Starting phenix.real_space_refine on Mon May 26 13:23:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8reb_19081/05_2025/8reb_19081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8reb_19081/05_2025/8reb_19081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8reb_19081/05_2025/8reb_19081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8reb_19081/05_2025/8reb_19081.map" model { file = "/net/cci-nas-00/data/ceres_data/8reb_19081/05_2025/8reb_19081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8reb_19081/05_2025/8reb_19081.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 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 101 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 17684 2.51 5 N 5093 2.21 5 O 5702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.31s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28681 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 875 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "R" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna3p': 5} Chain: "T" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1072 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9682 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 840 Unresolved non-hydrogen dihedrals: 585 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 441 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2194 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 1 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 739 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 22, 'PHE:plan': 2, 'GLU:plan': 26, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 341 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 16779 SG CYS D 70 106.543 114.667 92.090 1.00 66.62 S ATOM 16908 SG CYS D 88 104.966 114.784 95.832 1.00 66.10 S ATOM 22401 SG CYS D 814 100.730 47.899 85.807 1.00 47.44 S ATOM 23021 SG CYS D 898 98.212 47.559 85.093 1.00 25.73 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.71 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.71 Time building chain proxies: 16.66, per 1000 atoms: 0.58 Number of scatterers: 28681 At special positions: 0 Unit cell: (140.98, 172.78, 166.42, 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 98 16.00 P 101 15.00 Mg 1 11.99 O 5702 8.00 N 5093 7.00 C 17684 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: 7.67 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6748 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 45 sheets defined 39.3% alpha, 14.2% beta 40 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 9.49 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.857A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.743A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.957A pdb=" N ASP A 164 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 263 through 273 removed outlier: 4.018A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.592A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.773A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.832A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.663A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.689A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.738A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.196A 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 280 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.544A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 422 through 438 removed outlier: 4.018A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.605A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.330A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.593A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.963A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.529A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.631A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 4.106A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 865 removed outlier: 4.146A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.805A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.729A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.299A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.708A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) 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 1242 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 1311 removed outlier: 3.954A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.519A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 4.079A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.588A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.765A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.707A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.949A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.790A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) 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 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.786A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 599 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.172A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.755A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.622A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.739A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.543A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1259 removed outlier: 3.743A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.743A pdb=" N VAL D1298 " --> pdb=" O ASN D1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1314 removed outlier: 3.961A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.551A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.991A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.170A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 4.019A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.539A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.740A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 183 Processing helix chain 'M' and resid 194 through 205 removed outlier: 3.633A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 218 removed outlier: 4.033A pdb=" N LEU M 218 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 230 Processing helix chain 'M' and resid 234 through 240 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.538A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 351 Processing helix chain 'M' and resid 351 through 356 removed outlier: 4.295A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.556A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 466 removed outlier: 3.895A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 8.777A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.702A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.599A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.513A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 