Starting phenix.real_space_refine on Sun Jul 5 13:49:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8reb_19081/07_2026/8reb_19081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8reb_19081/07_2026/8reb_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 { model { file = "/net/cci-nas-00/data/ceres_data/8reb_19081/07_2026/8reb_19081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8reb_19081/07_2026/8reb_19081.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8reb_19081/07_2026/8reb_19081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8reb_19081/07_2026/8reb_19081.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8reb_19081/07_2026/8reb_19081.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8reb_19081/07_2026/8reb_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.55, per 1000 atoms: 0.19 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: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6748 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 45 sheets defined 39.3% alpha, 14.2% beta 40 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 3.43 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: 8.12 Time building geometry restraints manager: 3.41 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=" C3' DA T 16 " pdb=" C2' DA T 16 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C1' DT N 6 " pdb=" N1 DT N 6 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" C3' DA T 17 " pdb=" C2' DA T 17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA T 18 " pdb=" C2' DA T 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.82e+00 ... (remaining 29296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 40037 3.51 - 7.03: 195 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: 3702 0.050 - 0.100: 861 0.100 - 0.150: 208 0.150 - 0.200: 16 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: 0.510 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: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 33.790 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3435 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= 0.272 Angle : 0.734 17.573 40250 Z= 0.444 Chirality : 0.045 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 are 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/Z covalent geometry : bond 0.00515 / 0.27 (29301) covalent geometry : angle 0.73401 / 0.44 (40250) hydrogen bonds : bond 0.16025 / 15.76 ( 1237) hydrogen bonds : angle 5.67167 / 7.20 ( 3427) metal coordination : bond 0.00284 / 0.14 ( 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 : 0.935 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: 0.2086 time to fit residues: 245.5611 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 : 1.262 ------------------------------------------------------------------------------- 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... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 283 GLN B 93 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 ASN C 808 ASN C1108 ASN C1111 GLN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1175 ASN C1244 HIS ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 186 GLN D 309 ASN D 450 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN D 867 GLN D1249 ASN D1350 ASN M 121 GLN M 205 GLN M 387 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.091996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.070182 restraints weight = 111507.039| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 4.32 r_work: 0.3250 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 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 = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29305 Z= 0.216 Angle : 0.818 11.727 40250 Z= 0.425 Chirality : 0.048 0.253 4788 Planarity : 0.007 0.119 4929 Dihedral : 16.544 166.795 5044 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 6.25 % Allowed : 27.99 % Favored : 65.76 % 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 are not related in a simple way. whole: -0.84 (0.14), residues: 3612 helix: 0.48 (0.14), residues: 1323 sheet: 0.40 (0.26), residues: 392 loop : -1.57 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D1345 TYR 0.036 0.003 TYR D 349 PHE 0.042 0.003 PHE C 195 TRP 0.031 0.003 TRP D 115 HIS 0.026 0.003 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 (29301) covalent geometry : angle 0.81751 / 0.42 (40250) hydrogen bonds : bond 0.04824 / 4.80 ( 1237) hydrogen bonds : angle 4.79542 / 6.00 ( 3427) metal coordination : bond 0.00316 / 0.25 ( 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 