Starting phenix.real_space_refine on Mon Aug 25 13:28:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8reb_19081/08_2025/8reb_19081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8reb_19081/08_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_19081/08_2025/8reb_19081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8reb_19081/08_2025/8reb_19081.map" model { file = "/net/cci-nas-00/data/ceres_data/8reb_19081/08_2025/8reb_19081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8reb_19081/08_2025/8reb_19081.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'ARG:plan': 5} 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, 'GLU:plan': 22, 'ARG:plan': 18, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 15, 'PHE:plan': 5, 'TYR:plan': 3, 'TRP:plan': 1} 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, 'ASP:plan': 18, 'GLU:plan': 31, 'ASN:plan1': 5, 'PHE:plan': 9, 'ARG:plan': 18, 'HIS:plan': 1, 'TYR:plan': 3, 'TRP:plan': 2} 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: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 4} 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: {'ASN:plan1': 7, 'ASP:plan': 22, 'TYR:plan': 2, 'GLN:plan1': 9, 'GLU:plan': 26, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 2, 'ARG:plan': 10} 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: 6.05, per 1000 atoms: 0.21 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: 2.10 Conformation dependent library (CDL) restraints added in 865.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.17 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: 7.76 Time building geometry restraints manager: 2.80 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.430 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- 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 : 10.86 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG M 184 TYR 0.036 0.002 TYR C1053 PHE 0.015 0.002 PHE M 355 TRP 0.036 0.002 TRP C 183 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00488 (29301) covalent geometry : angle 0.71054 (40250) hydrogen bonds : bond 0.16025 ( 1237) hydrogen bonds : angle 5.67167 ( 3427) metal coordination : bond 0.00284 ( 4) *********************** 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 : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.1980 time to fit residues: 231.4437 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 : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.0040 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.0270 overall best weight: 3.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 C1257 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 232 ASN D 309 ASN D 419 HIS D 477 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS D1249 ASN ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN M 121 GLN M 205 GLN M 265 GLN M 290 ASN M 387 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.092642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.071171 restraints weight = 114591.432| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 4.44 r_work: 0.3284 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 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 = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 29305 Z= 0.269 Angle : 0.934 17.337 40250 Z= 0.479 Chirality : 0.051 0.342 4788 Planarity : 0.008 0.127 4929 Dihedral : 16.494 170.925 5044 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.49 % Rotamer: Outliers : 7.36 % Allowed : 27.42 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.13), residues: 3612 helix: -0.03 (0.14), residues: 1334 sheet: 0.30 (0.28), residues: 359 loop : -1.57 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG D1345 TYR 0.046 0.003 TYR C 726 PHE 0.036 0.004 PHE M 355 TRP 0.018 0.003 TRP D 33 HIS 0.017 0.003 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00589 (29301) covalent geometry : angle 0.93366 (40250) hydrogen bonds : bond 0.05037 ( 1237) hydrogen bonds : angle 4.85210 ( 3427) metal coordination : bond 0.00326 ( 4) *********************** 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 761 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 569 time to evaluate : 0.855 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: A 200 LYS cc_start: 0.8887 (ptmt) cc_final: 0.8597 (ptmm) REVERT: A 257 VAL cc_start: 0.7322 (OUTLIER) cc_final: 0.7067 (m) REVERT: B 47 LEU cc_start: 0.8630 (mt) cc_final: 0.8367 (mt) REVERT: B 51 MET cc_start: 0.8023 (mmt) cc_final: 0.7740 (mmm) REVERT: B 77 ASP cc_start: 0.7982 (t0) cc_final: 0.7545 (t0) REVERT: B 200 LYS cc_start: 0.8298 (ttpt) cc_final: 0.7750 (tmtt) REVERT: C 47 TYR cc_start: 0.4302 (OUTLIER) cc_final: 0.3577 (p90) REVERT: C 57 PHE cc_start: 0.6009 (m-80) cc_final: 0.5286 (m-80) REVERT: C 116 ASP cc_start: 0.8179 (t0) cc_final: 0.7620 (m-30) REVERT: C 409 LEU cc_start: 0.7893 (mt) cc_final: 0.7663 (tp) REVERT: C 414 ILE cc_start: 0.5853 (OUTLIER) cc_final: 0.5257 (mm) REVERT: C 651 ASP cc_start: 0.5741 (t70) cc_final: 0.5371 (t0) REVERT: C 671 LEU cc_start: 0.9029 (tp) cc_final: 0.8395 (tp) REVERT: C 702 THR cc_start: 0.8285 (m) cc_final: 0.7638 (m) REVERT: C 800 MET cc_start: 0.7766 (tpp) cc_final: 0.7351 (mpp) REVERT: C 900 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5551 (mttt) REVERT: C 957 LYS cc_start: 0.8705 (pptt) cc_final: 0.8273 (pttt) REVERT: C 1049 ILE cc_start: 0.5579 (mm) cc_final: 0.5296 (mm) REVERT: C 1167 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6964 (tm-30) REVERT: C 1168 GLU cc_start: 0.7929 (mp0) cc_final: 0.7037 (mm-30) REVERT: D 135 