Starting phenix.real_space_refine on Mon Jul 6 04:12:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p18_20233/07_2026/6p18_20233.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p18_20233/07_2026/6p18_20233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6p18_20233/07_2026/6p18_20233.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p18_20233/07_2026/6p18_20233.cif" model { file = "/net/cci-nas-00/data/ceres_data/6p18_20233/07_2026/6p18_20233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p18_20233/07_2026/6p18_20233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p18_20233/07_2026/6p18_20233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p18_20233/07_2026/6p18_20233.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 123 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 20120 2.51 5 N 5793 2.21 5 O 6491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32673 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1153 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "2" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1142 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10568 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10319 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1271} Chain breaks: 2 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2665 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 6, 'TRANS': 318} Chain breaks: 2 Chain: "P" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1165 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "Q" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1261 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "R" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 244 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16874 SG CYS D 70 58.979 119.013 85.312 1.00 46.06 S ATOM 16888 SG CYS D 72 60.321 122.141 84.051 1.00 47.41 S ATOM 16996 SG CYS D 85 58.195 120.359 81.163 1.00 51.55 S ATOM 17020 SG CYS D 88 61.752 119.701 81.629 1.00 46.73 S ATOM 22708 SG CYS D 814 58.114 52.188 74.105 1.00 40.48 S ATOM 23273 SG CYS D 888 60.903 55.573 74.913 1.00 31.50 S ATOM 23324 SG CYS D 895 58.341 53.893 77.348 1.00 27.28 S ATOM 23345 SG CYS D 898 60.983 51.584 76.680 1.00 26.31 S Time building chain proxies: 6.47, per 1000 atoms: 0.20 Number of scatterers: 32673 At special positions: 0 Unit cell: (158.834, 179.088, 172.692, 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 143 16.00 P 123 15.00 Mg 1 11.99 O 6491 8.00 N 5793 7.00 C 20120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " Number of angles added : 12 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 47 sheets defined 43.7% alpha, 13.1% beta 50 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.531A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.222A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.657A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.044A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.884A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.799A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.192A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.887A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.737A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.552A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.629A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 549' Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.812A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.065A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 removed outlier: 4.095A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.777A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1334 removed outlier: 3.921A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.694A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.606A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.907A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 515 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.522A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.573A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.596A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.763A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.991A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.325A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.941A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.798A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.343A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1361 through 1375 removed outlier: 4.515A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 114 through 135 removed outlier: 3.690A pdb=" N ASP F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 216 through 232 Processing helix chain 'F' and resid 243 through 257 removed outlier: 3.673A pdb=" N LYS F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 294 removed outlier: 4.195A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 315 through 321 Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.681A pdb=" N