Starting phenix.real_space_refine on Tue Jun 24 09:51:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8reb_19081/06_2025/8reb_19081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8reb_19081/06_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_19081/06_2025/8reb_19081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8reb_19081/06_2025/8reb_19081.map" model { file = "/net/cci-nas-00/data/ceres_data/8reb_19081/06_2025/8reb_19081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8reb_19081/06_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): 0.41s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.72, per 1000 atoms: 0.62 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: 7.95 Conformation dependent library (CDL) restraints added in 3.4 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: 10.41 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: 16.44 Time building geometry restraints manager: 9.20 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 84.150 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.140 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.840 ------------------------------------------------------------------------------- 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 : 3.226 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: 0.4680 time to fit residues: 546.2211 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 : 3.121 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.092328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.070750 restraints weight = 115757.683| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 4.45 r_work: 0.3277 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- 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: 0.6537 moved from start: 0.5940 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 17.735 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 : 16.57 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: -1.28 (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 0.05330 ( 1237) hydrogen bonds : angle 5.00655 ( 3427) metal coordination : bond 0.00487 ( 4) covalent geometry : bond 0.00645 (29301) covalent geometry : angle 0.97563 (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 : 3.154 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: 0.8195 (pttt) cc_final: 0.7961 (pttm) REVERT: A 200 LYS cc_start: 0.8832 (ptmt) cc_final: 0.8558 (ptmm) REVERT: A 257 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7289 (m) REVERT: B 47 LEU cc_start: 0.8756 (mt) cc_final: 0.8453 (mt) REVERT: B 51 MET cc_start: 0.8141 (mmt) cc_final: 0.7866 (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: 0.7691 (tttt) REVERT: C 20 GLN cc_start: 0.8097 (pt0) cc_final: 0.7865 (tt0) REVERT: C 47 TYR cc_start: 0.4545 (OUTLIER) cc_final: 0.3773 (p90) REVERT: C 57 PHE cc_start: 0.6117 (m-80) cc_final: 0.5416 (m-80) REVERT: C 116 ASP cc_start: 0.8284 (t0) cc_final: 0.7772 (m-30) REVERT: C 183 TRP cc_start: 0.5029 (OUTLIER) cc_final: 0.4494 (m-10) REVERT: C 409 LEU cc_start: 0.8118 (mt) cc_final: 0.7888 (tp) REVERT: C 451 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5388 (ptp-170) REVERT: C 581 THR cc_start: 0.7940 (p) cc_final: 0.7707 (p) REVERT: C 609 ILE cc_start: 0.8418 (pt) cc_final: 0.8055 (pt) REVERT: C 671 LEU cc_start: 0.9163 (tp) cc_final: 0.8529 (tp) REVERT: C 741 MET cc_start: 0.8037 (ppp) cc_final: 0.7639 (mmt) REVERT: C 742 TYR cc_start: 0.7804 (m-80) cc_final: 0.7276 (m-10) REVERT: C 900 LYS cc_start: 0.6242 (OUTLIER) cc_final: 0.5585 (mttt) REVERT: C 957 LYS cc_start: 0.8763 (pptt) cc_final: 0.8209 (ptpp) REVERT: C 1022 LYS cc_start: 0.8221 (mttp) cc_final: 0.8021 (mmmt) REVERT: C 1049 ILE cc_start: 0.5571 (mm) cc_final: 0.5261 (mm) REVERT: C 1128 ILE cc_start: 0.8690 (mm) cc_final: 0.8451 (mt) REVERT: C 1168 GLU cc_start: 0.8011 (mp0) cc_final: 0.7512 (mm-30) REVERT: C 1175 ASN cc_start: 0.8314 (m-40) cc_final: 0.7984 (m110) REVERT: C 1204 LEU cc_start: 0.8250 (mp) cc_final: 0.8042 (mp) REVERT: C 1276 TRP cc_start: 0.5804 (m-10) cc_final: 0.4957 (m-10) REVERT: D 135 ILE cc_start: 0.6394 (OUTLIER) cc_final: 0.5721 (tt) REVERT: D 165 TYR cc_start: 0.9070 (t80) cc_final: 0.8862 (t80) REVERT: D 402 GLU cc_start: 0.7328 (tp30) cc_final: 0.7021 (tp30) REVERT: D 445 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7340 (mtpt) REVERT: D 447 ILE cc_start: 0.8288 (mt) cc_final: 0.7967 (mt) REVERT: D 506 VAL cc_start: 0.8787 (t) cc_final: 0.8519 (m) REVERT: D 534 GLU cc_start: 0.8766 (tp30) cc_final: 0.8289 (tp30) REVERT: D 625 MET cc_start: 0.6035 (ttm) cc_final: 0.5701 (tmm) REVERT: D 759 ILE cc_start: 0.7749 (mt) cc_final: 0.7045 (mt) REVERT: D 1040 MET cc_start: 0.3461 (tpt) cc_final: 0.2792 (tpt) REVERT: D 1230 THR cc_start: 0.8026 (m) cc_final: 0.7733 (m) REVERT: D 1287 ILE cc_start: 0.4870 (OUTLIER) cc_final: 0.4435 (mt) REVERT: D 1320 ILE cc_start: 0.7912 (mm) cc_final: 0.7585 (mm) REVERT: M 178 VAL cc_start: 0.6757 (m) cc_final: 0.6485 (p) REVERT: M 196 ARG cc_start: 0.6051 (tpt170) cc_final: 0.5756 (tpm170) REVERT: M 200 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7310 (mt) REVERT: M 265 GLN cc_start: 0.2104 (OUTLIER) cc_final: 0.1873 (mp10) REVERT: M 270 GLU cc_start: 0.7090 (tp30) cc_final: 0.5531 (tp30) outliers start: 192 outliers final: 55 residues processed: 724 average time/residue: 0.4163 time to fit residues: 475.2172 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 : 3.717 ------------------------------------------------------------------------------- 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: 20.0000 chunk 353 optimal weight: 8.9990 chunk 232 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 323 optimal weight: 0.1980 chunk 33 optimal