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5587 (tt) REVERT: D 402 GLU cc_start: 0.7140 (tp30) cc_final: 0.6809 (tp30) REVERT: D 428 THR cc_start: 0.8055 (m) cc_final: 0.6800 (m) REVERT: D 445 LYS cc_start: 0.7684 (mttt) cc_final: 0.7458 (mtpt) REVERT: D 447 ILE cc_start: 0.7930 (mt) cc_final: 0.7683 (mt) REVERT: D 534 GLU cc_start: 0.8649 (tp30) cc_final: 0.8141 (tp30) REVERT: D 609 TYR cc_start: 0.7940 (t80) cc_final: 0.7696 (t80) REVERT: D 614 LEU cc_start: 0.7600 (tp) cc_final: 0.6959 (mp) REVERT: D 625 MET cc_start: 0.5553 (ttm) cc_final: 0.5262 (tmm) REVERT: D 736 GLN cc_start: 0.8003 (mt0) cc_final: 0.7738 (pt0) REVERT: D 759 ILE cc_start: 0.7404 (mt) cc_final: 0.6533 (mt) REVERT: D 1040 MET cc_start: 0.3369 (tpt) cc_final: 0.2720 (tpt) REVERT: D 1229 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.8039 (p) REVERT: D 1230 THR cc_start: 0.7841 (m) cc_final: 0.7536 (m) REVERT: D 1320 ILE cc_start: 0.7820 (mm) cc_final: 0.7515 (mm) REVERT: M 178 VAL cc_start: 0.6603 (m) cc_final: 0.6331 (p) REVERT: M 196 ARG cc_start: 0.5828 (tpt170) cc_final: 0.5601 (tpm170) REVERT: M 200 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7209 (mt) REVERT: M 265 GLN cc_start: 0.1939 (OUTLIER) cc_final: 0.1443 (mp10) REVERT: M 270 GLU cc_start: 0.7032 (tp30) cc_final: 0.5560 (tp30) outliers start: 192 outliers final: 53 residues processed: 719 average time/residue: 0.1736 time to fit residues: 199.7300 Evaluate side-chains 495 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 434 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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 30 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 414 ILE 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 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 1233 LEU Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 115 TRP 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 423 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 564 VAL 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 907 HIS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1351 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 363 optimal weight: 0.0020 chunk 367 optimal weight: 50.0000 chunk 246 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 358 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 339 optimal weight: 0.4980 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN 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 C 832 HIS ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN C1116 HIS C1175 ASN C1244 HIS C1313 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 265 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.093501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.072017 restraints weight = 115559.385| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.46 r_work: 0.3311 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 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 = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29305 Z= 0.144 Angle : 0.703 14.669 40250 Z= 0.355 Chirality : 0.044 0.195 4788 Planarity : 0.005 0.089 4929 Dihedral : 16.292 171.627 5044 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 3.60 % Allowed : 31.33 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.14), residues: 3612 helix: 0.48 (0.14), residues: 1347 sheet: 0.25 (0.26), residues: 391 loop : -1.43 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 678 TYR 0.022 0.002 TYR A 177 PHE 0.021 0.002 PHE D 62 TRP 0.020 0.002 TRP C 807 HIS 0.010 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00326 (29301) covalent geometry : angle 0.70333 (40250) hydrogen bonds : bond 0.03730 ( 1237) hydrogen bonds : angle 4.36195 ( 3427) metal coordination : bond 0.00101 ( 4) *********************** 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 568 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 474 time to evaluate : 0.804 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: A 141 SER cc_start: 0.7056 (OUTLIER) cc_final: 0.6570 (m) REVERT: A 257 VAL cc_start: 0.7533 (OUTLIER) cc_final: 0.7262 (m) REVERT: B 47 LEU cc_start: 0.8899 (mt) cc_final: 0.8480 (mt) REVERT: B 51 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7936 (mmm) REVERT: B 77 ASP cc_start: 0.8099 (t0) cc_final: 0.7784 (t0) REVERT: B 93 GLN cc_start: 0.7969 (mm110) cc_final: 0.7692 (mm-40) REVERT: B 127 GLN cc_start: 0.9195 (pm20) cc_final: 0.8786 (pm20) REVERT: C 57 PHE cc_start: 0.6063 (m-80) cc_final: 0.5520 (m-80) REVERT: C 116 ASP cc_start: 0.8267 (t0) cc_final: 0.7666 (m-30) REVERT: C 405 PHE cc_start: 0.6691 (t80) cc_final: 0.6295 (t80) REVERT: C 409 LEU cc_start: 0.8210 (mt) cc_final: 0.7981 (mp) REVERT: C 704 MET cc_start: 0.6338 (mpp) cc_final: 0.6100 (mpp) REVERT: C 741 MET cc_start: 0.7970 (ppp) cc_final: 0.7668 (mmt) REVERT: C 800 MET cc_start: 0.7691 (tpp) cc_final: 0.7216 (mpp) REVERT: C 900 LYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5531 (mttt) REVERT: C 1049 ILE cc_start: 0.5844 (mm) cc_final: 0.5592 (mm) REVERT: C 1168 GLU cc_start: 0.8022 (mp0) cc_final: 0.7641 (mm-30) REVERT: D 113 HIS cc_start: 0.4870 (t70) cc_final: 0.4635 (t70) REVERT: D 116 PHE cc_start: 0.3272 (m-10) cc_final: 0.2965 (m-10) REVERT: D 301 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6762 (pt0) REVERT: D 428 THR cc_start: 0.7886 (m) cc_final: 0.7391 (p) REVERT: D 445 LYS cc_start: 0.7544 (mttt) cc_final: 0.7302 (mtpt) REVERT: D 513 MET cc_start: 0.7643 (tpp) cc_final: 0.7187 (ttm) REVERT: D 625 MET cc_start: 0.6347 (ttm) cc_final: 0.5667 (tmm) REVERT: D 736 