3.982A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.541A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.822A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.941A 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: 6.098A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.941A 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: 6.098A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.081A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.638A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.995A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 634 through 636 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.445A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 723 through 727 removed outlier: 6.644A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.376A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.319A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 841 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: 6.723A 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 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AD6, first strand: chain 'D' and resid 104 through 111 removed outlier: 8.651A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 removed outlier: 4.134A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 825 through 827 removed outlier: 7.070A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 848 through 849 removed outlier: 7.017A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 957 through 961 Processing sheet with id=AE6, first strand: chain 'D' and resid 966 through 967 removed outlier: 5.056A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D1003 " --> pdb=" O LEU D 973 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1059 through 1062 removed outlier: 3.863A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE9, first strand: chain 'M' and resid 277 through 278 removed outlier: 7.148A pdb=" N LEU M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 1151 hydrogen bonds defined for protein. 3225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 13.76 Time building geometry restraints manager: 8.79 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: 8931 1.33 - 1.46: 4565 1.46 - 1.58: 15433 1.58 - 1.70: 202 1.70 - 1.82: 170 Bond restraints: 29301 Sorted by residual: bond pdb=" CG PRO M 258 " pdb=" CD PRO M 258 " ideal model delta sigma weight residual 1.503 1.304 0.199 3.40e-02 8.65e+02 3.42e+01 bond pdb=" N PRO M 258 " pdb=" CA PRO M 258 " ideal model delta sigma weight residual 1.469 1.429 0.039 1.28e-02 6.10e+03 9.39e+00 bond pdb=" CG PRO D1139 " pdb=" CD PRO D1139 " ideal model delta sigma weight residual 1.503 1.401 0.102 3.40e-02 8.65e+02 8.93e+00 bond pdb=" N PRO M 258 " pdb=" CD PRO M 258 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.18e+00 bond pdb=" CB PRO M 258 " pdb=" CG PRO M 258 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.35e+00 ... (remaining 29296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 40038 3.51 - 7.03: 194 7.03 - 10.54: 14 10.54 - 14.06: 1 14.06 - 17.57: 3 Bond angle restraints: 40250 Sorted by residual: angle pdb=" CA PRO M 258 " pdb=" N PRO M 258 " pdb=" CD PRO M 258 " ideal model delta sigma weight residual 112.00 94.43 17.57 1.40e+00 5.10e-01 1.58e+02 angle pdb=" N PRO M 258 " pdb=" CD PRO M 258 " pdb=" CG PRO M 258 " ideal model delta sigma weight residual 103.20 88.97 14.23 1.50e+00 4.44e-01 9.01e+01 angle pdb=" CA PRO D1139 " pdb=" N PRO D1139 " pdb=" CD PRO D1139 " ideal model delta sigma weight residual 112.00 101.82 10.18 1.40e+00 5.10e-01 5.28e+01 angle pdb=" N ILE A 159 " pdb=" CA ILE A 159 " pdb=" C ILE A 159 " ideal model delta sigma weight residual 113.53 107.94 5.59 9.80e-01 1.04e+00 3.25e+01 angle pdb=" C ASP D 67 " pdb=" CA ASP D 67 " pdb=" CB ASP D 67 " ideal model delta sigma weight residual 116.54 110.16 6.38 1.15e+00 7.56e-01 3.07e+01 ... (remaining 40245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 16635 34.34 - 68.68: 918 68.68 - 103.02: 42 103.02 - 137.36: 2 137.36 - 171.70: 2 Dihedral angle restraints: 17599 sinusoidal: 7140 harmonic: 10459 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 141.02 38.98 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA PHE C 15 " pdb=" C PHE C 15 " pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE D 338 " pdb=" C PHE D 338 " pdb=" N ARG D 339 " pdb=" CA ARG D 339 " ideal model delta harmonic sigma weight residual -180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 17596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3787 0.050 - 0.100: 797 0.100 - 0.150: 188 0.150 - 0.200: 15 0.200 - 0.250: 1 Chirality restraints: 4788 Sorted by residual: chirality pdb=" CB ILE D 159 " pdb=" CA ILE D 159 " pdb=" CG1 ILE D 159 " pdb=" CG2 ILE D 159 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU D 324 " pdb=" CB LEU D 324 " pdb=" CD1 LEU D 324 " pdb=" CD2 LEU D 324 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" CB ILE M 144 " pdb=" CA ILE M 144 " pdb=" CG1 ILE M 144 " pdb=" CG2 ILE M 144 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 4785 not shown) Planarity restraints: 4929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " 0.131 5.00e-02 4.00e+02 1.90e-01 5.80e+01 pdb=" N PRO D1139 " -0.329 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP M 257 " 0.100 5.00e-02 4.00e+02 1.36e-01 2.95e+01 pdb=" N PRO M 258 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO M 258 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO M 258 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 273 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO M 274 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO M 274 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO M 274 " -0.056 5.00e-02 4.00e+02 ... (remaining 4926 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 228 2.58 - 3.16: 24131 3.16 - 3.74: 44604 3.74 - 4.32: 58615 4.32 - 4.90: 97701 Nonbonded interactions: 225279 Sorted by model distance: nonbonded pdb=" O3' G R 4 " pdb="MG MG D1501 " model vdw 2.006 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.037 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 2.091 2.170 nonbonded pdb=" OG SER D 326 " pdb=" OD1 ASP D 329 " model vdw 2.141 3.040 nonbonded pdb=" NH1 ARG D 799 " pdb=" OE2 GLU D1146 " model vdw 2.153 3.120 ... (remaining 225274 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.270 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 77.730 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3518 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 0.199 29305 Z= 0.202 Angle : 0.711 17.573 40250 Z= 0.386 Chirality : 0.043 0.250 4788 Planarity : 0.006 0.190 4929 Dihedral : 19.202 171.697 10851 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.67 % Favored : 93.30 % Rotamer: Outliers : 0.38 % Allowed : 29.98 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3612 helix: 0.95 (0.15), residues: 1276 sheet: 0.46 (0.27), residues: 396 loop : -1.55 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 183 HIS 0.005 0.001 HIS D 113 PHE 0.015 0.002 PHE M 355 TYR 0.036 0.002 TYR C1053 ARG 0.008 0.001 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.16025 ( 1237) hydrogen bonds : angle 5.67167 ( 3427) metal coordination : bond 0.00284 ( 4) covalent geometry : bond 0.00488 (29301) covalent geometry : angle 0.71054 (40250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 760 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.4880 (m-80) cc_final: 0.4605 (m-10) REVERT: A 223 ILE cc_start: 0.5677 (mt) cc_final: 0.5458 (mt) REVERT: B 236 ASP cc_start: 0.5041 (t0) cc_final: 0.4717 (t0) REVERT: C 189 ASP cc_start: 0.4148 (t70) cc_final: 0.3929 (t0) REVERT: C 726 TYR cc_start: 0.3265 (t80) cc_final: 0.2905 (t80) REVERT: D 1040 MET cc_start: 0.2818 (tpt) cc_final: 0.2010 (tpt) REVERT: D 1357 ILE cc_start: 0.1264 (pt) cc_final: 0.0823 (pt) REVERT: E 54 ILE cc_start: 0.3741 (mt) cc_final: 0.3363 (mt) REVERT: M 270 GLU cc_start: 0.5301 (tp30) cc_final: 0.4568 (tm-30) REVERT: M 365 MET cc_start: 0.0162 (pmm) cc_final: -0.1949 (ppp) outliers start: 10 outliers final: 0 residues processed: 767 average time/residue: 0.4517 time to fit residues: 527.7153 Evaluate side-chains 468 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 290 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 336 optimal weight: 10.0000 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 283 GLN B 93 GLN C 462 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 762 ASN C 932 GLN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 186 GLN D 232 ASN D 309 ASN D 419 HIS D 477 GLN D 865 HIS D1249 ASN D1366 HIS M 121 GLN M 205 GLN M 265 GLN M 290 ASN M 387 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.092391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.070874 restraints weight = 115772.677| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 4.44 r_work: 0.3278 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 29305 Z= 0.291 Angle : 0.976 17.739 40250 Z= 0.502 Chirality : 0.052 0.288 4788 Planarity : 0.008 0.126 4929 Dihedral : 16.579 170.216 5044 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.84 % Favored : 93.13 % Rotamer: Outliers : 7.36 % Allowed : 26.76 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3612 helix: -0.15 (0.13), residues: 1330 sheet: 0.21 (0.28), residues: 359 loop : -1.60 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP D 115 HIS 0.015 0.003 HIS D 80 PHE 0.043 0.004 PHE M 355 TYR 0.042 0.003 TYR C 726 ARG 0.038 0.002 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.05331 ( 1237) hydrogen bonds : angle 5.00691 ( 3427) metal coordination : bond 0.00487 ( 4) covalent geometry : bond 0.00645 (29301) covalent geometry : angle 0.97583 (40250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 575 time to evaluate : 3.114 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 95 LYS cc_start: 0.8197 (pttt) cc_final: 0.7963 (pttm) REVERT: A 200 LYS cc_start: 0.8829 (ptmt) cc_final: 0.8558 (ptmm) REVERT: A 257 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7275 (m) REVERT: B 47 LEU cc_start: 0.8760 (mt) cc_final: 0.8455 (mt) REVERT: B 51 MET cc_start: 0.8146 (mmt) cc_final: 0.7873 (mmm) REVERT: B 77 ASP cc_start: 0.8104 (t0) cc_final: 0.7749 (t0) REVERT: B 200 LYS cc_start: 0.8482 (ttpt) cc_final: 0.7686 (tttt) REVERT: C 20 GLN cc_start: 0.8080 (pt0) cc_final: 0.7856 (tt0) REVERT: C 47 TYR cc_start: 0.4546 (OUTLIER) cc_final: 0.3773 (p90) REVERT: C 57 PHE cc_start: 0.6110 (m-80) cc_final: 0.5409 (m-80) REVERT: C 116 ASP cc_start: 0.8267 (t0) cc_final: 0.7754 (m-30) REVERT: C 183 TRP cc_start: 0.5043 (OUTLIER) cc_final: 0.4501 (m-10) REVERT: C 409 LEU cc_start: 0.8119 (mt) cc_final: 0.7889 (tp) REVERT: C 451 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5389 (ptp-170) REVERT: C 581 THR cc_start: 0.7943 (p) cc_final: 0.7711 (p) REVERT: C 609 ILE cc_start: 0.8418 (pt) cc_final: 0.8055 (pt) REVERT: C 671 LEU cc_start: 0.9162 (tp) cc_final: 0.8530 (tp) REVERT: C 741 MET cc_start: 0.8034 (ppp) cc_final: 0.7638 (mmt) REVERT: C 742 TYR cc_start: 0.7794 (m-80) cc_final: 0.7267 (m-10) REVERT: C 900 LYS cc_start: 0.6242 (OUTLIER) cc_final: 0.5584 (mttt) REVERT: C 957 LYS cc_start: 0.8766 (pptt) cc_final: 0.8211 (ptpp) REVERT: C 1022 LYS cc_start: 0.8222 (mttp) cc_final: 0.8021 (mmmt) REVERT: C 1049 ILE cc_start: 0.5573 (mm) cc_final: 0.5262 (mm) REVERT: C 1128 ILE cc_start: 0.8689 (mm) cc_final: 0.8451 (mt) REVERT: C 1168 GLU cc_start: 0.8015 (mp0) cc_final: 0.7515 (mm-30) REVERT: C 1175 ASN cc_start: 0.8314 (m-40) cc_final: 0.7982 (m110) REVERT: C 1204 LEU cc_start: 0.8248 (mp) cc_final: 0.8041 (mp) REVERT: C 1276 TRP cc_start: 0.5800 (m-10) cc_final: 0.4954 (m-10) REVERT: D 135 ILE cc_start: 0.6375 (OUTLIER) cc_final: 0.5704 (tt) REVERT: D 165 TYR cc_start: 0.9062 (t80) cc_final: 0.8853 (t80) REVERT: D 402 GLU cc_start: 0.7352 (tp30) cc_final: 0.7043 (tp30) REVERT: D 445 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7339 (mtpt) REVERT: D 447 ILE cc_start: 0.8287 (mt) cc_final: 0.7966 (mt) REVERT: D 506 VAL cc_start: 0.8786 (t) cc_final: 0.8518 (m) REVERT: D 534 GLU cc_start: 0.8764 (tp30) cc_final: 0.8286 (tp30) REVERT: D 625 MET cc_start: 0.6036 (ttm) cc_final: 0.5701 (tmm) REVERT: D 759 ILE cc_start: 0.7751 (mt) cc_final: 0.7048 (mt) REVERT: D 1040 MET cc_start: 0.3449 (tpt) cc_final: 0.2790 (tpt) REVERT: D 1230 THR cc_start: 0.8030 (m) cc_final: 0.7738 (m) REVERT: D 1287 ILE cc_start: 0.4876 (OUTLIER) cc_final: 0.4440 (mt) REVERT: D 1320 ILE cc_start: 0.7911 (mm) cc_final: 0.7582 (mm) REVERT: M 178 VAL cc_start: 0.6749 (m) cc_final: 0.6477 (p) REVERT: M 196 ARG cc_start: 0.6022 (tpt170) cc_final: 0.5736 (tpm170) REVERT: M 200 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7299 (mt) REVERT: M 265 GLN cc_start: 0.2113 (OUTLIER) cc_final: 0.1893 (mp10) REVERT: M 270 GLU cc_start: 0.7092 (tp30) cc_final: 0.5535 (tp30) outliers start: 192 outliers final: 55 residues processed: 724 average time/residue: 0.4035 time to fit residues: 461.7123 Evaluate side-chains 507 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 442 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 265 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 78 optimal weight: 4.9990 chunk 353 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 323 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 339 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 GLN C 462 ASN C 519 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN C 832 HIS C1108 ASN C1116 HIS C1175 ASN C1244 HIS C1257 GLN C1313 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.093026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071379 restraints weight = 115273.359| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 4.41 r_work: 0.3294 