687 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 524 time to evaluate : 1.028 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.6810 (m-80) cc_final: 0.5971 (m-80) REVERT: A 203 ILE cc_start: 0.8346 (mt) cc_final: 0.8090 (mp) REVERT: A 205 MET cc_start: 0.8258 (mpp) cc_final: 0.7871 (mpp) REVERT: A 257 VAL cc_start: 0.7164 (OUTLIER) cc_final: 0.6892 (m) REVERT: B 77 ASP cc_start: 0.7415 (t0) cc_final: 0.7176 (t0) REVERT: C 47 TYR cc_start: 0.4038 (OUTLIER) cc_final: 0.3229 (p90) REVERT: C 116 ASP cc_start: 0.7989 (t0) cc_final: 0.7445 (m-30) REVERT: C 124 MET cc_start: 0.5014 (pmm) cc_final: 0.3541 (ttp) REVERT: C 183 TRP cc_start: 0.3475 (OUTLIER) cc_final: 0.3247 (m-10) REVERT: C 189 ASP cc_start: 0.5807 (t70) cc_final: 0.5521 (t0) REVERT: C 487 LEU cc_start: 0.8509 (tp) cc_final: 0.8259 (tp) REVERT: C 614 TYR cc_start: 0.6964 (m-80) cc_final: 0.6373 (m-80) REVERT: C 726 TYR cc_start: 0.5947 (t80) cc_final: 0.5736 (t80) REVERT: C 734 ILE cc_start: 0.3769 (OUTLIER) cc_final: 0.3560 (tt) REVERT: C 741 MET cc_start: 0.8252 (ppp) cc_final: 0.7632 (mmt) REVERT: C 840 SER cc_start: 0.7090 (OUTLIER) cc_final: 0.6824 (m) REVERT: C 900 LYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5671 (mttt) REVERT: C 1049 ILE cc_start: 0.5322 (mm) cc_final: 0.5031 (mm) REVERT: C 1061 GLN cc_start: 0.6381 (pt0) cc_final: 0.6180 (pt0) REVERT: C 1101 LEU cc_start: 0.5193 (mt) cc_final: 0.4678 (mt) REVERT: C 1165 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7779 (t) REVERT: C 1175 ASN cc_start: 0.7960 (m110) cc_final: 0.7658 (m-40) REVERT: C 1319 MET cc_start: 0.3245 (OUTLIER) cc_final: 0.2659 (tpp) REVERT: D 116 PHE cc_start: 0.3120 (m-10) cc_final: 0.2847 (m-10) REVERT: D 192 MET cc_start: 0.0560 (ptm) cc_final: 0.0118 (ppp) REVERT: D 402 GLU cc_start: 0.7061 (tp30) cc_final: 0.6542 (tp30) REVERT: D 698 MET cc_start: 0.8483 (tpp) cc_final: 0.8169 (mmm) REVERT: D 725 MET cc_start: 0.7392 (mtt) cc_final: 0.7135 (mtt) REVERT: D 736 GLN cc_start: 0.8005 (mt0) cc_final: 0.7799 (pt0) REVERT: D 739 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7709 (mm-40) REVERT: D 1040 MET cc_start: 0.3279 (tpt) cc_final: 0.2836 (tpt) REVERT: D 1242 ARG cc_start: 0.7490 (tpt90) cc_final: 0.7217 (ttp-110) REVERT: D 1262 ARG cc_start: 0.4582 (mmm160) cc_final: 0.3849 (mmm160) REVERT: D 1325 PHE cc_start: 0.4621 (OUTLIER) cc_final: 0.3720 (t80) outliers start: 163 outliers final: 57 residues processed: 654 average time/residue: 0.1931 time to fit residues: 200.2193 Evaluate side-chains 496 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 430 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 174 ASP 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 48 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1302 THR Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 921 GLN Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 363 optimal weight: 0.7980 chunk 367 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 358 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 288 optimal weight: 0.0270 chunk 102 optimal weight: 8.9990 chunk 339 optimal weight: 0.0040 overall best weight: 0.5650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN B 37 HIS C 463 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 628 HIS C 808 ASN C 932 GLN C1108 ASN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS C1257 GLN C1313 HIS C1336 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D1218 HIS D1249 ASN D1289 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.093621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.072062 restraints weight = 110706.764| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 4.31 r_work: 0.3300 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 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 = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29305 Z= 0.152 Angle : 0.738 14.382 40250 Z= 0.376 Chirality : 0.045 0.375 4788 Planarity : 0.005 0.090 4929 Dihedral : 16.483 167.225 5044 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.19 % Rotamer: Outliers : 5.02 % Allowed : 29.60 % Favored : 65.38 % 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 are not related in a simple way. whole: -0.70 (0.14), residues: 3612 helix: 0.66 (0.14), residues: 1337 sheet: 0.27 (0.26), residues: 385 loop : -1.49 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 196 TYR 0.025 0.002 TYR D 537 PHE 0.021 0.002 PHE C 35 TRP 0.024 0.002 TRP D 115 HIS 0.010 0.002 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (29301) covalent