GLN cc_start: 0.8130 (mt0) cc_final: 0.7596 (mp10) REVERT: D 759 ILE cc_start: 0.7899 (mt) cc_final: 0.7589 (mt) REVERT: D 1040 MET cc_start: 0.3551 (tpt) cc_final: 0.3107 (tpt) REVERT: D 1262 ARG cc_start: 0.5370 (mmm160) cc_final: 0.4022 (mmm160) REVERT: D 1320 ILE cc_start: 0.7912 (mm) cc_final: 0.7625 (mm) REVERT: M 178 VAL cc_start: 0.6558 (m) cc_final: 0.6325 (p) REVERT: M 206 PHE cc_start: 0.6364 (OUTLIER) cc_final: 0.5234 (m-80) REVERT: M 265 GLN cc_start: 0.3573 (OUTLIER) cc_final: 0.3282 (mt0) REVERT: M 270 GLU cc_start: 0.6995 (tp30) cc_final: 0.5633 (tp30) outliers start: 94 outliers final: 46 residues processed: 530 average time/residue: 0.1685 time to fit residues: 143.6335 Evaluate side-chains 476 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 423 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 318 LEU 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 30 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1275 VAL 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 528 THR Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 706 VAL 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 1244 GLN Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 80 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 218 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 494 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D 594 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.092604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.070137 restraints weight = 116563.228| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.47 r_work: 0.3262 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 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 = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.9932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 29305 Z= 0.246 Angle : 0.830 24.700 40250 Z= 0.424 Chirality : 0.048 0.363 4788 Planarity : 0.006 0.087 4929 Dihedral : 16.456 168.221 5044 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 93.00 % Rotamer: Outliers : 6.06 % Allowed : 29.29 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.14), residues: 3612 helix: 0.18 (0.14), residues: 1340 sheet: 0.35 (0.27), residues: 359 loop : -1.53 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 407 TYR 0.026 0.003 TYR M 461 PHE 0.033 0.003 PHE D 116 TRP 0.073 0.005 TRP D 115 HIS 0.015 0.002 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00551 (29301) covalent geometry : angle 0.83016 (40250) hydrogen bonds : bond 0.04389 ( 1237) hydrogen bonds : angle 4.67926 ( 3427) metal coordination : bond 0.00409 ( 4) *********************** 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 623 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 465 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8627 (mmm) cc_final: 0.8146 (mmt) REVERT: A 142 MET cc_start: 0.8131 (ppp) cc_final: 0.7740 (ptt) REVERT: A 177 TYR cc_start: 0.8140 (m-80) cc_final: 0.7847 (m-80) REVERT: A 257 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7797 (m) REVERT: B 35 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8653 (t80) REVERT: B 77 ASP cc_start: 0.8364 (t0) cc_final: 0.8116 (t0) REVERT: B 93 GLN cc_start: 0.8542 (mm110) cc_final: 0.8209 (mm-40) REVERT: C 22 LEU cc_start: 0.8669 (pp) cc_final: 0.8171 (pp) REVERT: C 57 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.5970 (m-80) REVERT: C 100 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7213 (pt) REVERT: C 116 ASP cc_start: 0.8558 (t0) cc_final: 0.7996 (m-30) REVERT: C 405 PHE cc_start: 0.8057 (t80) cc_final: 0.7804 (t80) REVERT: C 409 LEU cc_start: 0.8419 (mt) cc_final: 0.8217 (mt) REVERT: C 430 LYS cc_start: 0.5522 (mmtt) cc_final: 0.5296 (tptt) REVERT: C 487 LEU cc_start: 0.8569 (tp) cc_final: 0.8196 (tp) REVERT: C 494 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7908 (p0) REVERT: C 541 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6393 (tm-30) REVERT: C 583 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6065 (tm-30) REVERT: C 681 MET cc_start: 0.8489 (ptp) cc_final: 0.8250 (ptp) REVERT: C 762 ASN cc_start: 0.8588 (m-40) cc_final: 0.8268 (m-40) REVERT: C 862 LEU cc_start: 0.8220 (mp) cc_final: 0.7929 (tt) REVERT: C 957 LYS cc_start: 0.9080 (pptt) cc_final: 0.8714 (pttt) REVERT: C 968 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: C 1049 ILE cc_start: 0.6265 (mm) cc_final: 0.5978 (mm) REVERT: C 1216 ARG cc_start: 0.8263 (mtm180) cc_final: 0.8050 (mtm-85) REVERT: C 1304 MET cc_start: 0.8445 (tmm) cc_final: 0.8237 (tpt) REVERT: C 1310 ASP cc_start: 0.7688 (m-30) cc_final: 0.7477 (t0) REVERT: D 117 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6985 (tp) REVERT: D 301 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6800 (pt0) REVERT: D 324 LEU cc_start: 0.6746 (mt) cc_final: 0.6496 (tp) REVERT: D 483 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8948 (mt) REVERT: D 590 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8672 (t) REVERT: D 592 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9311 (p) REVERT: D 634 ARG cc_start: 0.8899 (tpp80) cc_final: 0.8171 (tpp80) REVERT: D 725 MET cc_start: 0.8925 (mtt) cc_final: 0.8699 (mtt) REVERT: D 772 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.6613 (m-80) REVERT: D 861 ASN cc_start: 0.8213 (m-40) cc_final: 0.7788 (m110) REVERT: D 892 PHE cc_start: 0.8085 (m-80) cc_final: 0.7864 (m-80) REVERT: D 1040 MET cc_start: 0.3651 (tpt) cc_final: 0.3203 (tpt) REVERT: D 1287 ILE cc_start: 0.6190 (OUTLIER) cc_final: 0.5941 (mt) REVERT: E 15 ASN cc_start: 0.7204 (t0) cc_final: 0.6996 (t0) REVERT: M 178 VAL cc_start: 0.6691 (m) cc_final: 0.6446 (p) REVERT: M 199 LEU cc_start: 0.8239 (mm) cc_final: 0.7788 (tt) REVERT: M 200 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7394 (mt) REVERT: M 270 GLU cc_start: 0.7580 (tp30) cc_final: 0.6005 (tp30) outliers start: 158 outliers final: 61 residues processed: 584 average time/residue: 0.1645 time to fit residues: 155.4875 Evaluate side-chains 433 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 356 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 201 LEU 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 43 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 968 GLU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 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 114 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 177 ASP 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 338 PHE Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 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 D residue 1287 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1350 ASN Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 278 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 237 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 367 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 320 optimal weight: 8.9990 chunk 348 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C1108 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 504 GLN ** D 805 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 = 0.3915 r_free = 0.3915 target = 0.091216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.067907 restraints weight = 116510.490| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 4.47 r_work: 0.3198 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 1.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29305 Z= 0.186 Angle : 0.727 14.067 40250 Z= 0.369 Chirality : 0.045 0.277 4788 Planarity : 0.005 0.077 4929 Dihedral : 16.352 169.420 5044 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 3.91 % Allowed : 32.82 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.14), residues: 3612 helix: 0.47 (0.14), residues: 1359 sheet: 0.25 (0.27), residues: 368 loop : -1.51 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 310 TYR 0.020 0.002 TYR D1232 PHE 0.025 0.002 PHE C 505 TRP 0.013 0.002 TRP D 868 HIS 0.009 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00422 (29301) covalent geometry : angle 0.72737 (40250) hydrogen bonds : bond 0.03681 ( 1237) hydrogen bonds : angle 4.39072 ( 3427) metal coordination : bond 0.00324 ( 4) *********************** 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 471 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 369 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8584 (pt0) cc_final: 0.8220 (pt0) REVERT: A 257 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7849 (m) REVERT: B 37 HIS cc_start: 0.9216 (OUTLIER) cc_final: 0.8139 (t-90) REVERT: B 77 ASP cc_start: 0.8555 (t0) cc_final: 0.8316 (t0) REVERT: B 93 GLN cc_start: 0.8537 (mm110) cc_final: 0.8172 (mm-40) REVERT: C 47 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.5726 (p90) REVERT: C 57 PHE cc_start: 0.6771 (m-80) cc_final: 0.6470 (m-80) REVERT: C 116 ASP cc_start: 0.8427 (t0) cc_final: 0.7820 (m-30) REVERT: C 405 PHE cc_start: 0.8057 (t80) cc_final: 0.7802 (t80) REVERT: C 826 ASP cc_start: 0.8168 (m-30) cc_final: 0.7963 (t0) REVERT: C 862 LEU cc_start: 0.8418 (mp) cc_final: 0.8112 (tt) REVERT: C 900 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6149 (mttt) REVERT: C 1066 MET cc_start: 0.9174 (ttm) cc_final: 0.8965 (ttm) REVERT: C 1108 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8840 (p0) REVERT: C 1119 MET cc_start: 0.9162 (tpp) cc_final: 0.8903 (tpp) REVERT: C 1216 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8044 (mtm-85) REVERT: C 1278 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9060 (mt) REVERT: C 1289 GLU cc_start: 0.8159 (pp20) cc_final: 0.7830 (pt0) REVERT: C 1315 MET cc_start: 0.7318 (mmm) cc_final: 0.6832 (mmt) REVERT: D 77 ARG cc_start: 0.5228 (OUTLIER) cc_final: 0.5022 (tpm170) REVERT: D 119 SER cc_start: 0.6177 (OUTLIER) cc_final: 0.5732 (p) REVERT: D 314 ARG cc_start: 0.6742 (mmp80) cc_final: 0.6521 (mmp80) REVERT: D 324 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7078 (tp) REVERT: D 372 MET cc_start: 0.8601 (mtp) cc_final: 0.8386 (mtm) REVERT: D 441 LEU cc_start: 0.9074 (mt) cc_final: 0.8845 (mp) REVERT: D 466 MET cc_start: 0.8886 (mtp) cc_final: 0.8631 (mtt) REVERT: D 483 LEU cc_start: 0.9320 (mt) cc_final: 0.9074 (mp) REVERT: D 680 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8591 (t0) REVERT: D 725 MET cc_start: 0.8933 (mtt) cc_final: 0.8728 (mtt) REVERT: D 772 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: D 802 ASP cc_start: 0.8313 (m-30) cc_final: 0.8096 (t0) REVERT: D 861 ASN cc_start: 0.8193 (m-40) cc_final: 0.7855 (m-40) REVERT: D 1040 MET cc_start: 0.3242 (tpt) cc_final: 0.2700 (tpt) REVERT: D 1330 ARG cc_start: 0.5261 (mmt90) cc_final: 0.4972 (mmm160) REVERT: E 15 ASN cc_start: 0.7374 (t0) cc_final: 0.7162 (t0) REVERT: M 172 LEU cc_start: 0.8558 (tt) cc_final: 0.8125 (pp) REVERT: M 199 LEU cc_start: 0.8424 (mm) cc_final: 0.7997 (tt) REVERT: M 259 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7616 (ptp-110) REVERT: M 262 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: M 270 GLU cc_start: 0.7643 (tp30) cc_final: 0.6236 (tp30) outliers start: 102 outliers final: 45 residues processed: 449 average time/residue: 0.1833 time to fit residues: 132.9646 