weight: 0.2980 chunk 190 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 339 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 462 ASN C 494 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN C1116 HIS C1244 HIS C1257 GLN C1313 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 265 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.093572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.072077 restraints weight = 115501.733| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.43 r_work: 0.3315 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29305 Z= 0.137 Angle : 0.710 13.996 40250 Z= 0.359 Chirality : 0.044 0.259 4788 Planarity : 0.005 0.088 4929 Dihedral : 16.381 172.162 5044 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.80 % Rotamer: Outliers : 4.10 % Allowed : 30.25 % Favored : 65.64 % 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: -0.89 (0.14), residues: 3612 helix: 0.39 (0.14), residues: 1350 sheet: 0.17 (0.26), residues: 396 loop : -1.54 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 580 HIS 0.010 0.001 HIS D 80 PHE 0.025 0.002 PHE D 62 TYR 0.027 0.002 TYR A 177 ARG 0.010 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1237) hydrogen bonds : angle 4.44905 ( 3427) metal coordination : bond 0.00157 ( 4) covalent geometry : bond 0.00306 (29301) covalent geometry : angle 0.70986 (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 574 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 467 time to evaluate : 2.883 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 257 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7425 (m) REVERT: B 35 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8092 (t80) REVERT: B 51 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8033 (mmm) REVERT: B 77 ASP cc_start: 0.8026 (t0) cc_final: 0.7700 (t0) REVERT: B 93 GLN cc_start: 0.7936 (mm110) cc_final: 0.7639 (mm-40) REVERT: B 127 GLN cc_start: 0.9214 (pm20) cc_final: 0.8788 (pm20) REVERT: C 20 GLN cc_start: 0.8000 (pt0) cc_final: 0.7763 (tt0) REVERT: C 57 PHE cc_start: 0.6113 (m-80) cc_final: 0.5549 (m-80) REVERT: C 116 ASP cc_start: 0.8292 (t0) cc_final: 0.7645 (m-30) REVERT: C 141 THR cc_start: 0.7015 (m) cc_final: 0.6704 (p) REVERT: C 409 LEU cc_start: 0.8072 (mt) cc_final: 0.7833 (mp) REVERT: C 515 MET cc_start: 0.8151 (tpp) cc_final: 0.7905 (tmm) REVERT: C 629 PHE cc_start: 0.8339 (m-80) cc_final: 0.7987 (t80) REVERT: C 652 TYR cc_start: 0.7120 (m-80) cc_final: 0.6847 (m-10) REVERT: C 704 MET cc_start: 0.6402 (mpp) cc_final: 0.6109 (mpp) REVERT: C 900 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5528 (mttt) REVERT: C 946 LEU cc_start: 0.8634 (mt) cc_final: 0.8405 (mt) REVERT: C 1049 ILE cc_start: 0.5675 (mm) cc_final: 0.5349 (mm) REVERT: C 1175 ASN cc_start: 0.8201 (m-40) cc_final: 0.7987 (m110) REVERT: C 1204 LEU cc_start: 0.8818 (mp) cc_final: 0.8399 (mp) REVERT: C 1312 ASN cc_start: 0.6967 (t0) cc_final: 0.6759 (t0) REVERT: D 34 SER cc_start: 0.4040 (OUTLIER) cc_final: 0.3573 (t) REVERT: D 116 PHE cc_start: 0.3630 (m-10) cc_final: 0.3429 (m-10) REVERT: D 301 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: D 445 LYS cc_start: 0.7604 (mttt) cc_final: 0.7180 (mtpt) REVERT: D 447 ILE cc_start: 0.8452 (mt) cc_final: 0.8221 (mt) REVERT: D 466 MET cc_start: 0.6601 (mtp) cc_final: 0.6379 (mtt) REVERT: D 506 VAL cc_start: 0.8976 (t) cc_final: 0.8713 (m) REVERT: D 534 GLU cc_start: 0.8862 (tp30) cc_final: 0.8176 (tp30) REVERT: D 591 ILE cc_start: 0.9243 (pt) cc_final: 0.9025 (tp) REVERT: D 625 MET cc_start: 0.6075 (ttm) cc_final: 0.5521 (tmm) REVERT: D 759 ILE cc_start: 0.8000 (mt) cc_final: 0.7668 (mt) REVERT: D 861 ASN cc_start: 0.7443 (m-40) cc_final: 0.7136 (m110) REVERT: D 1040 MET cc_start: 0.3664 (tpt) cc_final: 0.3212 (tpt) REVERT: D 1262 ARG cc_start: 0.5512 (mmm160) cc_final: 0.4175 (mmm160) REVERT: D 1320 ILE cc_start: 0.7924 (mm) cc_final: 0.7637 (mm) REVERT: M 178 VAL cc_start: 0.6757 (m) cc_final: 0.6527 (p) REVERT: M 206 PHE cc_start: 0.4454 (m-80) cc_final: 0.3981 (m-80) REVERT: M 270 GLU cc_start: 0.7091 (tp30) cc_final: 0.5761 (tp30) REVERT: M 401 TYR cc_start: 0.5511 (t80) cc_final: 0.5308 (t80) outliers start: 107 outliers final: 42 residues processed: 531 average time/residue: 0.3830 time to fit residues: 326.9226 Evaluate side-chains 470 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 422 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 304 LYS 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 51 MET 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 100 LEU 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 735 LYS Chi-restraints excluded: chain C residue 794 LEU 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 1082 ILE 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 1198 LEU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1275 VAL 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 301 GLU Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 528 THR 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 820 ILE 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: 0.1980 chunk 221 optimal weight: 0.3980 chunk 370 optimal weight: 50.0000 chunk 161 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 317 optimal weight: 6.9990 chunk 334 optimal weight: 9.9990 chunk 286 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 309 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN C 808 ASN C1108 ASN C1336 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.093711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.071792 restraints weight = 117110.497| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 4.53 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 