LEU F 330 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 381 removed outlier: 3.576A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.528A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.642A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 4.309A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 444 removed outlier: 4.644A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 467 Processing helix chain 'P' and resid 9 through 29 removed outlier: 3.801A pdb=" N SER P 29 " --> pdb=" O ALA P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 44 Processing helix chain 'P' and resid 59 through 74 removed outlier: 3.779A pdb=" N GLY P 63 " --> pdb=" O ASN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 89 Processing helix chain 'P' and resid 93 through 103 removed outlier: 3.500A pdb=" N ILE P 97 " --> pdb=" O SER P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 150 Proline residue: P 143 - end of helix Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 29 through 31 No H-bonds generated for 'chain 'Q' and resid 29 through 31' Processing helix chain 'Q' and resid 38 through 48 Processing helix chain 'Q' and resid 60 through 74 Processing helix chain 'Q' and resid 77 through 89 Processing helix chain 'Q' and resid 93 through 104 Processing helix chain 'Q' and resid 122 through 151 removed outlier: 3.536A pdb=" N CYS Q 126 " --> pdb=" O SER Q 122 " (cutoff:3.500A) Proline residue: Q 143 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 6.812A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.518A pdb=" N GLU A 60 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.560A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 16 removed outlier: 4.013A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 105 removed outlier: 6.286A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.509A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.186A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.440A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.891A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 68 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 98 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.151A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 160 removed outlier: 3.640A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AC1, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.966A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.089A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.526A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.526A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.783A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.962A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 1065 through 1066 removed outlier: 7.099A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.677A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 877 " --> pdb=" O GLY C 926 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.850A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.548A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.623A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD7, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.689A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.228A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.942A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.513A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.645A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 958 through 961 removed outlier: 3.503A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 984 " --> pdb=" O GLU D 993 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 966 removed outlier: 4.040A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1025 through 1026 removed outlier: 3.962A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.571A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D1077 " --> pdb=" O THR D1038 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AE9, first strand: chain 'D' and resid 1164 through 1165 Processing sheet with id=AF1, first strand: chain 'D' and resid 1280 through 1281 removed outlier: 4.008A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 108 through 109 1363 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 8.44 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8109 1.33 - 1.45: 6360 1.45 - 1.57: 18478 1.57 - 1.69: 244 1.69 - 1.81: 249 Bond restraints: 33440 Sorted by residual: bond pdb=" C3' DC 2 55 " pdb=" C2' DC 2 55 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA 1 12 " pdb=" C2' DA 1 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC 2 27 " pdb=" C2' DC 2 27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DC 2 47 " pdb=" C2' DC 2 47 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.85e+00 bond pdb=" C3' DA 1 24 " pdb=" C2' DA 1 24 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.47e+00 ... (remaining 33435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 44544 2.17 - 4.34: 1005 4.34 - 6.51: 88 6.51 - 8.68: 28 8.68 - 