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29305 Z= 0.156 Angle : 0.710 11.463 40250 Z= 0.362 Chirality : 0.044 0.221 4788 Planarity : 0.005 0.087 4929 Dihedral : 16.371 172.629 5044 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.80 % Rotamer: Outliers : 4.37 % Allowed : 29.83 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3612 helix: 0.44 (0.14), residues: 1349 sheet: 0.15 (0.26), residues: 383 loop : -1.50 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 580 HIS 0.011 0.001 HIS D 80 PHE 0.031 0.002 PHE D 62 TYR 0.028 0.002 TYR A 177 ARG 0.011 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 1237) hydrogen bonds : angle 4.45380 ( 3427) metal coordination : bond 0.00169 ( 4) covalent geometry : bond 0.00352 (29301) covalent geometry : angle 0.70965 (40250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 470 time to evaluate : 2.995 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: A 141 SER cc_start: 0.7483 (OUTLIER) cc_final: 0.7063 (m) REVERT: A 257 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7389 (m) REVERT: B 35 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8130 (t80) REVERT: B 47 LEU cc_start: 0.9047 (mt) cc_final: 0.8821 (mt) REVERT: B 77 ASP cc_start: 0.8082 (t0) cc_final: 0.7756 (t0) REVERT: B 93 GLN cc_start: 0.7913 (mm110) cc_final: 0.7627 (mm-40) REVERT: B 127 GLN cc_start: 0.9212 (pm20) cc_final: 0.8805 (pm20) REVERT: C 20 GLN cc_start: 0.8131 (pt0) cc_final: 0.7843 (tt0) REVERT: C 57 PHE cc_start: 0.6308 (m-80) cc_final: 0.5635 (m-80) REVERT: C 103 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7738 (t) REVERT: C 116 ASP cc_start: 0.8395 (t0) cc_final: 0.7616 (m-30) REVERT: C 409 LEU cc_start: 0.8305 (mt) cc_final: 0.7964 (mp) REVERT: C 581 THR cc_start: 0.8176 (p) cc_final: 0.7944 (p) REVERT: C 736 VAL cc_start: 0.4874 (t) cc_final: 0.3237 (p) REVERT: C 741 MET cc_start: 0.8034 (ppp) cc_final: 0.7790 (mmt) REVERT: C 742 TYR cc_start: 0.7751 (m-80) cc_final: 0.7111 (m-10) REVERT: C 900 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5617 (mttt) REVERT: C 946 LEU cc_start: 0.8545 (mt) cc_final: 0.8320 (mt) REVERT: C 1049 ILE cc_start: 0.5841 (mm) cc_final: 0.5515 (mm) REVERT: C 1175 ASN cc_start: 0.8321 (m110) cc_final: 0.8119 (m110) REVERT: C 1186 VAL cc_start: 0.8775 (t) cc_final: 0.8403 (p) REVERT: C 1204 LEU cc_start: 0.8804 (mp) cc_final: 0.8388 (mp) REVERT: C 1304 MET cc_start: 0.7707 (tmm) cc_final: 0.7399 (tpp) REVERT: C 1312 ASN cc_start: 0.7440 (t0) cc_final: 0.7157 (t0) REVERT: D 34 SER cc_start: 0.4241 (OUTLIER) cc_final: 0.3409 (t) REVERT: D 116 PHE cc_start: 0.3732 (m-10) cc_final: 0.3504 (m-10) REVERT: D 301 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6591 (pt0) REVERT: D 428 THR cc_start: 0.8275 (m) cc_final: 0.7987 (p) REVERT: D 506 VAL cc_start: 0.9099 (t) cc_final: 0.8851 (m) REVERT: D 625 MET cc_start: 0.6917 (ttm) cc_final: 0.6173 (tmm) REVERT: D 759 ILE cc_start: 0.8191 (mt) cc_final: 0.7934 (mt) REVERT: D 861 ASN cc_start: 0.7446 (m-40) cc_final: 0.7031 (m110) REVERT: D 1040 MET cc_start: 0.3763 (tpt) cc_final: 0.3296 (tpt) REVERT: D 1320 ILE cc_start: 0.7977 (mm) cc_final: 0.7712 (mm) REVERT: M 178 VAL cc_start: 0.6846 (m) cc_final: 0.6608 (p) REVERT: M 206 PHE cc_start: 0.4813 (m-80) cc_final: 0.4167 (m-80) REVERT: M 270 GLU cc_start: 0.7166 (tp30) cc_final: 0.5826 (tp30) outliers start: 114 outliers final: 45 residues processed: 539 average time/residue: 0.3913 time to fit residues: 338.8080 Evaluate side-chains 461 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 409 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1227 HIS Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 70 optimal weight: 20.0000 chunk 271 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 370 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 317 optimal weight: 0.9980 chunk 334 optimal weight: 7.9990 chunk 286 optimal weight: 0.0050 chunk 83 optimal weight: 0.9980 chunk 309 optimal weight: 50.0000 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.092978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.070726 restraints weight = 116948.225| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.52 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.8367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29305 Z= 0.157 Angle : 0.699 13.949 40250 Z= 0.353 Chirality : 0.043 0.161 4788 Planarity : 0.005 0.084 4929 Dihedral : 16.300 171.351 5044 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 4.68 % Allowed : 29.91 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3612 helix: 0.60 (0.14), residues: 1343 sheet: 0.22 (0.26), residues: 391 loop : -1.47 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 115 HIS 0.011 0.001 HIS C 150 PHE 0.028 0.002 PHE C1323 TYR 0.023 0.002 TYR A 177 ARG 0.015 0.001 ARG D 101 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 1237) hydrogen bonds : angle 4.33720 ( 3427) metal coordination : bond 0.00175 ( 4) covalent geometry : bond 0.00353 (29301) covalent geometry : angle 0.69925 (40250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 458 time to evaluate : 2.990 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: A 142 MET cc_start: 0.7129 (ppp) cc_final: 0.6506 (ptt) REVERT: A 199 ASP cc_start: 0.7578 (m-30) cc_final: 0.7301 (m-30) REVERT: A 201 LEU cc_start: 0.9104 (tp) cc_final: 0.8868 (tt) REVERT: A 257 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7316 (m) REVERT: A 260 LEU cc_start: 0.6070 (mp) cc_final: 0.5663 (mm) REVERT: B 77 ASP cc_start: 0.8144 (t0) cc_final: 0.7909 (t0) REVERT: B 93 GLN cc_start: 0.8247 (mm110) cc_final: 0.8021 (mm-40) REVERT: C 57 PHE cc_start: 0.5935 (m-80) cc_final: 0.5514 (m-80) REVERT: C 116 ASP cc_start: 0.8067 (t0) cc_final: 0.7304 (m-30) REVERT: C 187 GLU cc_start: 0.5210 (tp30) cc_final: 0.4905 (pm20) REVERT: C 581 THR cc_start: 0.8501 (p) cc_final: 0.8229 (p) REVERT: C 583 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5259 (tm-30) REVERT: C 765 ILE cc_start: 0.7599 (mm) cc_final: 0.6981 (mp) REVERT: C 946 LEU cc_start: 0.8617 (mt) cc_final: 0.8368 (mt) REVERT: C 1049 ILE cc_start: 0.5637 (mm) cc_final: 0.5373 (mm) REVERT: C 1175 ASN cc_start: 0.8405 (m110) cc_final: 0.8138 (m-40) REVERT: C 1186 VAL cc_start: 0.9036 (t) cc_final: 0.8725 (p) REVERT: C 1204 LEU cc_start: 0.8876 (mp) cc_final: 0.8460 (mp) REVERT: C 1312 ASN cc_start: 0.7951 (t0) cc_final: 0.7676 (t0) REVERT: D 113 HIS cc_start: 0.5689 (t70) cc_final: 0.5401 (t70) REVERT: D 260 PHE cc_start: 0.4857 (m-80) cc_final: 0.4448 (p90) REVERT: D 301 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6150 (pt0) REVERT: D 483 LEU cc_start: 0.8574 (mt) cc_final: 0.8316 (mt) REVERT: D 513 MET cc_start: 0.8268 (tpp) cc_final: 0.7902 (ttt) REVERT: D 579 LEU cc_start: 0.8690 (mt) cc_final: 0.8324 (mt) REVERT: D 618 VAL cc_start: 0.9259 (t) cc_final: 0.9002 (p) REVERT: D 625 MET cc_start: 0.7580 (ttm) cc_final: 0.7129 (tmm) REVERT: D 759 ILE cc_start: 0.8434 (mt) cc_final: 0.8186 (mt) REVERT: D 1040 MET cc_start: 0.3256 (tpt) cc_final: 0.2606 (tpt) REVERT: M 185 PHE cc_start: 0.5164 (m-10) cc_final: 0.4870 (m-10) REVERT: M 199 LEU cc_start: 0.8030 (mm) cc_final: 0.7663 (tt) REVERT: M 200 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7307 (mt) REVERT: M 206 PHE cc_start: 0.4909 (m-80) cc_final: 0.4524 (m-80) REVERT: M 265 GLN cc_start: 0.4433 (OUTLIER) cc_final: 0.3870 (mt0) REVERT: M 270 GLU cc_start: 0.7325 (tp30) cc_final: 0.5941 (tp30) REVERT: M 355 PHE cc_start: 0.5080 (OUTLIER) cc_final: 0.4081 (m-80) outliers start: 122 outliers final: 59 residues processed: 542 average time/residue: 0.3736 time to fit residues: 327.5118 Evaluate side-chains 470 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 405 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 293 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 206 optimal weight: 8.9990 chunk 196 optimal weight: 0.9980 chunk 288 optimal weight: 0.0970 chunk 190 optimal weight: 0.6980 chunk 365 optimal weight: 40.0000 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1108 ASN C1175 ASN D 186 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 861 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.092849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.070509 restraints weight = 116191.244| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.50 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.9323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29305 Z= 0.143 Angle : 0.676 14.035 40250 Z= 0.340 Chirality : 0.043 0.196 4788 Planarity : 0.005 0.071 4929 Dihedral : 16.262 172.775 5044 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.23 % Favored : 94.71 % Rotamer: Outliers : 4.10 % Allowed : 31.56 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3612 helix: 0.79 (0.14), residues: 1339 sheet: 0.21 (0.26), residues: 388 loop : -1.41 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 33 HIS 0.009 0.001 HIS C 150 PHE 0.034 0.002 PHE D1325 TYR 0.022 0.002 TYR D1232 ARG 0.010 0.001 ARG M 259 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 1237) hydrogen bonds : angle 4.24032 ( 3427) metal coordination : bond 0.00197 ( 4) covalent geometry : bond 0.00322 (29301) covalent geometry : angle 0.67587 (40250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 438 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.7529 (ppp) cc_final: 0.7080 (ptt) REVERT: A 199 ASP cc_start: 0.7743 (m-30) cc_final: 0.7422 (m-30) REVERT: A 201 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8993 (tt) REVERT: A 231 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8293 (t80) REVERT: A 257 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7551 (m) REVERT: A 316 MET cc_start: 0.8347 (tmm) cc_final: 0.8076 (tmm) REVERT: A 318 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7185 (tp) REVERT: B 77 ASP cc_start: 0.8362 (t0) cc_final: 0.8124 (t0) REVERT: B 93 GLN cc_start: 0.8427 (mm110) cc_final: 0.8189 (mm-40) REVERT: B 200 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8103 (tmtt) REVERT: C 14 ASP cc_start: 0.6689 (t0) cc_final: 0.6486 (t0) REVERT: C 47 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.4547 (p90) REVERT: C 116 ASP cc_start: 0.8188 (t0) cc_final: 0.7481 (m-30) REVERT: C 409 LEU cc_start: 0.8674 (mt) cc_final: 0.8462 (mp) REVERT: C 581 THR cc_start: 0.8727 (p) cc_final: 0.8507 (p) REVERT: C 704 MET cc_start: 0.7154 (mtm) cc_final: 0.6864 (mtm) REVERT: C 742 TYR cc_start: 0.7417 (m-10) cc_final: 0.6866 (m-10) REVERT: C 788 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.7965 (t) REVERT: C 862 LEU cc_start: 0.7944 (mp) cc_final: 0.7692 (tt) REVERT: C 900 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.5871 (mttt) REVERT: C 1049 ILE cc_start: 0.5993 (mm) cc_final: 0.5679 (mm) REVERT: C 1101 LEU cc_start: 0.7973 (mm) cc_final: 0.7655 (mt) REVERT: C 1186 VAL cc_start: 0.9060 (t) cc_final: 0.8790 (p) REVERT: C 1312 ASN cc_start: 0.8111 (t0) cc_final: 0.7734 (t0) REVERT: D 324 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5680 (tt) REVERT: D 483 LEU cc_start: 0.8960 (mt) cc_final: 0.8685 (mt) REVERT: D 513 MET cc_start: 0.8455 (tpp) cc_final: 0.8213 (ttm) REVERT: D 579 LEU cc_start: 0.8752 (mt) cc_final: 0.8326 (mt) REVERT: D 772 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.5668 (m-80) REVERT: D 1040 MET cc_start: 0.3134 (tpt) cc_final: 0.2725 (tpt) REVERT: D 1344 LEU cc_start: 0.7182 (mm) cc_final: 0.6804 (mm) REVERT: M 199 LEU cc_start: 0.8212 (mm) cc_final: 0.7838 (tt) REVERT: M 200 LEU cc_start: 0.7677 (mt) cc_final: 0.7333 (mt) REVERT: M 206 PHE cc_start: 0.4932 (m-80) cc_final: 0.4475 (m-80) REVERT: M 262 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7664 (pp30) REVERT: M 270 GLU cc_start: 0.7320 (tp30) cc_final: 0.5969 (tp30) REVERT: M 355 PHE cc_start: 0.5317 (OUTLIER) cc_final: 0.4375 (m-80) outliers start: 107 outliers final: 47 residues processed: 512 average time/residue: 0.3561 time to fit residues: 298.2073 Evaluate side-chains 445 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 386 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 349 optimal weight: 30.0000 chunk 322 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 88 optimal weight: 0.0170 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 262 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 305 optimal weight: 0.0980 chunk 238 optimal weight: 0.6980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN C 60 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 861 ASN D1227 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.093519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.071137 restraints weight = 115492.932| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.50 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.9618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29305 Z= 0.120 Angle : 0.659 12.484 40250 Z= 0.329 Chirality : 0.042 0.232 4788 Planarity : 0.004 0.064 4929 Dihedral : 16.219 172.629 5044 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 3.34 % Allowed : 32.29 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3612 helix: 0.85 (0.14), residues: 1347 sheet: 0.50 (0.27), residues: 377 loop : -1.40 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1276 HIS 0.008 0.001 HIS D 80 PHE 0.023 0.002 PHE C1323 TYR 0.026 0.001 TYR M 112 ARG 0.009 0.000 ARG D 293 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 1237) hydrogen bonds : angle 4.16688 ( 3427) metal coordination : bond 0.00104 ( 4) covalent geometry : bond 0.00272 (29301) covalent geometry : angle 0.65900 (40250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 421 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.7599 (ppp) cc_final: 0.7266 (ptt) REVERT: A 199 ASP cc_start: 0.7830 (m-30) cc_final: 0.7538 (m-30) REVERT: A 231 