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 = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.7541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29305 Z= 0.140 Angle : 0.669 13.290 40250 Z= 0.338 Chirality : 0.043 0.173 4788 Planarity : 0.005 0.079 4929 Dihedral : 16.256 170.894 5044 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.81 % Favored : 94.16 % Rotamer: Outliers : 4.22 % Allowed : 30.06 % Favored : 65.72 % 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: -0.67 (0.14), residues: 3612 helix: 0.64 (0.14), residues: 1341 sheet: 0.23 (0.26), residues: 392 loop : -1.44 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 115 HIS 0.010 0.001 HIS D 80 PHE 0.029 0.002 PHE C1323 TYR 0.020 0.002 TYR A 152 ARG 0.006 0.001 ARG C 758 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 1237) hydrogen bonds : angle 4.27209 ( 3427) metal coordination : bond 0.00107 ( 4) covalent geometry : bond 0.00311 (29301) covalent geometry : angle 0.66921 (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 562 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 452 time to evaluate : 3.103 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 199 ASP cc_start: 0.7591 (m-30) cc_final: 0.7279 (m-30) REVERT: A 257 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7337 (m) REVERT: A 260 LEU cc_start: 0.5941 (mp) cc_final: 0.5585 (mm) REVERT: B 35 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7868 (t80) REVERT: B 47 LEU cc_start: 0.8946 (mt) cc_final: 0.8692 (mt) REVERT: B 77 ASP cc_start: 0.8119 (t0) cc_final: 0.7889 (t0) REVERT: B 93 GLN cc_start: 0.8066 (mm110) cc_final: 0.7802 (mm-40) REVERT: C 57 PHE cc_start: 0.5706 (m-80) cc_final: 0.5447 (m-80) REVERT: C 116 ASP cc_start: 0.8343 (t0) cc_final: 0.7634 (m-30) REVERT: C 409 LEU cc_start: 0.8328 (mt) cc_final: 0.7971 (tt) REVERT: C 515 MET cc_start: 0.8112 (tpp) cc_final: 0.7659 (tmm) REVERT: C 581 THR cc_start: 0.8116 (p) cc_final: 0.7870 (p) REVERT: C 629 PHE cc_start: 0.8379 (m-80) cc_final: 0.8144 (t80) REVERT: C 704 MET cc_start: 0.6812 (mpp) cc_final: 0.6425 (mpp) REVERT: C 762 ASN cc_start: 0.7721 (m-40) cc_final: 0.7485 (m-40) REVERT: C 946 LEU cc_start: 0.8609 (mt) cc_final: 0.8363 (mt) REVERT: C 1049 ILE cc_start: 0.5401 (mm) cc_final: 0.5178 (mm) REVERT: C 1165 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7541 (p) REVERT: C 1312 ASN cc_start: 0.7493 (t0) cc_final: 0.7283 (t0) REVERT: D 34 SER cc_start: 0.4109 (OUTLIER) cc_final: 0.3147 (t) REVERT: D 483 LEU cc_start: 0.8004 (mt) cc_final: 0.7784 (mt) REVERT: D 506 VAL cc_start: 0.9152 (t) cc_final: 0.8939 (m) REVERT: D 625 MET cc_start: 0.6858 (ttm) cc_final: 0.6189 (tmm) REVERT: D 759 ILE cc_start: 0.8155 (mt) cc_final: 0.7899 (mt) REVERT: D 861 ASN cc_start: 0.7155 (m-40) cc_final: 0.6818 (m110) REVERT: D 1040 MET cc_start: 0.3113 (tpt) cc_final: 0.2753 (tpt) REVERT: M 206 PHE cc_start: 0.4616 (m-80) cc_final: 0.4336 (m-80) REVERT: M 270 GLU cc_start: 0.7269 (tp30) cc_final: 0.5923 (tp30) REVERT: M 355 PHE cc_start: 0.5099 (OUTLIER) cc_final: 0.4102 (m-80) outliers start: 110 outliers final: 51 residues processed: 526 average time/residue: 0.3967 time to fit residues: 336.1404 Evaluate side-chains 473 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 417 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 257 VAL 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 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1082 ILE 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 1233 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 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 329 ASP Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 592 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 882 VAL Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain E residue 4 VAL 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: 7.9990 chunk 7 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 196 optimal weight: 0.6980 chunk 288 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 365 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN D 186 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.093193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.070782 restraints weight = 116349.837| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 4.51 r_work (final): 0.3428 ------------------------------------------------------------------------------- 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: 0.7186 moved from start: 0.9356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 29305 Z= 0.172 Angle : 0.720 13.313 40250 Z= 0.362 Chirality : 0.044 0.268 4788 Planarity : 0.005 0.072 4929 Dihedral : 16.281 171.013 5044 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 4.41 % Allowed : 29.64 % Favored : 65.95 % 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: -0.62 (0.14), residues: 3612 helix: 0.66 (0.14), residues: 1341 sheet: 0.31 (0.27), residues: 373 loop : -1.39 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 115 HIS 0.010 0.001 HIS C 150 PHE 0.032 0.002 PHE C 645 TYR 0.020 0.002 TYR D 165 ARG 0.022 0.001 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 1237) hydrogen bonds : angle 4.27498 ( 3427) metal coordination : bond 0.00209 ( 4) covalent geometry : bond 0.00386 (29301) covalent geometry : angle 0.71953 (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 577 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 462 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.7670 (ppp) cc_final: 0.7184 (ptt) REVERT: A 199 ASP cc_start: 0.7773 (m-30) cc_final: 0.7481 (m-30) REVERT: A 257 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7633 (m) REVERT: B 93 GLN cc_start: 0.8403 (mm110) cc_final: 0.8136 (mm-40) REVERT: C 47 TYR cc_start: 0.5522 (OUTLIER) cc_final: 0.4458 (p90) REVERT: C 84 GLU cc_start: 0.7837 (mp0) cc_final: 0.7142 (mp0) REVERT: C 116 ASP cc_start: 0.8308 (t0) cc_final: 0.7692 (m-30) REVERT: C 187 GLU cc_start: 0.5571 (tp30) cc_final: 0.4909 (pm20) REVERT: C 517 GLN cc_start: 0.7811 (tp40) cc_final: 0.7567 (tp-100) REVERT: C 583 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.5695 (tm-30) REVERT: C 653 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7794 (tpt) REVERT: C 862 LEU cc_start: 0.7900 (mp) cc_final: 0.7530 (tt) REVERT: C 900 LYS cc_start: 0.6358 (OUTLIER) cc_final: 0.5685 (mttt) REVERT: C 953 LEU cc_start: 0.9056 (pp) cc_final: 0.8821 (pp) REVERT: C 1049 ILE cc_start: 0.5960 (mm) cc_final: 0.5646 (mm) REVERT: C 1066 MET cc_start: 0.8546 (ttm) cc_final: 0.8321 (ttm) REVERT: C 1244 HIS cc_start: 0.6607 (t70) cc_final: 0.6378 (t70) REVERT: C 1275 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.9080 (p) REVERT: C 1312 ASN cc_start: 0.8074 (t0) cc_final: 0.7617 (t0) REVERT: D 301 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6207 (pt0) REVERT: D 483 LEU cc_start: 0.9029 (mt) cc_final: 0.8706 (mt) REVERT: D 618 VAL cc_start: 0.9415 (t) cc_final: 0.9190 (p) REVERT: D 746 LEU cc_start: 0.8787 (mp) cc_final: 0.8563 (mt) REVERT: D 747 MET cc_start: 0.7599 (pmm) cc_final: 0.7189 (pmm) REVERT: D 1040 MET cc_start: 0.2902 (tpt) cc_final: 0.2496 (tpt) REVERT: M 199 LEU cc_start: 0.8198 (mm) cc_final: 0.7777 (tt) REVERT: M 270 GLU cc_start: 0.7373 (tp30) cc_final: 0.6000 (tp30) REVERT: M 355 PHE cc_start: 0.5014 (OUTLIER) cc_final: 0.4083 (m-80) outliers start: 115 outliers final: 48 residues processed: 545 average time/residue: 0.3838 time to fit residues: 336.8726 Evaluate side-chains 439 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 383 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 83 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 735 LYS 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 1082 ILE 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 1275 VAL Chi-restraints excluded: chain C residue 1295 SER 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 223 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 415 VAL 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 803 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 259 ARG 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: 4.9990 chunk 184 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 262 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 305 optimal weight: 0.7980 chunk 238 optimal weight: 0.0980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN C 36 GLN C 60 GLN C 517 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 ASN M 265 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.092643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.069775 restraints weight = 115803.828| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.52 r_work: 0.3253 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 1.0295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29305 Z= 0.152 Angle : 0.703 11.380 40250 Z= 0.352 Chirality : 0.044 0.205 4788 Planarity : 0.005 0.086 4929 Dihedral : 16.249 170.700 5044 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 3.80 % Allowed : 31.94 % Favored : 64.26 % 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: -0.56 (0.14), residues: 3612 helix: 0.78 (0.14), residues: 1338 sheet: 0.31 (0.27), residues: 378 loop : -1.40 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 115 HIS 0.008 0.001 HIS D 80 PHE 0.030 0.002 PHE D1325 TYR 0.024 0.002 TYR D1232 ARG 0.018 0.001 ARG M 196 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 1237) hydrogen bonds : angle 4.29255 ( 3427) metal coordination : bond 0.00294 ( 4) covalent geometry : bond 0.00347 (29301) covalent geometry : angle 0.70269 (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 498 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 399 time to evaluate : 4.154 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: A 142 MET cc_start: 0.8035 (ppp) cc_final: 0.7801 (ptt) REVERT: A 147 GLN cc_start: 0.8130 (tt0) cc_final: 0.7886 (tt0) REVERT: A 199 ASP cc_start: 0.8081 (m-30) cc_final: 0.7793 (m-30) REVERT: A 231 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8290 (t80) REVERT: A 257 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7766 (m) REVERT: B 51 MET cc_start: 0.8936 (mmm) cc_final: 0.8313 (tmm) REVERT: B 93 GLN cc_start: 0.8509 (mm110) cc_final: 0.8176 (mm-40) REVERT: C 47 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.5206 (p90) REVERT: C 84 GLU cc_start: 0.8185 (mp0) cc_final: 0.7899 (mp0) REVERT: C 116 ASP cc_start: 0.8372 (t0) cc_final: 0.7754 (m-30) REVERT: C 151 ARG cc_start: 0.7595 (mmp80) cc_final: 0.6958 (mmm-85) REVERT: C 461 GLU cc_start: 0.7917 (pt0) cc_final: 0.7553 (pp20) REVERT: C 654 ASP cc_start: 0.7424 (t0) cc_final: 0.6521 (t0) REVERT: C 741 MET cc_start: 0.7976 (ppp) cc_final: 0.7643 (mmm) REVERT: C 862 LEU cc_start: 0.8107 (mp) cc_final: 0.7854 (tt) REVERT: C 900 LYS cc_start: 0.6487 (OUTLIER) cc_final: 0.5928 (mttt) REVERT: C 1049 ILE cc_start: 0.6621 (mm) cc_final: 0.6224 (mm) REVERT: C 1244 HIS cc_start: 0.7463 (t70) cc_final: 0.7204 (t70) REVERT: C 1276 TRP cc_start: 0.7870 (m-10) cc_final: 0.7505 (m-10) REVERT: D 301 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6990 (pt0) REVERT: D 324 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6589 (tt) REVERT: D 483 LEU cc_start: 0.9153 (mt) cc_final: 0.8777 (mt) REVERT: D 625 MET cc_start: 0.9158 (ttp) cc_final: 0.8733 (tmm) REVERT: D 772 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: D 1040 MET cc_start: 0.3601 (tpt) cc_final: 0.3036 (tpt) REVERT: D 