10.85: 11 Bond angle restraints: 45676 Sorted by residual: angle pdb=" C GLY B 209 " pdb=" N THR B 210 " pdb=" CA THR B 210 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C MET F 322 " pdb=" N ASN F 323 " pdb=" CA ASN F 323 " ideal model delta sigma weight residual 121.54 131.64 -10.10 1.91e+00 2.74e-01 2.80e+01 angle pdb=" O4' DG 1 43 " pdb=" C4' DG 1 43 " pdb=" C3' DG 1 43 " ideal model delta sigma weight residual 106.00 102.90 3.10 6.00e-01 2.78e+00 2.67e+01 angle pdb=" O4' DA 2 21 " pdb=" C4' DA 2 21 " pdb=" C3' DA 2 21 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 angle pdb=" N LYS C 991 " pdb=" CA LYS C 991 " pdb=" C LYS C 991 " ideal model delta sigma weight residual 113.28 107.33 5.95 1.22e+00 6.72e-01 2.38e+01 ... (remaining 45671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17329 17.93 - 35.86: 2092 35.86 - 53.78: 630 53.78 - 71.71: 157 71.71 - 89.64: 30 Dihedral angle restraints: 20238 sinusoidal: 9221 harmonic: 11017 Sorted by residual: dihedral pdb=" CA LEU C 397 " pdb=" C LEU C 397 " pdb=" N SER C 398 " pdb=" CA SER C 398 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASP D 710 " pdb=" C ASP D 710 " pdb=" N GLY D 711 " pdb=" CA GLY D 711 " ideal model delta harmonic sigma weight residual 180.00 154.53 25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA SER C 398 " pdb=" C SER C 398 " pdb=" N ALA C 399 " pdb=" CA ALA C 399 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 20235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4444 0.073 - 0.145: 671 0.145 - 0.218: 53 0.218 - 0.291: 2 0.291 - 0.364: 5 Chirality restraints: 5175 Sorted by residual: chirality pdb=" CB ILE D 707 " pdb=" CA ILE D 707 " pdb=" CG1 ILE D 707 " pdb=" CG2 ILE D 707 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL D1280 " pdb=" CA VAL D1280 " pdb=" CG1 VAL D1280 " pdb=" CG2 VAL D1280 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 5172 not shown) Planarity restraints: 5519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 324 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO F 325 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 325 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 325 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO C 190 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO C 520 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.039 5.00e-02 4.00e+02 ... (remaining 5516 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 564 2.67 - 3.23: 27476 3.23 - 3.78: 51384 3.78 - 4.34: 67563 4.34 - 4.90: 109894 Nonbonded interactions: 256881 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.110 2.170 nonbonded pdb=" O3' A R 11 " pdb="MG MG D1503 " model vdw 2.116 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.144 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.191 2.170 nonbonded pdb=" OE2 GLU D 981 " pdb=" OG SER D 994 " model vdw 2.302 3.040 ... (remaining 256876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = (chain 'P' and resid 7 through 150) selection = (chain 'Q' and resid 7 through 150) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 36.630 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.005 0.246 33448 Z= 0.267 Angle : 0.822 28.967 45688 Z= 0.498 Chirality : 0.051 0.364 5175 Planarity : 0.006 0.080 5519 Dihedral : 17.291 89.640 13144 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.28 % Allowed : 6.54 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: -3.80 (0.10), residues: 3802 helix: -2.17 (0.09), residues: 1574 sheet: -2.23 (0.23), residues: 399 loop : -2.89 (0.11), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 69 TYR 0.021 0.001 TYR D 679 PHE 0.028 0.002 PHE F 266 TRP 0.025 0.001 TRP F 326 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.25 (33440) covalent geometry : angle 0.78025 / 0.50 (45676) hydrogen bonds : bond 0.16515 / 18.04 ( 1481) hydrogen bonds : angle 7.31176 / 9.39 ( 4166) metal coordination : bond 0.17411 / 14.81 ( 8) metal coordination : angle 15.91434 / 24.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 582 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7947 (ttpp) REVERT: A 117 HIS cc_start: 0.7606 (p-80) cc_final: 0.7341 (p-80) REVERT: B 229 GLU cc_start: 0.7479 (tp30) cc_final: 0.7140 (tp30) REVERT: C 524 ILE cc_start: 0.8837 (tt) cc_final: 0.8593 (tt) REVERT: C 696 ASP cc_start: 0.7953 (t70) cc_final: 0.7636 (t70) REVERT: C 952 GLN cc_start: 0.8164 (mt0) cc_final: 0.7928 (mt0) REVERT: D 140 TYR cc_start: 0.7162 (m-10) cc_final: 0.6832 (m-80) REVERT: D 802 ASP cc_start: 0.7850 (m-30) cc_final: 0.7609 (m-30) REVERT: D 984 LEU cc_start: 0.8002 (tt) cc_final: 0.7770 (tt) REVERT: D 1146 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6932 (tm-30) REVERT: D 1243 LEU cc_start: 0.8188 (tp) cc_final: 0.7977 (tp) REVERT: F 276 MET cc_start: 0.7472 (ppp) cc_final: 0.7185 (ppp) REVERT: P 87 TYR cc_start: 0.8795 (t80) cc_final: 0.8287 (t80) REVERT: Q 21 GLU cc_start: 0.7842 (tp30) cc_final: 0.7623 (mm-30) REVERT: Q 90 HIS cc_start: 0.8294 (t70) cc_final: 0.8066 (t-170) outliers