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8386 (t80) REVERT: A 257 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7605 (m) REVERT: B 77 ASP cc_start: 0.8377 (t0) cc_final: 0.8163 (t0) REVERT: B 93 GLN cc_start: 0.8466 (mm110) cc_final: 0.8180 (mm-40) REVERT: C 116 ASP cc_start: 0.8082 (t0) cc_final: 0.7389 (m-30) REVERT: C 160 ASP cc_start: 0.8189 (p0) cc_final: 0.7835 (p0) REVERT: C 704 MET cc_start: 0.7159 (mtm) cc_final: 0.6886 (mtm) REVERT: C 788 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.7907 (t) REVERT: C 862 LEU cc_start: 0.7978 (mp) cc_final: 0.7731 (tt) REVERT: C 900 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.5961 (mttt) REVERT: C 1049 ILE cc_start: 0.6125 (mm) cc_final: 0.5801 (mm) REVERT: C 1066 MET cc_start: 0.8511 (ttm) cc_final: 0.8263 (ttm) REVERT: C 1101 LEU cc_start: 0.8145 (mm) cc_final: 0.7937 (mt) REVERT: C 1186 VAL cc_start: 0.9013 (t) cc_final: 0.8770 (p) REVERT: C 1217 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7552 (t) REVERT: D 441 LEU cc_start: 0.8883 (mt) cc_final: 0.8508 (mp) REVERT: D 579 LEU cc_start: 0.8726 (mt) cc_final: 0.8331 (mt) REVERT: D 618 VAL cc_start: 0.9408 (t) cc_final: 0.9182 (p) REVERT: D 680 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8644 (t0) REVERT: D 772 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.5315 (m-80) REVERT: D 821 MET cc_start: 0.9038 (tpp) cc_final: 0.8818 (tpp) REVERT: D 1040 MET cc_start: 0.3114 (tpt) cc_final: 0.2632 (tpt) REVERT: D 1325 PHE cc_start: 0.6497 (t80) cc_final: 0.6284 (t80) REVERT: D 1344 LEU cc_start: 0.7238 (mm) cc_final: 0.6868 (mm) REVERT: M 199 LEU cc_start: 0.8246 (mm) cc_final: 0.7819 (tt) REVERT: M 200 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7409 (mt) REVERT: M 206 PHE cc_start: 0.4888 (m-80) cc_final: 0.4523 (m-80) REVERT: M 262 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7475 (pp30) REVERT: M 270 GLU cc_start: 0.7460 (tp30) cc_final: 0.6074 (tp30) outliers start: 87 outliers final: 50 residues processed: 484 average time/residue: 0.3653 time to fit residues: 289.2059 Evaluate side-chains 449 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 390 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 614 TYR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 262 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 158 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 304 optimal weight: 40.0000 chunk 247 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 370 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 60 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN M 265 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.090791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.068121 restraints weight = 114292.074| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.44 r_work: 0.3202 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 1.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 29305 Z= 0.189 Angle : 0.722 11.197 40250 Z= 0.366 Chirality : 0.045 0.535 4788 Planarity : 0.005 0.064 4929 Dihedral : 16.241 171.040 5044 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.72 % Rotamer: Outliers : 3.91 % Allowed : 32.48 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3612 helix: 0.72 (0.14), residues: 1335 sheet: 0.26 (0.26), residues: 390 loop : -1.44 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 115 HIS 0.010 0.001 HIS D 450 PHE 0.029 0.002 PHE C1323 TYR 0.024 0.002 TYR D 165 ARG 0.009 0.001 ARG C 678 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1237) hydrogen bonds : angle 4.36063 ( 3427) metal coordination : bond 0.00446 ( 4) covalent geometry : bond 0.00433 (29301) covalent geometry : angle 0.72190 (40250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 389 time to evaluate : 3.235 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: A 51 MET cc_start: 0.8917 (mmm) cc_final: 0.8601 (mmt) REVERT: A 134 THR cc_start: 0.7944 (m) cc_final: 0.7618 (p) REVERT: A 142 MET cc_start: 0.8366 (ppp) cc_final: 0.8153 (ptp) REVERT: A 199 ASP cc_start: 0.8348 (m-30) cc_final: 0.8045 (m-30) REVERT: A 231 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8409 (t80) REVERT: A 257 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7954 (m) REVERT: B 77 ASP cc_start: 0.8509 (t0) cc_final: 0.8271 (t0) REVERT: B 93 GLN cc_start: 0.8496 (mm110) cc_final: 0.8171 (mm-40) REVERT: C 47 TYR cc_start: 0.6588 (OUTLIER) cc_final: 0.5975 (p90) REVERT: C 461 GLU cc_start: 0.8131 (pt0) cc_final: 0.7734 (pp20) REVERT: C 541 GLU cc_start: 0.7186 (tp30) cc_final: 0.6651 (tm-30) REVERT: C 742 TYR cc_start: 0.7724 (m-10) cc_final: 0.7062 (m-10) REVERT: C 788 SER cc_start: 0.9135 (OUTLIER) cc_final: 0.8816 (t) REVERT: C 862 LEU cc_start: 0.8580 (mp) cc_final: 0.8270 (tt) REVERT: C 900 LYS cc_start: 0.6708 (OUTLIER) cc_final: 0.6122 (mttt) REVERT: C 1066 MET cc_start: 0.9032 (ttm) cc_final: 0.8823 (ttm) REVERT: D 130 MET cc_start: 0.4222 (mtt) cc_final: 0.3967 (mtt) REVERT: D 301 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: D 314 ARG cc_start: 0.6714 (mmp80) cc_final: 0.6384 (mmp80) REVERT: D 330 MET cc_start: 0.7233 (tpp) cc_final: 0.6820 (ttm) REVERT: D 564 VAL cc_start: 0.7881 (OUTLIER) cc_final: 0.7635 (p) REVERT: D 614 LEU cc_start: 0.9018 (tp) cc_final: 0.8808 (tp) REVERT: D 680 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8635 (t0) REVERT: D 707 ILE cc_start: 0.9054 (mt) cc_final: 0.8820 (mm) REVERT: D 772 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: D 1040 MET cc_start: 0.3287 (tpt) cc_final: 0.2718 (tpt) REVERT: M 199 LEU cc_start: 0.8407 (mm) cc_final: 0.7884 (tt) REVERT: M 200 LEU cc_start: 0.8119 (mt) cc_final: 0.7651 (mt) REVERT: M 262 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8040 (pp30) REVERT: M 265 GLN cc_start: 0.5194 (OUTLIER) cc_final: 0.4874 (mt0) REVERT: M 270 GLU cc_start: 0.7817 (tp30) cc_final: 0.6913 (tp30) REVERT: M 355 PHE cc_start: 0.5661 (OUTLIER) cc_final: 0.4945 (m-80) outliers start: 102 outliers final: 52 residues processed: 460 average time/residue: 0.4045 time to fit residues: 310.6610 Evaluate side-chains 393 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 329 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1323 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 994 SER Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 332 optimal weight: 1.9990 chunk 259 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 366 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 288 optimal weight: 0.8980 chunk 219 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS C 519 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D1218 HIS D1249 ASN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.088769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.064729 restraints weight = 114107.319| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 4.35 r_work: 0.3123 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 1.