Evaluate side-chains 371 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 313 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 37 HIS Chi-restraints excluded: chain B residue 61 ILE 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 177 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 677 ASN 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 927 THR Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain D residue 21 LYS 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 114 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1350 ASN Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 206 PHE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 247 optimal weight: 7.9990 chunk 324 optimal weight: 9.9990 chunk 50 optimal weight: 0.0870 chunk 120 optimal weight: 7.9990 chunk 296 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 285 optimal weight: 10.0000 chunk 95 optimal weight: 40.0000 chunk 221 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 overall best weight: 3.5764 ------------------------------------------------------------------------------- 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** C 150 HIS C 519 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS D 186 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS D1249 ASN M 121 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.088737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.064733 restraints weight = 113720.819| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 4.32 r_work: 0.3119 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 1.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29305 Z= 0.195 Angle : 0.755 15.088 40250 Z= 0.385 Chirality : 0.046 0.293 4788 Planarity : 0.006 0.137 4929 Dihedral : 16.353 170.097 5044 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.41 % Allowed : 31.75 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.14), residues: 3612 helix: 0.52 (0.14), residues: 1344 sheet: 0.06 (0.26), residues: 373 loop : -1.46 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 293 TYR 0.024 0.002 TYR A 68 PHE 0.023 0.002 PHE C 35 TRP 0.022 0.002 TRP D 115 HIS 0.019 0.002 HIS D1218 Details of bonding type rmsd covalent geometry : bond 0.00445 (29301) covalent geometry : angle 0.75454 (40250) hydrogen bonds : bond 0.03874 ( 1237) hydrogen bonds : angle 4.45601 ( 3427) metal coordination : bond 0.00478 ( 4) *********************** 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 451 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 336 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8707 (pp20) cc_final: 0.8410 (pp20) REVERT: B 86 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8261 (tttt) REVERT: B 93 GLN cc_start: 0.8620 (mm110) cc_final: 0.8132 (mm-40) REVERT: C 47 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6837 (p90) REVERT: C 57 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: C 183 TRP cc_start: 0.8002 (OUTLIER) cc_final: 0.7073 (m-90) REVERT: C 541 GLU cc_start: 0.7510 (tp30) cc_final: 0.6951 (tm-30) REVERT: C 788 SER cc_start: 0.9307 (OUTLIER) cc_final: 0.8849 (p) REVERT: C 862 LEU cc_start: 0.8883 (mp) cc_final: 0.8631 (tt) REVERT: C 882 ILE cc_start: 0.8794 (mp) cc_final: 0.8368 (tp) REVERT: C 1157 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8743 (pt0) REVERT: C 1216 ARG cc_start: 0.8714 (mtm180) cc_final: 0.8410 (mtm-85) REVERT: D 301 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: D 330 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7504 (ttp) REVERT: D 337 ARG cc_start: 0.7384 (mmp80) cc_final: 0.7111 (mmp80) REVERT: D 340 GLN cc_start: 0.8363 (pm20) cc_final: 0.8102 (pm20) REVERT: D 591 ILE cc_start: 0.9518 (tp) cc_final: 0.9286 (tp) REVERT: D 725 MET cc_start: 0.9042 (mtt) cc_final: 0.8774 (mtt) REVERT: D 772 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: D 788 LEU cc_start: 0.9316 (pp) cc_final: 0.9009 (mt) REVERT: D 822 MET cc_start: 0.8613 (tpp) cc_final: 0.8397 (tpt) REVERT: D 1040 MET cc_start: 0.3441 (tpt) cc_final: 0.2796 (tpt) REVERT: D 1244 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8310 (tm-30) REVERT: D 1249 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8801 (t0) REVERT: E 11 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8645 (mm-30) REVERT: M 155 THR cc_start: 0.6807 (OUTLIER) cc_final: 0.6443 (t) REVERT: M 172 LEU cc_start: 0.8740 (tt) cc_final: 0.8277 (pp) REVERT: M 199 LEU cc_start: 0.8643 (mm) cc_final: 0.8091 (tt) REVERT: M 262 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8294 (pp30) REVERT: M 270 GLU cc_start: 0.7877 (tp30) cc_final: 0.6961 (tp30) REVERT: M 455 ARG cc_start: 0.6472 (tpt90) cc_final: 0.4288 (tmm160) outliers start: 115 outliers final: 56 residues processed: 419 average time/residue: 0.1649 time to fit residues: 112.6852 Evaluate side-chains 348 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 280 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 75 GLN 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 A residue 260 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 57 PHE 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 408 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 1162 ILE Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1350 ASN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 264 ILE 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 346 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 87 optimal weight: 50.0000 chunk 265 optimal weight: 7.9990 chunk 279 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 309 optimal weight: 30.0000 chunk 325 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 95 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** 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 504 GLN D 897 HIS ** D1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS D1249 ASN E 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.084010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.059498 restraints weight = 111386.502| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.14 r_work: 0.2975 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 1.