start: 9 outliers final: 1 residues processed: 588 average time/residue: 0.2214 time to fit residues: 200.3063 Evaluate side-chains 396 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 150 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 93 GLN B 37 HIS B 128 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 447 HIS C 622 ASN C 673 HIS C1108 ASN C1313 HIS D 196 GLN D 232 ASN D 294 ASN D 300 GLN D 450 HIS D 504 GLN D 777 HIS D 875 ASN D1098 GLN D1108 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1252 HIS D1259 GLN F 128 ASN F 258 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN P 68 GLN P 90 HIS ** Q 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.177087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145342 restraints weight = 41613.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147092 restraints weight = 107839.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147535 restraints weight = 50327.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147623 restraints weight = 33486.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148195 restraints weight = 28098.356| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 33448 Z= 0.211 Angle : 0.640 9.186 45688 Z= 0.341 Chirality : 0.044 0.205 5175 Planarity : 0.005 0.067 5519 Dihedral : 15.968 89.538 5589 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.68 % Allowed : 12.44 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.12), residues: 3802 helix: -0.38 (0.12), residues: 1584 sheet: -2.14 (0.23), residues: 401 loop : -2.51 (0.12), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 117 TYR 0.024 0.002 TYR C 70 PHE 0.027 0.002 PHE F 306 TRP 0.019 0.001 TRP F 326 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (33440) covalent geometry : angle 0.63374 / 0.34 (45676) hydrogen bonds : bond 0.04937 / 5.36 ( 1481) hydrogen bonds : angle 4.95350 / 6.40 ( 4166) metal coordination : bond 0.00952 / 0.91 ( 8) metal coordination : angle 5.46718 / 8.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 419 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.8695 (ttm) cc_final: 0.8455 (ttm) REVERT: C 158 ASP cc_start: 0.6966 (t70) cc_final: 0.6676 (t70) REVERT: C 516 ASP cc_start: 0.7349 (t0) cc_final: 0.7032 (t0) REVERT: C 524 ILE cc_start: 0.8711 (tt) cc_final: 0.8411 (tt) REVERT: C 696 ASP cc_start: 0.8167 (t70) cc_final: 0.7830 (t70) REVERT: C 1108 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8391 (p0) REVERT: D 96 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7966 (ptpt) REVERT: D 140 TYR cc_start: 0.7186 (m-10) cc_final: 0.6855 (m-80) REVERT: D 697 MET cc_start: 0.7924 (tmm) cc_final: 0.7529 (tmm) REVERT: D 802 ASP cc_start: 0.7940 (m-30) cc_final: 0.7709 (m-30) REVERT: D 1146 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6917 (tm-30) REVERT: D 1208 ASP cc_start: 0.5681 (t0) cc_final: 0.5429 (t0) REVERT: F 276 MET cc_start: 0.6771 (ppp) cc_final: 0.6482 (ppp) REVERT: P 7 ASN cc_start: 0.7458 (m-40) cc_final: 0.7127 (t0) REVERT: P 12 GLN cc_start: 0.4861 (tp40) cc_final: 0.2540 (tp40) REVERT: P 132 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7147 (tm-30) REVERT: Q 90 HIS cc_start: 0.8127 (t70) cc_final: 0.7882 (t-170) outliers start: 55 outliers final: 34 residues processed: 450 average time/residue: 0.1963 time to fit residues: 139.8612 Evaluate side-chains 413 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 377 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 38 optimal weight: 10.0000 chunk 357 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 281 optimal weight: 30.0000 chunk 258 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 141 optimal weight: 0.0970 chunk 53 optimal weight: 0.0370 chunk 83 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 overall best weight: 1.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C1008 GLN C1108 ASN D 196 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.177890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148738 restraints weight = 41317.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149687 restraints weight = 105821.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148026 restraints weight = 43728.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148345 restraints weight = 30657.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148618 restraints weight = 24594.166| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33448 Z= 0.158 Angle : 0.589 8.594 45688 Z= 0.314 Chirality : 0.043 0.201 5175 Planarity : 0.004 0.062 5519 Dihedral : 15.905 89.715 5589 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.11 % Allowed : 14.19 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.13), residues: 3802 helix: 0.38 (0.13), residues: 1594 sheet: -1.91 (0.24), residues: 391 loop : -2.24 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1345 TYR 0.029 0.002 TYR F 148 PHE 0.034 0.001 PHE F 302 TRP 0.016 0.001 TRP F 326 HIS 0.005 0.001 HIS P 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (33440) covalent geometry : angle 0.58436 / 0.31 (45676) hydrogen bonds : bond 0.04214 / 4.57 ( 1481) hydrogen bonds : angle 4.62806 / 5.94 ( 4166) metal coordination : bond 0.00582 / 0.54 ( 8) metal coordination : angle 4.54237 / 7.