1232 TYR cc_start: 0.8202 (t80) cc_final: 0.7973 (t80) REVERT: M 199 LEU cc_start: 0.8499 (mm) cc_final: 0.8051 (tt) REVERT: M 270 GLU cc_start: 0.7564 (tp30) cc_final: 0.6120 (tp30) REVERT: M 355 PHE cc_start: 0.5589 (OUTLIER) cc_final: 0.4761 (m-80) outliers start: 99 outliers final: 51 residues processed: 471 average time/residue: 0.5230 time to fit residues: 408.1130 Evaluate side-chains 410 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 351 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 90 VAL 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 17 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 LEU 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 122 VAL Chi-restraints excluded: chain C residue 130 MET 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 558 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 616 ILE 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 1023 HIS Chi-restraints excluded: chain C residue 1060 ILE 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 1275 VAL Chi-restraints excluded: chain C residue 1323 PHE 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 262 THR Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 415 VAL 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 882 VAL Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 158 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 257 optimal weight: 0.2980 chunk 164 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 304 optimal weight: 30.0000 chunk 247 optimal weight: 20.0000 chunk 187 optimal weight: 6.9990 chunk 370 optimal weight: 40.0000 chunk 168 optimal weight: 7.9990 overall best weight: 3.4584 ------------------------------------------------------------------------------- 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 60 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS C1070 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D1227 HIS ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.090208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.066831 restraints weight = 115930.997| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 4.41 r_work: 0.3172 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 1.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 29305 Z= 0.211 Angle : 0.794 15.570 40250 Z= 0.404 Chirality : 0.047 0.284 4788 Planarity : 0.006 0.130 4929 Dihedral : 16.328 170.367 5044 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 3.80 % Allowed : 32.40 % Favored : 63.80 % 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: -0.80 (0.14), residues: 3612 helix: 0.58 (0.14), residues: 1338 sheet: 0.10 (0.27), residues: 367 loop : -1.51 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 868 HIS 0.010 0.001 HIS D 80 PHE 0.034 0.002 PHE C 505 TYR 0.031 0.002 TYR D 555 ARG 0.033 0.001 ARG D 337 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 1237) hydrogen bonds : angle 4.58655 ( 3427) metal coordination : bond 0.00386 ( 4) covalent geometry : bond 0.00478 (29301) covalent geometry : angle 0.79439 (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 461 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 362 time to evaluate : 3.542 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: A 199 ASP cc_start: 0.8521 (m-30) cc_final: 0.8130 (m-30) REVERT: A 231 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8586 (t80) REVERT: B 51 MET cc_start: 0.9216 (mmm) cc_final: 0.8766 (tmm) REVERT: B 93 GLN cc_start: 0.8539 (mm110) cc_final: 0.8120 (mm-40) REVERT: C 47 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6561 (p90) REVERT: C 494 ASN cc_start: 0.8360 (t0) cc_final: 0.8052 (t0) REVERT: C 541 GLU cc_start: 0.7427 (tp30) cc_final: 0.6927 (tm-30) REVERT: C 783 LEU cc_start: 0.9052 (mt) cc_final: 0.8713 (mp) REVERT: C 862 LEU cc_start: 0.8668 (mp) cc_final: 0.8387 (tt) REVERT: C 882 ILE cc_start: 0.8673 (mp) cc_final: 0.8168 (tp) REVERT: C 900 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6161 (mttt) REVERT: C 1238 LEU cc_start: 0.8337 (mm) cc_final: 0.8070 (mt) REVERT: D 116 PHE cc_start: 0.6363 (m-10) cc_final: 0.5872 (m-10) REVERT: D 130 MET cc_start: 0.4620 (mtt) cc_final: 0.4408 (mtt) REVERT: D 192 MET cc_start: 0.2785 (ppp) cc_final: 0.2434 (ppp) REVERT: D 248 ASP cc_start: 0.8326 (m-30) cc_final: 0.7993 (t0) REVERT: D 301 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: D 330 MET cc_start: 0.7736 (tpt) cc_final: 0.7350 (ttm) REVERT: D 339 ARG cc_start: 0.8102 (tpp-160) cc_final: 0.7454 (tpp-160) REVERT: D 340 GLN cc_start: 0.7665 (pm20) cc_final: 0.7412 (pm20) REVERT: D 411 ILE cc_start: 0.9201 (tt) cc_final: 0.9001 (tp) REVERT: D 564 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7692 (p) REVERT: D 614 LEU cc_start: 0.9006 (tp) cc_final: 0.8759 (tp) REVERT: D 725 MET cc_start: 0.9002 (mtt) cc_final: 0.8763 (mtt) REVERT: D 756 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8808 (mt-10) REVERT: D 772 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.6962 (m-80) REVERT: D 1040 MET cc_start: 0.3439 (tpt) cc_final: 0.2877 (tpt) REVERT: D 1307 LEU cc_start: 0.8727 (mt) cc_final: 0.8290 (tp) REVERT: D 1330 ARG cc_start: 0.5288 (mmt180) cc_final: 0.5077 (mmm160) REVERT: M 154 LEU cc_start: 0.6645 (mt) cc_final: 0.5839 (tp) REVERT: M 172 LEU cc_start: 0.8619 (tt) cc_final: 0.8150 (pp) REVERT: M 199 LEU cc_start: 0.8439 (mm) cc_final: 0.8035 (tt) REVERT: M 259 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7819 (ptp90) REVERT: M 262 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8151 (pp30) REVERT: M 270 GLU cc_start: 0.7886 (tp30) cc_final: 0.6518 (tp30) REVERT: M 355 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5324 (m-80) outliers start: 99 outliers final: 44 residues