geometry : angle 0.73787 / 0.38 (40250) hydrogen bonds : bond 0.04237 / 4.29 ( 1237) hydrogen bonds : angle 4.52804 / 5.72 ( 3427) metal coordination : bond 0.00040 / 0.02 ( 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 581 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 450 time to evaluate : 1.029 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: A 147 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6784 (pt0) REVERT: A 257 VAL cc_start: 0.7269 (OUTLIER) cc_final: 0.6910 (m) REVERT: A 321 TRP cc_start: 0.4983 (m100) cc_final: 0.4678 (m100) REVERT: B 77 ASP cc_start: 0.7520 (t0) cc_final: 0.7293 (t0) REVERT: C 47 TYR cc_start: 0.4067 (OUTLIER) cc_final: 0.3279 (p90) REVERT: C 68 LEU cc_start: 0.8127 (tp) cc_final: 0.7709 (tt) REVERT: C 121 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6752 (mt-10) REVERT: C 124 MET cc_start: 0.5624 (pmm) cc_final: 0.4620 (ppp) REVERT: C 183 TRP cc_start: 0.3519 (OUTLIER) cc_final: 0.3045 (m-10) REVERT: C 405 PHE cc_start: 0.6073 (t80) cc_final: 0.5805 (t80) REVERT: C 409 LEU cc_start: 0.6358 (tp) cc_final: 0.5968 (tp) REVERT: C 487 LEU cc_start: 0.8184 (tp) cc_final: 0.7971 (tp) REVERT: C 498 ILE cc_start: 0.7043 (mm) cc_final: 0.6276 (mm) REVERT: C 609 ILE cc_start: 0.7580 (pt) cc_final: 0.7268 (pt) REVERT: C 736 VAL cc_start: 0.4556 (t) cc_final: 0.3202 (m) REVERT: C 741 MET cc_start: 0.7954 (ppp) cc_final: 0.7540 (mmt) REVERT: C 900 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5326 (mttt) REVERT: C 1107 MET cc_start: 0.6539 (mmm) cc_final: 0.6121 (tpp) REVERT: C 1243 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.5657 (mtm) REVERT: C 1319 MET cc_start: 0.3483 (OUTLIER) cc_final: 0.2713 (tpp) REVERT: D 525 MET cc_start: 0.6573 (mmm) cc_final: 0.5430 (mtt) REVERT: D 708 ASN cc_start: 0.6963 (OUTLIER) cc_final: 0.6235 (p0) REVERT: D 725 MET cc_start: 0.7357 (mtt) cc_final: 0.7125 (mtt) REVERT: D 736 GLN cc_start: 0.7902 (mt0) cc_final: 0.7244 (mp10) REVERT: D 1040 MET cc_start: 0.3212 (tpt) cc_final: 0.2817 (tpt) REVERT: D 1325 PHE cc_start: 0.4943 (OUTLIER) cc_final: 0.4059 (t80) REVERT: E 21 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.5729 (tt) REVERT: E 41 GLU cc_start: 0.7297 (tm-30) cc_final: 0.7079 (tm-30) outliers start: 131 outliers final: 59 residues processed: 545 average time/residue: 0.1852 time to fit residues: 162.8882 Evaluate side-chains 488 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 419 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 721 SER 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 1325 PHE Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 49 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 80 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 177 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 chunk 6 optimal weight: 40.0000 chunk 256 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 2 optimal weight: 50.0000 chunk 189 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS C 658 GLN C 686 GLN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 ASN C1108 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1175 ASN C1244 HIS C1313 HIS D 309 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 921 GLN D1249 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN M 265 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.092735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071152 restraints weight = 116000.963| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 4.33 r_work: 0.3287 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 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 = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.169 29305 Z= 0.277 Angle : 0.895 16.536 40250 Z= 0.467 Chirality : 0.052 0.544 4788 Planarity : 0.008 0.140 4929 Dihedral : 16.609 168.121 5044 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.84 % Favored : 93.08 % Rotamer: Outliers : 6.90 % Allowed : 26.80 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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 are not related in a simple way. whole: -1.21 (0.13), residues: 3612 helix: 0.05 (0.14), residues: 1358 sheet: 0.12 (0.26), residues: 379 loop : -1.68 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C1106 TYR 0.049 0.003 TYR D1365 PHE 0.038 0.004 PHE C 629 TRP 0.068 0.005 TRP D 580 HIS 0.018 0.003 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.28 (29301) covalent geometry : angle 0.89487 / 0.47 (40250) hydrogen bonds : bond 0.05117 / 5.11 ( 1237) hydrogen bonds : angle 