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 405 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 516 ASP cc_start: 0.7428 (t0) cc_final: 0.7036 (t0) REVERT: C 524 ILE cc_start: 0.8719 (tt) cc_final: 0.8473 (tt) REVERT: C 696 ASP cc_start: 0.8213 (t70) cc_final: 0.7938 (t70) REVERT: D 96 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8061 (ptpt) REVERT: D 136 GLU cc_start: 0.7756 (tp30) cc_final: 0.7404 (tp30) REVERT: D 140 TYR cc_start: 0.7275 (m-10) cc_final: 0.6941 (m-80) REVERT: D 1146 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6897 (tm-30) REVERT: P 12 GLN cc_start: 0.4302 (tp40) cc_final: 0.1735 (tp40) REVERT: P 132 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7203 (tm-30) REVERT: Q 21 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7426 (tm-30) REVERT: Q 90 HIS cc_start: 0.8133 (t70) cc_final: 0.7908 (t-170) outliers start: 69 outliers final: 48 residues processed: 450 average time/residue: 0.2065 time to fit residues: 148.5445 Evaluate side-chains 425 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 376 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 167 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 279 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 373 optimal weight: 4.9990 chunk 335 optimal weight: 50.0000 chunk 285 optimal weight: 0.0040 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN B 103 ASN B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN D 196 GLN D 341 ASN D 962 ASN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.177594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141950 restraints weight = 41199.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141150 restraints weight = 85110.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142720 restraints weight = 66589.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143567 restraints weight = 36535.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144698 restraints weight = 29977.486| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33448 Z= 0.161 Angle : 0.575 9.271 45688 Z= 0.305 Chirality : 0.043 0.164 5175 Planarity : 0.004 0.056 5519 Dihedral : 15.874 89.926 5589 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.51 % Allowed : 14.98 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 3802 helix: 0.75 (0.13), residues: 1596 sheet: -1.77 (0.25), residues: 385 loop : -2.05 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 278 TYR 0.045 0.002 TYR F 148 PHE 0.032 0.001 PHE F 302 TRP 0.017 0.001 TRP F 326 HIS 0.005 0.001 HIS P 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (33440) covalent geometry : angle 0.57121 / 0.31 (45676) hydrogen bonds : bond 0.04016 / 4.38 ( 1481) hydrogen bonds : angle 4.44938 / 5.70 ( 4166) metal coordination : bond 0.00716 / 0.65 ( 8) metal coordination : angle 3.92301 / 6.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 388 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.8801 (ttm) cc_final: 0.8569 (ttm) REVERT: C 516 ASP cc_start: 0.7426 (t0) cc_final: 0.6977 (t0) REVERT: C 524 ILE cc_start: 0.8728 (tt) cc_final: 0.8474 (tt) REVERT: C 696 ASP cc_start: 0.8247 (t70) cc_final: 0.7942 (t70) REVERT: C 1230 MET cc_start: 0.8425 (ttm) cc_final: 0.8205 (ttt) REVERT: D 96 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8229 (ptpt) REVERT: D 458 ASN cc_start: 0.8165 (t0) cc_final: 0.7864 (m-40) REVERT: D 649 LYS cc_start: 0.8196 (ptpp) cc_final: 0.7693 (mtpt) REVERT: D 822 MET cc_start: 0.8149 (mmm) cc_final: 0.7808 (tpt) REVERT: D 1146 GLU cc_start: 0.7253 (tm-30) cc_final: 0.7018 (tm-30) REVERT: E 55 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6316 (tp30) REVERT: F 362 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.7928 (t0) REVERT: P 12 GLN cc_start: 0.5422 (tp40) cc_final: 0.3406 (tp40) REVERT: P 15 TRP cc_start: 0.7363 (t60) cc_final: 0.6901 (t60) REVERT: P 64 MET cc_start: 0.7575 (tpp) cc_final: 0.7298 (tpp) REVERT: P 87 TYR cc_start: 0.8876 (t80) cc_final: 0.8564 (t80) REVERT: P 132 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7460 (tm-30) REVERT: Q 21 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7484 (tm-30) REVERT: Q 90 HIS cc_start: 0.8200 (t70) cc_final: 0.7983 (t-170) outliers start: 82 outliers final: 54 residues processed: 446 average time/residue: 0.1987 time to fit residues: 142.2341 Evaluate side-chains 418 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 361 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 369 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 204 optimal weight: 9.9990 chunk 267 optimal weight: 0.0970 chunk 122 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 371 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 359 optimal weight: 4.9990 chunk 315 optimal weight: 3.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146558 restraints weight = 41335.