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 29305 Z= 0.276 Angle : 0.819 13.050 40250 Z= 0.423 Chirality : 0.048 0.488 4788 Planarity : 0.006 0.093 4929 Dihedral : 16.428 167.632 5044 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 3.95 % Allowed : 33.05 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.14), residues: 3612 helix: 0.34 (0.14), residues: 1343 sheet: -0.06 (0.26), residues: 384 loop : -1.49 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 181 TYR 0.029 0.002 TYR D 555 PHE 0.032 0.003 PHE D 116 TRP 0.026 0.003 TRP D 236 HIS 0.009 0.002 HIS D1218 Details of bonding type rmsd covalent geometry : bond 0.00622 (29301) covalent geometry : angle 0.81917 (40250) hydrogen bonds : bond 0.04402 ( 1237) hydrogen bonds : angle 4.69848 ( 3427) metal coordination : bond 0.00663 ( 4) *********************** 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 388 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 285 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8948 (t0) cc_final: 0.8614 (t0) REVERT: A 79 LEU cc_start: 0.9713 (tp) cc_final: 0.9493 (tp) REVERT: A 102 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8572 (tp) REVERT: A 181 GLU cc_start: 0.8616 (pp20) cc_final: 0.8228 (pp20) REVERT: B 37 HIS cc_start: 0.9245 (OUTLIER) cc_final: 0.8220 (t-90) REVERT: C 47 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7581 (p90) REVERT: C 57 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: C 370 MET cc_start: 0.7738 (mmm) cc_final: 0.7472 (tpp) REVERT: C 408 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8336 (m) REVERT: C 494 ASN cc_start: 0.8912 (t0) cc_final: 0.8567 (t0) REVERT: C 503 LYS cc_start: 0.8993 (tptm) cc_final: 0.8571 (mptp) REVERT: C 541 GLU cc_start: 0.7984 (tp30) cc_final: 0.7610 (tm-30) REVERT: C 614 TYR cc_start: 0.9226 (m-80) cc_final: 0.8897 (m-80) REVERT: C 788 SER cc_start: 0.9401 (OUTLIER) cc_final: 0.9088 (p) REVERT: C 1107 MET cc_start: 0.8797 (tpp) cc_final: 0.8528 (mtt) REVERT: C 1325 VAL cc_start: 0.9520 (t) cc_final: 0.9261 (t) REVERT: D 39 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8350 (ptpp) REVERT: D 102 MET cc_start: 0.9130 (mmt) cc_final: 0.8835 (mmp) REVERT: D 330 MET cc_start: 0.8256 (tpt) cc_final: 0.7875 (ttp) REVERT: D 337 ARG cc_start: 0.7836 (mmp80) cc_final: 0.7330 (mmp80) REVERT: D 534 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8776 (tm-30) REVERT: D 591 ILE cc_start: 0.9517 (tp) cc_final: 0.9236 (tp) REVERT: D 725 MET cc_start: 0.9239 (mtt) cc_final: 0.8960 (mtt) REVERT: D 739 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8766 (pt0) REVERT: D 835 LEU cc_start: 0.8747 (pt) cc_final: 0.8379 (pp) REVERT: D 1040 MET cc_start: 0.4501 (tpt) cc_final: 0.4106 (tpt) REVERT: D 1155 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8570 (tp) REVERT: D 1249 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.8659 (t0) REVERT: M 172 LEU cc_start: 0.9032 (tt) cc_final: 0.8627 (mm) REVERT: M 270 GLU cc_start: 0.8112 (tp30) cc_final: 0.7081 (tp30) outliers start: 103 outliers final: 51 residues processed: 364 average time/residue: 0.1451 time to fit residues: 86.5590 Evaluate side-chains 296 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 75 GLN 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 37 HIS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain D residue 1350 ASN Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 91 optimal weight: 20.0000 chunk 363 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 197 optimal weight: 0.4980 chunk 354 optimal weight: 0.5980 chunk 264 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 326 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 504 GLN D 861 ASN D 897 HIS ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.085963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.061623 restraints weight = 112197.329| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.26 r_work: 0.3040 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 1.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29305 Z= 0.138 Angle : 0.700 11.718 40250 Z= 0.352 Chirality : 0.044 0.226 4788 Planarity : 0.005 0.078 4929 Dihedral : 16.296 171.105 5044 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 2.22 % Allowed : 34.36 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3612 helix: 0.67 (0.14), residues: 1323 sheet: 0.01 (0.27), residues: 382 loop : -1.34 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1149 TYR 0.019 0.001 TYR A 177 PHE 0.016 0.002 PHE D 380 TRP 0.030 0.002 TRP D 236 HIS 0.008 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00315 (29301) covalent geometry : angle 0.70014 (40250) hydrogen bonds : bond 0.03387 ( 1237) hydrogen bonds : angle 4.34370 ( 3427) metal coordination : bond 0.00305 ( 4) *********************** 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 340 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 15 ASP cc_start: 0.9009 (t0) cc_final: 0.8701 (t0) REVERT: A 79 LEU cc_start: 0.9705 (tp) cc_final: 0.9503 (tp) REVERT: A 102 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8486 (tp) REVERT: A 181 GLU cc_start: 0.8576 (pp20) cc_final: 0.8230 (pp20) REVERT: C 47 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.7393 (p90) REVERT: C 83 GLN cc_start: 0.8713 (mp10) cc_final: 0.8502 (pm20) REVERT: C 100 LEU cc_start: 0.8185 (tt) cc_final: 0.7558 (mp) REVERT: C 370 MET cc_start: 0.7708 (mmm) cc_final: 0.7484 (tpp) REVERT: C 494 ASN cc_start: 0.8886 (t0) cc_final: 0.8549 (t0) REVERT: C 503 LYS cc_start: 0.8953 (tptm) cc_final: 0.8493 (mttp) REVERT: C 541 GLU cc_start: 0.7830 (tp30) cc_final: 0.7447 (tm-30) REVERT: C 614 TYR cc_start: 0.9132 (m-80) cc_final: 0.8823 (m-80) REVERT: C 1319 MET cc_start: 0.9114 (tpp) cc_final: 0.8905 (tpp) REVERT: D 39 LYS cc_start: 0.8495 (mtmt) cc_final: 0.8269 (ptpp) REVERT: D 52 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: D 102 MET cc_start: 0.9097 (mmt) cc_final: 0.8836 (mmt) REVERT: D 192 MET cc_start: 0.3593 (ppp) cc_final: 0.3313 (ppp) REVERT: D 240 THR cc_start: 0.8482 (p) cc_final: 0.8221 (p) REVERT: D 304 ASP cc_start: 0.7811 (m-30) cc_final: 0.7567 (p0) REVERT: D 330 MET cc_start: 0.7871 (tpt) cc_final: 0.7441 (tmm) REVERT: D 337 ARG cc_start: 0.7883 (mmp80) cc_final: 0.7405 (mmp80) REVERT: D 340 GLN cc_start: 0.8896 (pm20) cc_final: 0.8639 (pm20) REVERT: D 534 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8740 (tm-30) REVERT: D 591 ILE cc_start: 0.9484 (tp) cc_final: 0.9222 (tp) REVERT: D 725 MET cc_start: 0.9151 (mtt) cc_final: 0.8888 (mtt) REVERT: D 739 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: D 835 LEU cc_start: 0.8771 (pt) cc_final: 0.8263 (tt) REVERT: D 1040 MET cc_start: 0.4282 (tpt) cc_final: 0.3887 (tpt) REVERT: D 1282 TYR cc_start: 0.8681 (m-10) cc_final: 0.8410 (m-10) REVERT: M 172 LEU cc_start: 0.9080 (tt) cc_final: 0.8726 (mm) REVERT: M 270 GLU cc_start: 0.8093 (tp30) cc_final: 0.6670 (tt0) outliers start: 58 outliers final: 34 residues processed: 329 average time/residue: 0.1716 time to fit residues: 91.6895 Evaluate side-chains 279 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 897 HIS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1350 ASN Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 226 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 44 optimal weight: 0.0070 chunk 5 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 overall best weight: 3.5802 ------------------------------------------------------------------------------- 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** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 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 = 0.3761 r_free = 0.3761 target = 0.083563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.059436 restraints weight = 111428.792| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.21 r_work: 0.2979 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 1.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29305 Z= 0.187 Angle : 0.725 11.550 40250 Z= 0.367 Chirality : 0.045 0.341 4788 Planarity : 0.005 0.075 4929 Dihedral : 16.277 172.334 5044 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 2.42 % Allowed : 33.82 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3612 helix: 0.69 (0.14), residues: 1339 sheet: 0.02 (0.27), residues: 366 loop : -1.36 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1149 TYR 0.046 0.002 TYR C 26 PHE 0.022 0.002 PHE D 380 TRP 0.033 0.002 TRP D 236 HIS 0.024 0.001 HIS D 897 Details of bonding type rmsd covalent geometry : bond 0.00434 (29301) covalent geometry : angle 0.72459 (40250) hydrogen bonds : bond 0.03531 ( 1237) hydrogen bonds : angle 4.36458 ( 3427) metal coordination : bond 0.01670 ( 4) *********************** 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 311 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 248 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8998 (t0) cc_final: 0.8673 (t0) REVERT: A 181 GLU cc_start: 0.8622 (pp20) cc_final: 0.8273 (pp20) REVERT: B 37 HIS cc_start: 0.9153 (OUTLIER) cc_final: 0.7973 (t-90) REVERT: C 83 GLN cc_start: 0.8810 (mp10) cc_final: 0.8586 (pm20) REVERT: C 100 LEU cc_start: 0.7763 (tt) cc_final: 0.7163 (mp) REVERT: C 370 MET cc_start: 0.7727 (mmm) cc_final: 0.7452 (tpp) REVERT: C 503 LYS cc_start: 0.9131 (tptm) cc_final: 0.8620 (mptp) REVERT: C 541 GLU cc_start: 0.7999 (tp30) cc_final: 0.7657 (tm-30) REVERT: C 614 TYR cc_start: 0.9204 (m-80) cc_final: 0.8854 (m-80) REVERT: C 936 ARG cc_start: 0.7153 (ttt180) cc_final: 0.6479 (ttp80) REVERT: D 39 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8480 (ptpp) REVERT: D 52 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: D 192 MET cc_start: 0.4275 (ppp) cc_final: 0.4070 (ppp) REVERT: D 330 MET cc_start: 0.8116 (tpt) cc_final: 0.7703 (tmm) REVERT: D 337 ARG cc_start: 0.7886 (mmp80) cc_final: 0.7253 (mmp80) REVERT: D 534 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8793 (tm-30) REVERT: D 591 ILE cc_start: 0.9484 (tp) cc_final: 0.9269 (tp) REVERT: D 725 MET cc_start: 0.9216 (mtt) cc_final: 0.8922 (mtt) REVERT: D 772 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: D 835 LEU cc_start: 0.8824 (pt) cc_final: 0.8391 (tt) REVERT: D 1040 MET cc_start: 0.4160 (tpt) cc_final: 0.3813 (tpt) REVERT: D 1334 GLU cc_start: 0.9281 (tp30) cc_final: 0.8816 (tp30) REVERT: M 172 LEU cc_start: 0.9148 (tt) cc_final: 0.8794 (mm) REVERT: M 173 GLU cc_start: 0.8675 (tp30) cc_final: 0.8470 (tm-30) REVERT: M 270 GLU cc_start: 0.8077 (tp30) cc_final: 0.6624 (tt0) outliers start: 63 outliers final: 43 residues processed: 300 average