processed: 440 average time/residue: 0.4995 time to fit residues: 358.2998 Evaluate side-chains 352 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 299 time to evaluate : 3.744 ------------------------------------------------------------------------------- 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 310 ARG Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 LEU 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 131 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1295 SER 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 239 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 624 ILE 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 1226 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 259 ARG Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 355 PHE Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 332 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 291 optimal weight: 50.0000 chunk 366 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C1108 ASN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN ** M 377 HIS ** 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 = 0.3869 r_free = 0.3869 target = 0.088742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.064760 restraints weight = 114743.260| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 4.38 r_work: 0.3126 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 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 = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 1.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29305 Z= 0.180 Angle : 0.737 13.179 40250 Z= 0.373 Chirality : 0.045 0.278 4788 Planarity : 0.006 0.103 4929 Dihedral : 16.261 169.605 5044 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 2.99 % Allowed : 33.40 % 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: -0.66 (0.14), residues: 3612 helix: 0.72 (0.14), residues: 1331 sheet: 0.11 (0.26), residues: 393 loop : -1.44 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 115 HIS 0.015 0.001 HIS M 377 PHE 0.030 0.002 PHE C 390 TYR 0.058 0.002 TYR C 742 ARG 0.008 0.001 ARG D1345 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1237) hydrogen bonds : angle 4.47593 ( 3427) metal coordination : bond 0.00418 ( 4) covalent geometry : bond 0.00413 (29301) covalent geometry : angle 0.73729 (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 417 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 339 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.9017 (t0) cc_final: 0.8725 (t0) REVERT: A 75 GLN cc_start: 0.8174 (pm20) cc_final: 0.7720 (pp30) REVERT: A 199 ASP cc_start: 0.8488 (m-30) cc_final: 0.8185 (m-30) REVERT: A 231 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8667 (t80) REVERT: A 233 ASP cc_start: 0.8378 (m-30) cc_final: 0.7300 (t0) REVERT: B 37 HIS cc_start: 0.9289 (OUTLIER) cc_final: 0.8002 (t-90) REVERT: B 51 MET cc_start: 0.9247 (mmm) cc_final: 0.8918 (tpp) REVERT: B 93 GLN cc_start: 0.8657 (mm110) cc_final: 0.8278 (mm-40) REVERT: B 95 LYS cc_start: 0.8604 (tptp) cc_final: 0.8256 (tptp) REVERT: C 47 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.7051 (p90) REVERT: C 492 MET cc_start: 0.5540 (mtm) cc_final: 0.4639 (mtm) REVERT: C 494 ASN cc_start: 0.8437 (t0) cc_final: 0.7866 (p0) REVERT: C 503 LYS cc_start: 0.8381 (tptm) cc_final: 0.8064 (mptp) REVERT: C 541 GLU cc_start: 0.7690 (tp30) cc_final: 0.7279 (tm-30) REVERT: C 741 MET cc_start: 0.7838 (mmt) cc_final: 0.7449 (ppp) REVERT: C 862 LEU cc_start: 0.8772 (mp) cc_final: 0.8457 (tt) REVERT: C 900 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6196 (mttt) REVERT: C 1053 TYR cc_start: 0.8919 (m-80) cc_final: 0.8705 (m-80) REVERT: C 1238 LEU cc_start: 0.8539 (mm) cc_final: 0.8282 (mt) REVERT: C 1319 MET cc_start: 0.8943 (tpp) cc_final: 0.8729 (tpp) REVERT: D 192 MET cc_start: 0.3449 (ppp) cc_final: 0.3164 (ppp) REVERT: D 330 MET cc_start: 0.7876 (tpt) cc_final: 0.7643 (ttm) REVERT: D 339 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.7812 (ttt180) REVERT: D 340 GLN cc_start: 0.8195 (pm20) cc_final: 0.7913 (pm20) REVERT: D 725 MET cc_start: 0.9009 (mtt) cc_final: 0.8721 (mtp) REVERT: D 747 MET cc_start: 0.7762 (pmm) cc_final: 0.7342 (pmm) REVERT: D 772 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: D 1040 MET cc_start: 0.3693 (tpt) cc_final: 0.3016 (tpt) REVERT: D 1155 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8188 (tp) REVERT: D 1249 ASN cc_start: 0.9360 (OUTLIER) cc_final: 0.9141 (t0) REVERT: D 1278 GLU cc_start: 0.6552 (pt0) cc_final: 0.5986 (pm20) REVERT: D 1279 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7615 (tp-100) REVERT: D 1330 ARG cc_start: 0.6115 (mmt180) cc_final: 0.5839 (mmm160) REVERT: E 11 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8761 (mm-30) REVERT: M 172 LEU cc_start: 0.8848 (tt) cc_final: 0.8506 (pp) REVERT: M 178 VAL cc_start: 0.7294 (m) cc_final: 0.7065 (p) REVERT: M 199 LEU cc_start: 0.8577 (mm) cc_final: 0.8165 (tt) REVERT: M 262 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: M 270 GLU cc_start: 0.8043 (tp30) cc_final: 0.6718 (tp30) REVERT: M 355 PHE cc_start: 0.5918 (OUTLIER) cc_final: 0.5455 (m-80) REVERT: M 363 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.5766 (mmmt) outliers start: 78 outliers final: 44 residues processed: 398 average time/residue: 0.4853 time to fit residues: 309.7810 Evaluate side-chains 345 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 291 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE 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 B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 900 LYS 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 1230 MET Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1323 