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148415 restraints weight = 108640.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148665 restraints weight = 48873.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148884 restraints weight = 32236.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149427 restraints weight = 27486.027| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33448 Z= 0.152 Angle : 0.560 10.454 45688 Z= 0.298 Chirality : 0.042 0.157 5175 Planarity : 0.004 0.055 5519 Dihedral : 15.843 89.823 5589 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.38 % Allowed : 16.51 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: -0.97 (0.13), residues: 3802 helix: 0.95 (0.13), residues: 1593 sheet: -1.64 (0.25), residues: 397 loop : -1.93 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1345 TYR 0.047 0.002 TYR F 148 PHE 0.025 0.001 PHE F 221 TRP 0.016 0.001 TRP F 326 HIS 0.005 0.001 HIS P 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (33440) covalent geometry : angle 0.55659 / 0.30 (45676) hydrogen bonds : bond 0.03885 / 4.25 ( 1481) hydrogen bonds : angle 4.34619 / 5.57 ( 4166) metal coordination : bond 0.00675 / 0.62 ( 8) metal coordination : angle 3.60931 / 5.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 381 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLN cc_start: 0.7338 (mm110) cc_final: 0.6724 (mm-40) REVERT: C 158 ASP cc_start: 0.6877 (t70) cc_final: 0.6571 (t70) REVERT: C 516 ASP cc_start: 0.7464 (t0) cc_final: 0.6986 (t0) REVERT: C 524 ILE cc_start: 0.8734 (tt) cc_final: 0.8480 (tt) REVERT: C 696 ASP cc_start: 0.8239 (t70) cc_final: 0.7869 (t70) REVERT: C 1108 ASN cc_start: 0.8785 (p0) cc_final: 0.8429 (p0) REVERT: C 1230 MET cc_start: 0.8428 (ttm) cc_final: 0.8217 (ttt) REVERT: C 1231 TYR cc_start: 0.9020 (t80) cc_final: 0.8195 (t80) REVERT: D 140 TYR cc_start: 0.7366 (m-10) cc_final: 0.7112 (m-80) REVERT: D 221 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8934 (mm) REVERT: D 458 ASN cc_start: 0.8195 (t0) cc_final: 0.7901 (m-40) REVERT: D 526 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8545 (m) REVERT: D 822 MET cc_start: 0.7962 (mmm) cc_final: 0.7755 (tpt) REVERT: D 1146 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6977 (tm-30) REVERT: D 1215 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5893 (pt0) REVERT: E 55 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6296 (tp30) REVERT: F 277 MET cc_start: 0.4994 (mmt) cc_final: 0.4773 (mmt) REVERT: F 362 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7359 (t0) REVERT: P 12 GLN cc_start: 0.3650 (tp40) cc_final: 0.3069 (tp40) REVERT: P 57 MET cc_start: 0.5423 (tpp) cc_final: 0.4939 (tpt) REVERT: P 142 TYR cc_start: 0.5822 (t80) cc_final: 0.5578 (t80) REVERT: Q 21 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7327 (tm-30) REVERT: Q 90 HIS cc_start: 0.8128 (t70) cc_final: 0.7909 (t-170) outliers start: 78 outliers final: 57 residues processed: 434 average time/residue: 0.1992 time to fit residues: 138.7352 Evaluate side-chains 419 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 357 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 135 ASN Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 145 optimal weight: 10.0000 chunk 356 optimal weight: 8.9990 chunk 387 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 286 optimal weight: 20.0000 chunk 347 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 384 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 651 HIS ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.178395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.137780 restraints weight = 41178.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.135709 restraints weight = 64418.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130768 restraints weight = 39777.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129712 restraints weight = 43018.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130391 restraints weight = 38411.343| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33448 Z= 0.136 Angle : 0.554 10.569 45688 Z= 0.294 Chirality : 0.042 0.238 5175 Planarity : 0.004 0.055 5519 Dihedral : 15.813 89.642 5589 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.66 % Allowed : 16.88 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 3802 helix: 1.05 (0.13), residues: 1601 sheet: -1.53 (0.25), residues: 402 loop : -1.82 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1345 TYR 0.045 0.001 TYR F 137 PHE 0.043 0.001 PHE F 221 TRP 0.016 0.001 TRP F 326 HIS 0.010 0.001 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (33440) covalent geometry : angle 0.55170 / 0.29 (45676) hydrogen bonds : bond 0.03760 / 4.11 ( 1481) hydrogen bonds : angle 4.28862 / 5.51 ( 4166) metal coordination : bond 0.00586 / 0.53 ( 8) metal coordination : angle 3.32468 / 5.