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 29305 Z= 0.223 Angle : 0.819 30.348 40250 Z= 0.410 Chirality : 0.047 0.372 4788 Planarity : 0.006 0.064 4929 Dihedral : 16.305 170.672 5044 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer: Outliers : 3.60 % Allowed : 33.82 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3612 helix: 0.63 (0.14), residues: 1334 sheet: 0.01 (0.26), residues: 376 loop : -1.49 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 115 HIS 0.010 0.001 HIS D 80 PHE 0.043 0.003 PHE D 116 TYR 0.058 0.002 TYR C 742 ARG 0.012 0.001 ARG D 275 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 1237) hydrogen bonds : angle 4.55731 ( 3427) metal coordination : bond 0.00468 ( 4) covalent geometry : bond 0.00492 (29301) covalent geometry : angle 0.81927 (40250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 342 time to evaluate : 4.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.9027 (t0) cc_final: 0.8713 (t0) REVERT: A 181 GLU cc_start: 0.8704 (pp20) cc_final: 0.8402 (pp20) REVERT: A 199 ASP cc_start: 0.8476 (m-30) cc_final: 0.8178 (m-30) REVERT: A 231 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8104 (t80) REVERT: B 77 ASP cc_start: 0.8700 (t0) cc_final: 0.8490 (t0) REVERT: B 93 GLN cc_start: 0.8661 (mm110) cc_final: 0.8301 (mm-40) REVERT: C 47 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.7249 (p90) REVERT: C 336 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7358 (tt) REVERT: C 461 GLU cc_start: 0.8409 (pt0) cc_final: 0.8046 (pp20) REVERT: C 503 LYS cc_start: 0.8552 (tptm) cc_final: 0.8199 (mptp) REVERT: C 541 GLU cc_start: 0.7770 (tp30) cc_final: 0.7250 (tm-30) REVERT: C 741 MET cc_start: 0.8135 (mmt) cc_final: 0.7500 (ppp) REVERT: C 788 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.8975 (t) REVERT: C 862 LEU cc_start: 0.8962 (mp) cc_final: 0.8626 (tt) REVERT: C 1234 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8872 (ttpt) REVERT: C 1290 MET cc_start: 0.9118 (mtt) cc_final: 0.8866 (ttm) REVERT: D 192 MET cc_start: 0.3375 (ppp) cc_final: 0.3132 (ppp) REVERT: D 478 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8384 (mm) REVERT: D 680 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8652 (t0) REVERT: D 724 MET cc_start: 0.9275 (mtt) cc_final: 0.9070 (mtt) REVERT: D 747 MET cc_start: 0.7822 (pmm) cc_final: 0.7114 (pmm) REVERT: D 772 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: D 1040 MET cc_start: 0.3784 (tpt) cc_final: 0.3123 (tpt) REVERT: D 1226 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8719 (p) REVERT: D 1230 THR cc_start: 0.9685 (OUTLIER) cc_final: 0.9278 (p) REVERT: D 1244 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8442 (tm-30) REVERT: D 1249 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8935 (t0) REVERT: D 1333 THR cc_start: 0.8734 (t) cc_final: 0.8494 (m) REVERT: E 11 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8719 (mm-30) REVERT: M 120 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7485 (tp) REVERT: M 154 LEU cc_start: 0.7684 (mt) cc_final: 0.6320 (pp) REVERT: M 155 THR cc_start: 0.6812 (OUTLIER) cc_final: 0.6501 (t) REVERT: M 172 LEU cc_start: 0.8708 (tt) cc_final: 0.8230 (pp) REVERT: M 270 GLU cc_start: 0.8000 (tp30) cc_final: 0.6628 (tp30) REVERT: M 355 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5574 (m-80) outliers start: 94 outliers final: 46 residues processed: 416 average time/residue: 0.3808 time to fit residues: 257.1336 Evaluate side-chains 344 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1234 LYS Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1323 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1162 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 355 PHE Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 212 optimal weight: 3.9990 chunk 337 optimal weight: 0.3980 chunk 342 optimal weight: 0.4980 chunk 293 optimal weight: 8.9990 chunk 283 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 315 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 330 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 147 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C1108 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 489 ASN D 504 GLN D1249 ASN E 7 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.089454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065702 restraints weight = 113536.932| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 4.33 r_work: 0.3148 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 1.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29305 Z= 0.138 Angle : 0.723 12.451 40250 Z= 0.359 Chirality : 0.043 0.245 4788 Planarity : 0.005 0.096 4929 Dihedral : 16.210 171.187 5044 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.87 % Favored : 94.08 % Rotamer: Outliers : 2.53 % Allowed : 34.82 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3612 helix: 0.82 (0.14), residues: 1335 sheet: 0.29 (0.27), residues: 366 loop : -1.44 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 236 HIS 0.009 0.001 HIS D 80 PHE 0.031 0.002 PHE C 390 TYR 0.026 0.002 TYR D 165 ARG 0.011 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 1237) hydrogen bonds : angle 4.32729 ( 3427) metal coordination : bond 0.00225 ( 4) covalent geometry : bond 0.00318 (29301) covalent geometry : angle 0.72299 (40250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 331 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8986 (t0) cc_final: 0.8739 (t0) REVERT: A 102 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8091 (tp) REVERT: A 134 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8135 (p) REVERT: A 181 GLU cc_start: 0.8607 (pp20) cc_final: 0.8360 (pp20) REVERT: A 199 ASP cc_start: 0.8443 (m-30) cc_final: 0.8151 (m-30) REVERT: A 231 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8287 (t80) REVERT: A 318 LEU cc_start: 0.8640 (tp) cc_final: 0.8406 (tp) REVERT: B 61 ILE cc_start: 0.9380 (pt) cc_final: 0.9088 (mm) REVERT: B 93 GLN cc_start: 0.8699 (mm110) cc_final: 0.8339 (mm-40) REVERT: C 47 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.7166 (p90) REVERT: C 183 TRP cc_start: 0.8243 (OUTLIER) cc_final: 0.7467 (m-90) REVERT: C 461 GLU cc_start: 0.8336 (pt0) cc_final: 0.8035 (pp20) REVERT: C 503 LYS cc_start: 0.8582 (tptm) cc_final: 0.8195 (mptp) REVERT: C 541 GLU cc_start: 0.7814 (tp30) cc_final: 0.7318 (tm-30) REVERT: C 741 MET cc_start: 0.7453 (mmt) cc_final: 0.6916 (ppp) REVERT: C 788 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.8789 (p) REVERT: C 862 LEU cc_start: 0.9039 (mp) cc_final: 0.8697 (tt) REVERT: C 900 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6261 (mttt) REVERT: C 1053 TYR cc_start: 0.8895 (m-80) cc_final: 0.8632 (m-80) REVERT: C 1108 ASN cc_start: 0.9301 (OUTLIER) cc_final: 0.8958 (p0) REVERT: C 1244 HIS cc_start: 0.8258 (t70) cc_final: 0.7843 (t70) REVERT: C 1279 GLU cc_start: 0.9306 (pt0) cc_final: 0.9106 (pt0) REVERT: C 1290 MET cc_start: 0.9207 (mtt) cc_final: 0.8974 (ttm) REVERT: C 1319 MET cc_start: 0.9060 (tpp) cc_final: 0.8788 (tpp) REVERT: D 217 LEU cc_start: 0.7980 (mm) cc_final: 0.7736 (pp) REVERT: D 330 MET cc_start: 0.8653 (ttp) cc_final: 0.8452 (ptm) REVERT: D 466 MET cc_start: 0.9088 (mtp) cc_final: 0.8887 (mtt) REVERT: D 625 MET cc_start: 0.9433 (ttp) cc_final: 0.8985 (ttp) REVERT: D 680 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8664 (t0) REVERT: D 747 MET cc_start: 0.7720 (pmm) cc_final: 0.7208 (pmm) REVERT: D 772 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: D 1040 MET cc_start: 0.3560 (tpt) cc_final: 0.3131 (tpt) REVERT: D 1244 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8509 (tm-30) REVERT: D 1333 THR cc_start: 0.8719 (t) cc_final: 0.8502 (t) REVERT: E 11 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8713 (mm-30) REVERT: M 172 LEU cc_start: 0.8746 (tt) cc_final: 0.8294 (pp) REVERT: M 270 GLU cc_start: 0.7989 (tp30) cc_final: 0.6553 (tp30) outliers start: 66 outliers final: 32 residues processed: 382 average time/residue: 0.3913 time to fit residues: 242.7875 Evaluate side-chains 333 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1323 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 316 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 36 optimal weight: 0.0070 chunk 210 optimal weight: 30.0000 chunk 224 optimal weight: 1.9990 chunk 294 optimal weight: 0.0670 chunk 177 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 302 optimal weight: 40.0000 chunk 238 optimal weight: 5.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 504 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.089350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.065494 restraints weight = 114019.984| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 4.35 r_work: 0.3141 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 1.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 29305 Z= 0.219 Angle : 0.960 59.197 40250 Z= 0.533 Chirality : 0.045 0.677 4788 Planarity : 0.005 0.105 4929 Dihedral : 16.218 171.192 5044 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer: Outliers : 1.80 % Allowed : 35.47 % Favored : 62.73 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3612 helix: 0.82 (0.14), residues: 1335 sheet: 0.29 (0.27), residues: 366 loop : -1.44 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 236 HIS 0.008 0.001 HIS D 80 PHE 0.049 0.002 PHE D 62 TYR 0.096 0.002 TYR A 177 ARG 0.013 0.001 ARG D 337 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 1237) hydrogen bonds : angle 4.33039 ( 3427) metal coordination : bond 0.00247 ( 4) covalent geometry : bond 0.00484 (29301) covalent geometry : angle 0.96018 (40250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 292 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8095 (tp) REVERT: A 134 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8126 (p) REVERT: A 181 GLU cc_start: 0.8631 (pp20) cc_final: 0.8370 (pp20) REVERT: A 199 ASP cc_start: 0.8461 (m-30) cc_final: 0.8165 (m-30) REVERT: A 231 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8301 (t80) REVERT: A 318 LEU cc_start: 0.8639 (tp) cc_final: 0.8400 (tp) REVERT: B 61 ILE cc_start: 0.9379 (pt) cc_final: 0.9085 (mm) REVERT: B 93 GLN cc_start: 0.8718 (mm110) cc_final: 0.8357 (mm-40) REVERT: C 47 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.7180 (p90) REVERT: C 183 TRP cc_start: 0.8238 (OUTLIER) cc_final: 0.7468 (m-90) REVERT: C 461 GLU cc_start: 0.8322 (pt0) cc_final: 0.8029 (pp20) REVERT: C 503 LYS cc_start: 0.8575 (tptm) cc_final: 0.8200 (mptp) REVERT: C 541 GLU cc_start: 0.7827 (tp30) cc_final: 0.7334 (tm-30) REVERT: C 741 MET cc_start: 0.7467 (mmt) cc_final: 0.6937 (ppp) REVERT: C 788 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.8792 (p) REVERT: C 862 LEU cc_start: 0.9026 (mp) cc_final: 0.8703 (tt) REVERT: C 900 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6285 (mttt) REVERT: C 1053 TYR cc_start: 0.8890 (m-80) cc_final: 0.8633 (m-80) REVERT: C 1244 HIS cc_start: 0.8276 (t70) cc_final: 0.7861 (t70) REVERT: C 1290 MET cc_start: 0.9219 (mtt) cc_final: 0.8980 (ttm) REVERT: C 1319 MET cc_start: 0.9061 (tpp) cc_final: 0.8790 (tpp) REVERT: D 29 MET cc_start: 0.7910 (tmm) cc_final: 0.7389 (ptm) REVERT: D 217 LEU cc_start: 0.7981 (mm) cc_final: 0.7736 (pp) REVERT: D 330 MET cc_start: 0.8647 (ttp) cc_final: 0.8429 (ptm) REVERT: D 466 MET cc_start: 0.9103 (mtp) cc_final: 0.8889 (mtt) REVERT: D 625 MET cc_start: 0.9422 (ttp) cc_final: 0.8963 (ttp) REVERT: D 680 ASN cc_start: 0.9166 (OUTLIER) cc_final: 0.8681 (t0) REVERT: D 747 MET cc_start: 0.7722 (pmm) cc_final: 0.7200 (pmm) REVERT: D 772 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: D 1040 MET cc_start: 0.3573 (tpt) cc_final: 0.3149 (tpt) REVERT: D 1244 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8513 (tm-30) REVERT: D 1305 ASP cc_start: 0.8244 (t0) cc_final: 0.7899 (m-30) REVERT: D 1333 THR cc_start: 0.8721 (t) cc_final: 0.8502 (t) REVERT: M 172 LEU cc_start: 0.8785 (tt) cc_final: 0.8327 (pp) REVERT: M 270 GLU cc_start: 0.8000 (tp30) cc_final: 0.6561 (tp30) outliers start: 47 outliers final: 34 residues processed: 329 average time/residue: 0.3786 time to fit residues: 204.9007 Evaluate side-chains 329 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1323 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 282 optimal weight: 6.9990 chunk 323 optimal weight: 10.0000 chunk 233 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 296 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 294 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 283 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.089267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.065411 restraints weight = 114021.414| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 4.35 r_work: 0.3139 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 1.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 29305 Z= 0.222 Angle : 0.988 59.182 40250 Z= 0.550 Chirality : 0.045 0.488 4788 Planarity : 0.005 0.126 4929 Dihedral : 16.214 171.187 5044 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer: Outliers : 1.92 % Allowed : 35.20 % Favored : 62.88 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3612 helix: 0.82 (0.14), residues: 1335 sheet: 0.28 (0.27), residues: 366 loop : -1.44 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 236 HIS 0.007 0.001 HIS D 80 PHE 0.043 0.002 PHE D 62 TYR 0.076 0.002 TYR A 177 ARG 0.012 0.000 ARG D 337 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 1237) hydrogen bonds : angle 4.32883 ( 3427) metal coordination : bond 0.00349 ( 4) covalent geometry : bond 0.00498 (29301) covalent geometry : angle 0.98817 (40250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15270.34 seconds wall clock time: 263 minutes 58.93 seconds (15838.93 seconds total)