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 249 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 518 VAL Chi-restraints excluded: chain D residue 674 THR 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 1155 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 355 PHE Chi-restraints excluded: chain M residue 363 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 212 optimal weight: 6.9990 chunk 337 optimal weight: 0.1980 chunk 342 optimal weight: 0.8980 chunk 293 optimal weight: 9.9990 chunk 283 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 chunk 315 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 330 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 314 ASN C 519 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.089798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066036 restraints weight = 114209.915| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 4.40 r_work: 0.3160 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 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 = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 1.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29305 Z= 0.132 Angle : 0.717 12.656 40250 Z= 0.359 Chirality : 0.044 0.237 4788 Planarity : 0.005 0.095 4929 Dihedral : 16.209 170.767 5044 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 2.07 % Allowed : 34.55 % Favored : 63.38 % 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: -0.53 (0.14), residues: 3612 helix: 0.86 (0.14), residues: 1322 sheet: 0.12 (0.27), residues: 396 loop : -1.38 (0.14), residues: 1894 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 0.033 0.002 PHE C 390 TYR 0.028 0.002 TYR C 26 ARG 0.010 0.001 ARG D1222 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 1237) hydrogen bonds : angle 4.33814 ( 3427) metal coordination : bond 0.00165 ( 4) covalent geometry : bond 0.00302 (29301) covalent geometry : angle 0.71716 (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 369 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8950 (t0) cc_final: 0.8715 (t0) REVERT: A 199 ASP cc_start: 0.8457 (m-30) cc_final: 0.8144 (m-30) REVERT: B 51 MET cc_start: 0.9203 (mmm) cc_final: 0.8842 (tpp) REVERT: B 95 LYS cc_start: 0.8597 (tptp) cc_final: 0.8220 (tptp) REVERT: C 47 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.7072 (p90) REVERT: C 392 GLU cc_start: 0.7388 (tp30) cc_final: 0.6998 (tm-30) REVERT: C 503 LYS cc_start: 0.8411 (tptm) cc_final: 0.8107 (mttp) REVERT: C 541 GLU cc_start: 0.7755 (tp30) cc_final: 0.7202 (tm-30) REVERT: C 741 MET cc_start: 0.7766 (mmt) cc_final: 0.7161 (ppp) REVERT: C 862 LEU cc_start: 0.8914 (mp) cc_final: 0.8610 (tt) REVERT: C 882 ILE cc_start: 0.8704 (mp) cc_final: 0.8272 (tp) REVERT: C 900 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6251 (mttt) REVERT: C 1053 TYR cc_start: 0.8941 (m-80) cc_final: 0.8671 (m-80) REVERT: C 1233 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9238 (mt) REVERT: C 1238 LEU cc_start: 0.8363 (mm) cc_final: 0.8144 (mt) REVERT: C 1315 MET cc_start: 0.8408 (tpp) cc_final: 0.8139 (tpp) REVERT: D 192 MET cc_start: 0.3543 (ppp) cc_final: 0.3157 (ppp) REVERT: D 217 LEU cc_start: 0.7944 (mm) cc_final: 0.7706 (pp) REVERT: D 330 MET cc_start: 0.7467 (tpt) cc_final: 0.7259 (ttm) REVERT: D 337 ARG cc_start: 0.7567 (mmp80) cc_final: 0.7245 (mmp80) REVERT: D 339 ARG cc_start: 0.8269 (tpp-160) cc_final: 0.7741 (ttt180) REVERT: D 340 GLN cc_start: 0.8562 (pm20) cc_final: 0.8311 (pm20) REVERT: D 747 MET cc_start: 0.7582 (pmm) cc_final: 0.6979 (pmm) REVERT: D 772 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7353 (m-80) REVERT: D 1040 MET cc_start: 0.3593 (tpt) cc_final: 0.3171 (tpt) REVERT: D 1244 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8599 (tm-30) REVERT: D 1278 GLU cc_start: 0.6407 (pt0) cc_final: 0.5939 (pm20) REVERT: D 1305 ASP cc_start: 0.8275 (t0) cc_final: 0.7915 (m-30) REVERT: M 172 LEU cc_start: 0.8756 (tt) cc_final: 0.8321 (pp) REVERT: M 199 LEU cc_start: 0.8587 (mm) cc_final: 0.8192 (tt) REVERT: M 270 GLU cc_start: 0.8076 (tp30) cc_final: 0.6723 (tp30) REVERT: M 355 PHE cc_start: 0.5905 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: M 363 LYS cc_start: 0.6408 (mtmm) cc_final: 0.5760 (mmmt) outliers start: 54 outliers final: 35 residues processed: 355 average time/residue: 0.4021 time to fit residues: 235.5543 Evaluate side-chains 331 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 291 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS 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 1233 LEU Chi-restraints excluded: chain C residue 1323 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 518 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 918 ILE Chi-restraints excluded: chain D residue 1162 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 355 PHE 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: 0.6980 chunk 50 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 36 optimal weight: 0.0470 chunk 210 optimal weight: 30.0000 chunk 224 optimal weight: 0.1980 chunk 294 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 302 optimal weight: 30.0000 chunk 238 optimal weight: 3.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 ASN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.089953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.066370 restraints weight = 114385.902| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.36 r_work: 0.3169 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 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 = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 1.