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 370 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 ARG cc_start: 0.7866 (ttm110) cc_final: 0.7435 (mtm110) REVERT: C 158 ASP cc_start: 0.6888 (t70) cc_final: 0.6636 (t70) REVERT: C 516 ASP cc_start: 0.7567 (t0) cc_final: 0.7092 (t0) REVERT: C 524 ILE cc_start: 0.8851 (tt) cc_final: 0.8581 (tt) REVERT: C 817 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8620 (tt) REVERT: C 1108 ASN cc_start: 0.8820 (p0) cc_final: 0.8474 (p0) REVERT: C 1230 MET cc_start: 0.8599 (ttm) cc_final: 0.8384 (ttt) REVERT: C 1231 TYR cc_start: 0.9033 (t80) cc_final: 0.8160 (t80) REVERT: D 136 GLU cc_start: 0.7818 (tp30) cc_final: 0.7599 (tp30) REVERT: D 214 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7439 (mmm-85) REVERT: D 221 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8953 (mm) REVERT: D 458 ASN cc_start: 0.8272 (t0) cc_final: 0.7990 (m-40) REVERT: D 1146 GLU cc_start: 0.7277 (tm-30) cc_final: 0.7057 (tm-30) REVERT: D 1189 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7648 (tpp) REVERT: D 1215 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6275 (pt0) REVERT: E 55 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6471 (tp30) REVERT: F 277 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6501 (mmt) REVERT: F 362 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8196 (t0) REVERT: P 12 GLN cc_start: 0.5301 (tp40) cc_final: 0.4745 (tp40) REVERT: P 57 MET cc_start: 0.6396 (tpp) cc_final: 0.5803 (tpt) REVERT: Q 21 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7543 (tm-30) REVERT: Q 90 HIS cc_start: 0.8375 (t70) cc_final: 0.8159 (t-170) outliers start: 87 outliers final: 60 residues processed: 430 average time/residue: 0.1763 time to fit residues: 121.7013 Evaluate side-chains 424 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 357 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 147 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 281 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 96 optimal weight: 0.9990 chunk 302 optimal weight: 7.9990 chunk 225 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 490 GLN D 196 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.176593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145610 restraints weight = 41285.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147128 restraints weight = 113361.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147481 restraints weight = 49932.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148090 restraints weight = 32571.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148238 restraints weight = 29016.199| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33448 Z= 0.193 Angle : 0.589 11.377 45688 Z= 0.311 Chirality : 0.043 0.219 5175 Planarity : 0.004 0.054 5519 Dihedral : 15.861 89.879 5589 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.78 % Allowed : 17.49 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 3802 helix: 1.03 (0.13), residues: 1601 sheet: -1.56 (0.25), residues: 415 loop : -1.79 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1345 TYR 0.035 0.002 TYR P 142 PHE 0.046 0.001 PHE F 221 TRP 0.015 0.001 TRP F 326 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (33440) covalent geometry : angle 0.58598 / 0.31 (45676) hydrogen bonds : bond 0.04038 / 4.41 ( 1481) hydrogen bonds : angle 4.33308 / 5.55 ( 4166) metal coordination : bond 0.00921 / 0.84 ( 8) metal coordination : angle 3.47808 / 5.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 367 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 516 ASP cc_start: 0.7516 (t0) cc_final: 0.7096 (t0) REVERT: C 524 ILE cc_start: 0.8742 (tt) cc_final: 0.8492 (tt) REVERT: D 221 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8907 (mm) REVERT: D 724 MET cc_start: 0.7804 (mtm) cc_final: 0.7549 (mtm) REVERT: D 1040 MET cc_start: 0.3977 (ttp) cc_final: 0.2627 (ptt) REVERT: D 1189 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7141 (tpp) REVERT: D 1215 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5890 (pt0) REVERT: E 55 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6343 (tp30) REVERT: F 362 ASN cc_start: 0.7561 (OUTLIER) cc_final: 0.7358 (t0) REVERT: Q 21 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7291 (tm-30) outliers start: 91 outliers final: 70 residues processed: 433 average time/residue: 0.1948 time to fit residues: 136.0347 Evaluate side-chains 432 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 357 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 6 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 340 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 40.0000 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 360 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 686 GLN D 157 GLN D 196 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.174558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142595 restraints weight = 41628.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144539 restraints weight = 112916.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144782 restraints weight = 45006.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145378 restraints weight = 30830.