time/residue: 0.1634 time to fit residues: 79.4799 Evaluate side-chains 275 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS 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 B residue 207 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1350 ASN Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 247 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 363 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 307 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 317 optimal weight: 5.9990 chunk 292 optimal weight: 40.0000 chunk 325 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 301 optimal weight: 0.4980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.082597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.058611 restraints weight = 110688.426| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.16 r_work: 0.2959 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 1.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29305 Z= 0.186 Angle : 0.727 11.264 40250 Z= 0.369 Chirality : 0.045 0.272 4788 Planarity : 0.005 0.081 4929 Dihedral : 16.279 172.371 5044 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 1.88 % Allowed : 34.39 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.14), residues: 3612 helix: 0.67 (0.14), residues: 1328 sheet: 0.05 (0.27), residues: 368 loop : -1.36 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 148 TYR 0.029 0.002 TYR C 26 PHE 0.018 0.002 PHE D 437 TRP 0.030 0.002 TRP D 236 HIS 0.010 0.001 HIS M 377 Details of bonding type rmsd covalent geometry : bond 0.00428 (29301) covalent geometry : angle 0.72714 (40250) hydrogen bonds : bond 0.03418 ( 1237) hydrogen bonds : angle 4.40742 ( 3427) metal coordination : bond 0.00164 ( 4) ********************** 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 302 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8975 (t0) cc_final: 0.8643 (t0) REVERT: A 181 GLU cc_start: 0.8604 (pp20) cc_final: 0.8213 (pp20) REVERT: B 37 HIS cc_start: 0.9122 (OUTLIER) cc_final: 0.7930 (t-90) REVERT: C 83 GLN cc_start: 0.8840 (mp10) cc_final: 0.8610 (pm20) REVERT: C 100 LEU cc_start: 0.8040 (tt) cc_final: 0.7444 (mp) REVERT: C 214 ASN cc_start: 0.9001 (m-40) cc_final: 0.8759 (p0) REVERT: C 370 MET cc_start: 0.7842 (mmm) cc_final: 0.7568 (tpp) REVERT: C 541 GLU cc_start: 0.7927 (tp30) cc_final: 0.7649 (tm-30) REVERT: C 614 TYR cc_start: 0.9229 (m-80) cc_final: 0.8942 (m-80) REVERT: C 696 ASP cc_start: 0.8907 (t0) cc_final: 0.8540 (t0) REVERT: C 741 MET cc_start: 0.8003 (mmm) cc_final: 0.7797 (mmm) REVERT: D 52 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: D 165 TYR cc_start: 0.9157 (t80) cc_final: 0.8893 (t80) REVERT: D 337 ARG cc_start: 0.7890 (mmp80) cc_final: 0.7197 (mmp80) REVERT: D 534 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8831 (tm-30) REVERT: D 591 ILE cc_start: 0.9469 (tp) cc_final: 0.9207 (tp) REVERT: D 725 MET cc_start: 0.9178 (mtt) cc_final: 0.8912 (mtt) REVERT: D 822 MET cc_start: 0.9018 (tpp) cc_final: 0.8604 (tpp) REVERT: D 835 LEU cc_start: 0.8779 (pt) cc_final: 0.8429 (tt) REVERT: D 1040 MET cc_start: 0.4452 (tpt) cc_final: 0.3776 (tpt) REVERT: D 1282 TYR cc_start: 0.8890 (m-10) cc_final: 0.8666 (m-10) REVERT: D 1330 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7951 (mmm160) REVERT: D 1334 GLU cc_start: 0.9339 (tp30) cc_final: 0.8955 (tp30) REVERT: E 7 GLN cc_start: 0.8350 (tp40) cc_final: 0.8039 (tp-100) REVERT: E 11 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8655 (mm-30) REVERT: M 172 LEU cc_start: 0.9279 (tt) cc_final: 0.8960 (mm) REVERT: M 193 LYS cc_start: 0.8306 (mmmm) cc_final: 0.8049 (mmmm) REVERT: M 270 GLU cc_start: 0.8273 (tp30) cc_final: 0.6837 (tt0) REVERT: M 355 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.5980 (m-80) outliers start: 49 outliers final: 40 residues processed: 294 average time/residue: 0.1728 time to fit residues: 82.8454 Evaluate side-chains 268 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS 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 B residue 207 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain D residue 1350 ASN Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 355 PHE Chi-restraints excluded: chain M residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 45 optimal weight: 3.9990 chunk 313 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.082956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.058978 restraints weight = 112746.456| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.09 r_work: 0.2999 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 1.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29305 Z= 0.152 Angle : 0.708 11.683 40250 Z= 0.357 Chirality : 0.044 0.291 4788 Planarity : 0.005 0.070 4929 Dihedral : 16.236 173.444 5044 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.70 % Favored : 94.24 % Rotamer: Outliers : 1.80 % Allowed : 34.78 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.14), residues: 3612 helix: 0.73 (0.14), residues: 1339 sheet: 0.10 (0.28), residues: 352 loop : -1.36 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 196 TYR 0.036 0.002 TYR C 26 PHE 0.018 0.002 PHE D 141 TRP 0.025 0.002 TRP D 236 HIS 0.007 0.001 HIS M 377 Details of bonding type rmsd covalent geometry : bond 0.00354 (29301) covalent geometry : angle 0.70840 (40250) hydrogen bonds : bond 0.03297 ( 1237) hydrogen bonds : angle 4.32224 ( 3427) metal coordination : bond 0.00408 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8045.44 seconds wall clock time: 138 minutes 8.43 seconds (8288.43 seconds total)