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29305 Z= 0.130 Angle : 0.707 12.494 40250 Z= 0.353 Chirality : 0.043 0.217 4788 Planarity : 0.005 0.082 4929 Dihedral : 16.174 172.128 5044 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.21 % Rotamer: Outliers : 1.61 % Allowed : 34.85 % Favored : 63.54 % 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: -0.44 (0.14), residues: 3612 helix: 0.98 (0.14), residues: 1323 sheet: 0.25 (0.28), residues: 371 loop : -1.36 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 236 HIS 0.007 0.001 HIS D 80 PHE 0.030 0.002 PHE C 390 TYR 0.023 0.001 TYR M 461 ARG 0.010 0.001 ARG D1222 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 1237) hydrogen bonds : angle 4.27904 ( 3427) metal coordination : bond 0.00135 ( 4) covalent geometry : bond 0.00300 (29301) covalent geometry : angle 0.70660 (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 350 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.9011 (tt0) cc_final: 0.8613 (mt0) REVERT: A 199 ASP cc_start: 0.8476 (m-30) cc_final: 0.8177 (m-30) REVERT: A 233 ASP cc_start: 0.8421 (m-30) cc_final: 0.7212 (t0) REVERT: A 318 LEU cc_start: 0.8214 (tp) cc_final: 0.7950 (tp) REVERT: B 51 MET cc_start: 0.9173 (mmm) cc_final: 0.8807 (tpp) REVERT: B 95 LYS cc_start: 0.8578 (tptp) cc_final: 0.8201 (tptp) REVERT: C 47 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.7178 (p90) REVERT: C 392 GLU cc_start: 0.7407 (tp30) cc_final: 0.7004 (tm-30) REVERT: C 503 LYS cc_start: 0.8480 (tptm) cc_final: 0.8149 (mptp) REVERT: C 541 GLU cc_start: 0.7811 (tp30) cc_final: 0.7341 (tm-30) REVERT: C 741 MET cc_start: 0.7813 (mmt) cc_final: 0.7133 (ppp) REVERT: C 862 LEU cc_start: 0.8975 (mp) cc_final: 0.8664 (tt) REVERT: C 882 ILE cc_start: 0.8798 (mp) cc_final: 0.8373 (tp) REVERT: C 1053 TYR cc_start: 0.8970 (m-80) cc_final: 0.8690 (m-80) REVERT: C 1085 MET cc_start: 0.8980 (mtp) cc_final: 0.8746 (mtt) REVERT: C 1233 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9230 (mt) REVERT: C 1238 LEU cc_start: 0.8351 (mm) cc_final: 0.8149 (mt) REVERT: C 1244 HIS cc_start: 0.8257 (t70) cc_final: 0.7880 (t70) REVERT: C 1291 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9211 (mt) REVERT: C 1315 MET cc_start: 0.8431 (tpp) cc_final: 0.8168 (tpp) REVERT: D 192 MET cc_start: 0.3514 (ppp) cc_final: 0.3180 (ppp) REVERT: D 217 LEU cc_start: 0.8062 (mm) cc_final: 0.7810 (pp) REVERT: D 330 MET cc_start: 0.7650 (tpt) cc_final: 0.7436 (ttm) REVERT: D 337 ARG cc_start: 0.7402 (mmp80) cc_final: 0.7047 (mmp80) REVERT: D 339 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.7895 (ttt180) REVERT: D 340 GLN cc_start: 0.8644 (pm20) cc_final: 0.8407 (pm20) REVERT: D 747 MET cc_start: 0.7723 (pmm) cc_final: 0.7314 (pmm) REVERT: D 772 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: D 1040 MET cc_start: 0.3798 (tpt) cc_final: 0.3347 (tpt) REVERT: D 1244 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8638 (tm-30) REVERT: D 1249 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.9079 (t0) REVERT: D 1278 GLU cc_start: 0.6281 (pt0) cc_final: 0.5921 (pm20) REVERT: D 1305 ASP cc_start: 0.8312 (t0) cc_final: 0.7972 (m-30) REVERT: E 46 THR cc_start: 0.9437 (m) cc_final: 0.9085 (t) REVERT: M 172 LEU cc_start: 0.8795 (tt) cc_final: 0.8362 (pp) REVERT: M 199 LEU cc_start: 0.8587 (mm) cc_final: 0.8205 (tt) REVERT: M 270 GLU cc_start: 0.7945 (tp30) cc_final: 0.6522 (tp30) outliers start: 42 outliers final: 31 residues processed: 343 average time/residue: 0.5720 time to fit residues: 332.2533 Evaluate side-chains 326 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 290 time to evaluate : 6.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET 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 B residue 146 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 967 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 1233 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 249 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 1162 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain M residue 155 THR 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: 10.0000 chunk 323 optimal weight: 0.4980 chunk 233 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 296 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 294 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 283 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 GLN D1249 ASN M 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.089848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.066218 restraints weight = 114319.415| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.37 r_work: 0.3166 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 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 = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 1.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 29305 Z= 0.185 Angle : 0.802 59.200 40250 Z= 0.427 Chirality : 0.047 1.202 4788 Planarity : 0.005 0.079 4929 Dihedral : 16.180 172.124 5044 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 1.76 % Allowed : 34.70 % Favored : 63.54 % Cbeta Deviations : 0.03 % 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: -0.44 (0.14), residues: 3612 helix: 0.98 (0.14), residues: 1323 sheet: 0.25 (0.28), residues: 371 loop : -1.37 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 236 HIS 0.006 0.001 HIS D 80 PHE 0.028 0.002 PHE C 390 TYR 0.022 0.001 TYR A 152 ARG 0.009 0.000 ARG D1222 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 1237) hydrogen bonds : angle 4.27991 ( 3427) metal coordination : bond 0.00193 ( 4) covalent geometry : bond 0.00395 (29301) covalent geometry : angle 0.80225 (40250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17855.99 seconds wall clock time: 317 minutes 40.47 seconds (19060.47 seconds total)