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145512 restraints weight = 27712.583| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 33448 Z= 0.256 Angle : 0.646 10.246 45688 Z= 0.338 Chirality : 0.044 0.195 5175 Planarity : 0.004 0.058 5519 Dihedral : 15.948 89.594 5589 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.54 % Allowed : 18.43 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.40 % 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: -0.87 (0.13), residues: 3802 helix: 0.92 (0.13), residues: 1605 sheet: -1.61 (0.25), residues: 420 loop : -1.75 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1345 TYR 0.048 0.002 TYR P 142 PHE 0.034 0.002 PHE F 221 TRP 0.042 0.002 TRP D1193 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.26 (33440) covalent geometry : angle 0.64305 / 0.34 (45676) hydrogen bonds : bond 0.04374 / 4.74 ( 1481) hydrogen bonds : angle 4.43307 / 5.68 ( 4166) metal coordination : bond 0.01255 / 1.16 ( 8) metal coordination : angle 3.78203 / 5.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7604 Ramachandran restraints generated. 3802 Oldfield, 0 Emsley, 3802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 369 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 ASP cc_start: 0.6963 (t70) cc_final: 0.6627 (t70) REVERT: C 239 MET cc_start: 0.7972 (tmm) cc_final: 0.7677 (tmm) REVERT: C 516 ASP cc_start: 0.7556 (t0) cc_final: 0.7194 (t0) REVERT: C 524 ILE cc_start: 0.8746 (tt) cc_final: 0.8519 (tt) REVERT: C 800 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8109 (mtm) REVERT: C 922 ASN cc_start: 0.7988 (m-40) cc_final: 0.7764 (m-40) REVERT: D 214 ARG cc_start: 0.7473 (tpp80) cc_final: 0.7140 (mmm-85) REVERT: D 221 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8980 (mm) REVERT: D 457 TYR cc_start: 0.8998 (m-80) cc_final: 0.8636 (m-80) REVERT: D 724 MET cc_start: 0.7970 (mtm) cc_final: 0.7722 (mtm) REVERT: D 802 ASP cc_start: 0.7858 (m-30) cc_final: 0.7609 (m-30) REVERT: D 1040 MET cc_start: 0.4658 (ttp) cc_final: 0.2974 (ptt) REVERT: D 1189 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7227 (tpp) REVERT: D 1215 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5982 (pt0) REVERT: E 55 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6405 (tp30) REVERT: P 12 GLN cc_start: 0.4651 (tp40) cc_final: 0.2896 (tp40) REVERT: Q 21 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7383 (tm-30) outliers start: 83 outliers final: 74 residues processed: 435 average time/residue: 0.1999 time to fit residues: 140.4622 Evaluate side-chains 435 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 356 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 961 SER Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1205 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 149 PHE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 133 ILE Chi-restraints excluded: chain Q residue 134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.2875 > 50: distance: 23 - 98: 32.177 distance: 26 - 95: 26.708 distance: 74 - 103: 28.683 distance: 91 - 95: 25.569 distance: 95 - 96: 12.710 distance: 96 - 97: 42.128 distance: 96 - 99: 31.986 distance: 97 - 98: 44.121 distance: 97 - 103: 34.853 distance: 99 - 100: 34.135 distance: 100 - 101: 48.784 distance: 101 - 102: 43.861 distance: 103 - 104: 56.905 distance: 104 - 105: 52.249 distance: 104 - 107: 41.590 distance: 105 - 106: 40.814 distance: 105 - 112: 58.309 distance: 107 - 108: 30.149 distance: 108 - 109: 22.475 distance: 109 - 110: 11.209 distance: 109 - 111: 21.548 distance: 112 - 113: 40.760 distance: 113 - 114: 27.536 distance: 113 - 116: 31.535 distance: 114 - 115: 46.708 distance: 114 - 119: 43.010 distance: 116 - 117: 28.317 distance: 116 - 118: 21.568 distance: 119 - 120: 26.168 distance: 120 - 121: 42.458 distance: 120 - 123: 20.098 distance: 121 - 122: 18.758 distance: 121 - 127: 48.978 distance: 123 - 124: 47.821 distance: 124 - 125: 43.819 distance: 124 - 126: 45.623 distance: 127 - 128: 42.637 distance: 128 - 129: 24.586 distance: 129 - 130: 36.654 distance: 129 - 131: 29.267 distance: 131 - 132: 53.633 distance: 132 - 133: 60.473 distance: 132 - 135: 34.670 distance: 133 - 134: 39.459 distance: 133 - 138: 61.483 distance: 135 - 136: 45.937 distance: 135 - 137: 34.197 distance: 138 - 139: 41.549 distance: 139 - 140: 60.528 distance: 139 - 142: 16.958 distance: 140 - 141: 62.008 distance: 140 - 146: 9.578 distance: 142 - 143: 29.703 distance: 142 - 144: 23.138 distance: 143 - 145: 44.557 distance: 146 - 147: 25.992 distance: 147 - 148: 66.287 distance: 147 - 150: 33.960 distance: 148 - 154: 57.827 distance: 149 - 176: 34.238 distance: 150 - 151: 61.435 distance: 151 - 152: 13.958 distance: 151 - 153: 34.730 distance: 154 - 155: 31.707 distance: 154 - 160: 35.059 distance: 155 - 156: 14.222 distance: 155 - 158: 39.643 distance: 156 - 157: 28.202 distance: 156 - 161: 32.774 distance: 157 - 181: 5.264 distance: 158 - 159: 18.844 distance: 159 - 160: 29.579 distance: 161 - 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