0.16), residues: 1102 sheet: 0.50 (0.25), residues: 435 loop : -0.53 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG J 133 TYR 0.011 0.001 TYR I 123 PHE 0.022 0.001 PHE J1199 TRP 0.005 0.001 TRP J 33 HIS 0.004 0.000 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (26609) covalent geometry : angle 0.51634 / 0.27 (36212) hydrogen bonds : bond 0.03886 / 2.37 ( 1122) hydrogen bonds : angle 3.98186 / 2.56 ( 3109) metal coordination : bond 0.00238 / 0.12 ( 8) metal coordination : angle 2.16474 / 1.44 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.8625 (tpp80) cc_final: 0.8319 (tpp-160) REVERT: G 57 THR cc_start: 0.9139 (m) cc_final: 0.8527 (p) REVERT: G 157 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7970 (m) REVERT: G 229 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7345 (mt-10) REVERT: H 96 ASP cc_start: 0.7970 (p0) cc_final: 0.7675 (m-30) REVERT: H 219 ARG cc_start: 0.7691 (mmm-85) cc_final: 0.7309 (mmt90) REVERT: I 74 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7570 (ttt-90) REVERT: I 370 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7247 (mmp) REVERT: I 518 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7152 (OUTLIER) REVERT: I 542 ARG cc_start: 0.6353 (ptt90) cc_final: 0.5220 (mmp80) REVERT: I 647 ARG cc_start: 0.8342 (ttt180) cc_final: 0.7438 (mtm180) REVERT: I 1064 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8276 (p0) REVERT: I 1079 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8170 (mt) REVERT: I 1119 MET cc_start: 0.8527 (ttm) cc_final: 0.8231 (ttm) REVERT: I 1143 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: J 227 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7335 (t80) REVERT: J 237 MET cc_start: 0.8995 (mtm) cc_final: 0.8720 (mtm) REVERT: J 534 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: J 552 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8943 (mt) REVERT: J 797 THR cc_start: 0.9097 (t) cc_final: 0.8398 (m) REVERT: J 802 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7703 (t0) REVERT: J 1189 MET cc_start: 0.7287 (tpp) cc_final: 0.6698 (tpp) outliers start: 65 outliers final: 45 residues processed: 335 average time/residue: 0.7817 time to fit residues: 299.5146 Evaluate side-chains 334 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 280 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 180 optimal weight: 0.1980 chunk 143 optimal weight: 6.9990 chunk 287 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 302 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 283 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 618 GLN I 620 ASN J 430 HIS J 651 HIS J 777 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.203415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137101 restraints weight = 28132.710| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.72 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26617 Z= 0.119 Angle : 0.539 11.716 36224 Z= 0.280 Chirality : 0.041 0.229 4150 Planarity : 0.004 0.077 4517 Dihedral : 13.098 128.327 4309 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.52 % Allowed : 17.96 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3148 helix: 2.00 (0.16), residues: 1102 sheet: 0.55 (0.25), residues: 421 loop : -0.54 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG J 133 TYR 0.011 0.001 TYR G 177 PHE 0.014 0.001 PHE J1319 TRP 0.004 0.001 TRP J1193 HIS 0.011 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (26609) covalent geometry : angle 0.53745 / 0.28 (36212) hydrogen bonds : bond 0.04395 / 2.67 ( 1122) hydrogen bonds : angle 4.00348 / 2.58 ( 3109) metal coordination : bond 0.00244 / 0.12 ( 8) metal coordination : angle 2.23849 / 1.49 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10527.80 seconds wall clock time: 179 minutes 20.45 seconds (10760.45 seconds total)