4.93633 / 6.33 ( 3427) metal coordination : bond 0.00342 / 0.31 ( 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 667 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 487 time to evaluate : 1.218 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: B 47 LEU cc_start: 0.8811 (mt) cc_final: 0.8386 (mt) REVERT: B 77 ASP cc_start: 0.7987 (t0) cc_final: 0.7713 (t0) REVERT: B 93 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7276 (mm-40) REVERT: C 47 TYR cc_start: 0.5043 (OUTLIER) cc_final: 0.4057 (p90) REVERT: C 57 PHE cc_start: 0.6886 (m-80) cc_final: 0.6638 (m-80) REVERT: C 116 ASP cc_start: 0.8307 (t0) cc_final: 0.7752 (m-30) REVERT: C 409 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6002 (tt) REVERT: C 524 ILE cc_start: 0.6727 (pp) cc_final: 0.6382 (pp) REVERT: C 685 MET cc_start: 0.7001 (ptp) cc_final: 0.6799 (ptp) REVERT: C 900 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5690 (mttt) REVERT: C 1094 VAL cc_start: 0.7371 (OUTLIER) cc_final: 0.7159 (t) REVERT: C 1219 GLU cc_start: 0.7204 (tp30) cc_final: 0.6717 (tt0) REVERT: C 1319 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4353 (tpp) REVERT: D 62 PHE cc_start: 0.3883 (m-80) cc_final: 0.3555 (m-80) REVERT: D 113 HIS cc_start: 0.5466 (t-170) cc_final: 0.5177 (t-170) REVERT: D 525 MET cc_start: 0.7584 (mmm) cc_final: 0.6681 (mtt) REVERT: D 736 GLN cc_start: 0.8098 (mt0) cc_final: 0.7854 (mt0) REVERT: D 759 ILE cc_start: 0.7502 (mt) cc_final: 0.7067 (mt) REVERT: D 1040 MET cc_start: 0.3562 (tpt) cc_final: 0.2875 (tpt) REVERT: D 1287 ILE cc_start: 0.4870 (OUTLIER) cc_final: 0.4605 (mt) REVERT: D 1320 ILE cc_start: 0.7869 (mm) cc_final: 0.7586 (mm) REVERT: M 125 MET cc_start: 0.7102 (tpp) cc_final: 0.6179 (mmp) REVERT: M 265 GLN cc_start: 0.2507 (OUTLIER) cc_final: 0.1788 (mp10) REVERT: M 270 GLU cc_start: 0.7216 (tp30) cc_final: 0.5678 (tp30) outliers start: 180 outliers final: 72 residues processed: 620 average time/residue: 0.1703 time to fit residues: 170.0406 Evaluate side-chains 486 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 407 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 299 SER 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 51 MET Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 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 147 SER Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 97 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 309 ASN Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 237 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 367 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 320 optimal weight: 10.0000 chunk 348 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 139 ASN C 463 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN C1108 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1175 ASN C1312 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D 921 GLN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.091804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.069616 restraints weight = 117866.835| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 4.47 r_work: 0.3251 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 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 = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 29305 Z= 0.255 Angle : 0.824 14.810 40250 Z= 0.434 Chirality : 0.049 0.377 4788 Planarity : 0.006 0.080 4929 Dihedral : 16.618 164.294 5044 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 4.91 % Allowed : 30.33 % Favored : 64.76 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -1.09 (0.13), residues: 3612 helix: 0.26 (0.14), residues: 1340 sheet: -0.03 (0.27), residues: 363 loop : -1.62 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG D 101 TYR 0.055 0.002 TYR A 177 PHE 0.024 0.003 PHE D 227 TRP 0.041 0.003 TRP D 580 HIS 0.015 0.002 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.25 (29301) covalent geometry : angle 0.82442 / 0.43 (40250) hydrogen bonds : bond 0.04372 / 4.52 ( 1237) hydrogen bonds : angle 4.69777 / 5.99 ( 3427) metal coordination : bond 0.00473 / 0.24 ( 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 570 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 442 time to evaluate : 1.108 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: A 142 MET cc_start: 0.7508 (ppp) cc_final: 0.6694 (ppp) REVERT: B 93 GLN cc_start: 0.8128 (mm110) cc_final: 0.7920 (mm-40) REVERT: C 20 GLN cc_start: 0.7527 (tt0) cc_final: 0.7021 (pp30) REVERT: C 47 TYR cc_start: 0.5410 (OUTLIER) cc_final: 0.4574 (p90) REVERT: C 116 ASP cc_start: 0.8418 (t0) cc_final: 0.7764 (m-30) REVERT: C 409 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6964 (tt) REVERT: C 541 GLU cc_start: 0.6626 (tp30) cc_final: 0.6330 (tt0) REVERT: C 581 THR cc_start: 0.8305 (p) cc_final: 0.8035 (p) REVERT: C 614 TYR cc_start: 0.7420 (m-80) cc_final: 0.7089 (m-80) REVERT: C 705 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: C 900 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5594 (mttt) REVERT: C 1187 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7958 (t80) REVERT: C 1222 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: C 1276 TRP cc_start: 0.7010 (m-10) cc_final: 0.6450 (m-10) REVERT: C 1312 ASN cc_start: 0.7355 (t0) cc_final: 0.7113 (t0) REVERT: D 102 MET cc_start: 0.4021 (mtp) cc_final: 0.2205 (mmt) REVERT: D 113 HIS cc_start: 0.5883 (t-170) cc_final: 0.5456 (t-170) REVERT: D 116 PHE cc_start: 0.5233 (m-10) cc_final: 0.4962 (m-10) REVERT: D 252 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6671 (mp) REVERT: D 301 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6689 (pt0) REVERT: D 330 MET cc_start: 0.6863 (tpt) cc_final: 0.6603 (tpp) REVERT: D 334 LYS cc_start: 0.2498 (OUTLIER) cc_final: 0.2182 (mmtm) REVERT: D 428 THR cc_start: 0.8894 (m) cc_final: 0.8494 (p) REVERT: D 525 MET cc_start: 0.7968 (mmm) cc_final: 0.7520 (mtt) REVERT: D 680 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8609 (t0) REVERT: D 736 GLN cc_start: 0.8394 (mt0) cc_final: 0.8173 (mt0) REVERT: D 759 ILE cc_start: 0.8132 (mt) cc_final: 0.7797 (mt) REVERT: D 772 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6536 (m-80) REVERT: D 1040 MET cc_start: 0.3725 (tpt) cc_final: 0.3010 (tpt) REVERT: D 1287 ILE cc_start: 0.5320 (OUTLIER) cc_final: 0.5096 (mt) REVERT: M 125 MET cc_start: 0.7544 (tpp) cc_final: 0.6506 (mmp) REVERT: M 154 LEU cc_start: 0.5279 (tt) cc_final: 0.4931 (mt) REVERT: M 199 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7779 (tt) REVERT: M 265 GLN cc_start: 0.3639 (OUTLIER) cc_final: 0.3052 (mt0) REVERT: M 270 GLU cc_start: 0.7394 (tp30) cc_final: 0.6445 (tp30) outliers start: 128 outliers final: 61 residues processed: 530 average time/residue: 0.1742 time to fit residues: 151.3317 Evaluate side-chains 472 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 397 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 228 LEU 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 138 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 719 LYS Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1187 PHE Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1325 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 244 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 247 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 331 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 504 GLN D 861 ASN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.091800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.069311 restraints weight = 116900.302| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 4.43 r_work: 0.3244 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.8981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 29305 Z= 0.190 Angle : 0.760 20.791 40250 Z= 0.387 Chirality : 0.047 0.279 4788 Planarity : 0.005 0.082 4929 Dihedral : 16.552 164.436 5044 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.59 % Favored : 93.36 % Rotamer: Outliers : 4.37 % Allowed : 31.60 % Favored : 64.03 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -0.98 (0.14), residues: 3612 helix: 0.38 (0.14), residues: 1342 sheet: 0.00 (0.26), residues: 381 loop : -1.59 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 101 TYR 0.024 0.002 TYR A 152 PHE 0.027 0.002 PHE C 35 TRP 0.028 0.003 TRP D 115 HIS 0.012 0.002 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (29301) covalent geometry : angle 0.76039 / 0.39 (40250) hydrogen bonds : bond 0.04032 / 4.09 ( 1237) hydrogen bonds : angle 4.62220 / 5.87 ( 3427) metal coordination : bond 0.00278 / 0.13 ( 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 540 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 426 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.7899 (pt0) cc_final: 0.7677 (pt0) REVERT: B 93 GLN cc_start: 0.7873 (mm110) cc_final: 0.7577 (mm-40) REVERT: C 38 PHE cc_start: 0.7899 (t80) cc_final: 0.7646 (t80) REVERT: C 47 TYR cc_start: 0.5832 (OUTLIER) cc_final: 0.4794 (p90) REVERT: C 116 ASP cc_start: 0.8412 (t0) cc_final: 0.7560 (m-30) REVERT: C 409 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7074 (tt) REVERT: C 517 GLN cc_start: 0.8436 (mm-40) cc_final: 0.7848 (tp40) REVERT: C 541 GLU cc_start: 0.6856 (tp30) cc_final: 0.6396 (tp30) REVERT: C 581 THR cc_start: 0.8623 (p) cc_final: 0.8404 (p) REVERT: C 680 LEU cc_start: 0.9035 (tt) cc_final: 0.8826 (tt) REVERT: C 741 MET cc_start: 0.8188 (ppp) cc_final: 0.7962 (mmt) REVERT: C 1204 LEU cc_start: 0.9151 (mt) cc_final: 0.8946 (mt) REVERT: C 1216 ARG cc_start: 0.7816 (mtm180) cc_final: 0.7582 (mtm-85) REVERT: C 1312 ASN cc_start: 0.7970 (t0) cc_final: 0.7569 (t0) REVERT: C 1315 MET cc_start: 0.6985 (mmp) cc_final: 0.6533 (mmt) REVERT: D 102 MET cc_start: 0.4455 (mtp) cc_final: 0.3156 (mmt) REVERT: D 301 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6484 (pt0) REVERT: D 330 MET cc_start: 0.7008 (tpt) cc_final: 0.6719 (tpp) REVERT: D 525 MET cc_start: 0.8197 (mmm) cc_final: 0.7911 (mtt) REVERT: D 618 VAL cc_start: 0.9436 (t) cc_final: 0.9211 (p) REVERT: D 680 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8608 (t0) REVERT: D 736 GLN cc_start: 0.8362 (mt0) cc_final: 0.7812 (mt0) REVERT: D 759 ILE cc_start: 0.8577 (mt) cc_final: 0.8277 (mt) REVERT: D 772 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.6606 (m-80) REVERT: D 901 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6649 (ptt180) REVERT: D 1040 MET cc_start: 0.3856 (tpt) cc_final: 0.3155 (tpt) REVERT: D 1206 ARG cc_start: 0.7090 (ttp80) cc_final: 0.6827 (tmm160) REVERT: D 1330 ARG cc_start: 0.4700 (mmt180) cc_final: 0.4107 (mmm160) REVERT: M 125 MET cc_start: 0.7540 (tpp) cc_final: 0.6502 (mmp) REVERT: M 154 LEU cc_start: 0.5724 (tt) cc_final: 0.5453 (mt) REVERT: M 199 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8017 (tt) REVERT: M 270 GLU cc_start: 0.7435 (tp30) cc_final: 0.5886 (tp30) outliers start: 114 outliers final: 65 residues processed: 509 average time/residue: 0.1715 time to fit residues: 144.8511 Evaluate side-chains 450 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 378 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL 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 B residue 207 THR Chi-restraints excluded: chain B residue 228 LEU 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 335 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 719 LYS Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 845 LEU 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 1047 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1187 PHE Chi-restraints excluded: chain C residue 1275 VAL 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 252 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 0.4980 chunk 163 optimal weight: 10.0000 chunk 87 optimal weight: 50.0000 chunk 265 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 309 optimal weight: 40.0000 chunk 325 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 95 optimal weight: 50.0000 overall best weight: 4.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 504 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 265 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.090321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.067090 restraints weight = 116106.840| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 4.44 r_work: 0.3184 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 1.0352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 29305 Z= 0.248 Angle : 0.848 21.499 40250 Z= 0.439 Chirality : 0.048 0.270 4788 Planarity : 0.006 0.141 4929 Dihedral : 16.614 163.870 5044 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.78 % Favored : 93.19 % Rotamer: Outliers : 5.10 % Allowed : 31.44 % Favored : 63.46 % 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 are not related in a simple way. whole: -1.08 (0.13), residues: 3612 helix: 0.28 (0.14), residues: 1350 sheet: -0.21 (0.26), residues: 376 loop : -1.60 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG D1341 TYR 0.034 0.002 TYR M 461 PHE 0.020 0.002 PHE C1323 TRP 0.027 0.003 TRP D 580 HIS 0.079 0.003 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.25 (29301) covalent geometry : angle 0.84754 / 0.44 (40250) hydrogen bonds : bond 0.04327 / 4.38 ( 1237) hydrogen bonds : angle 4.75194 / 6.04 ( 3427) metal coordination : bond 0.00273 / 0.20 ( 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 505 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 372 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8352 (mt) cc_final: 0.8137 (tt) REVERT: A 142 MET cc_start: 0.8304 (ppp) cc_final: 0.8051 (ppp) REVERT: A 147 GLN cc_start: 0.8215 (pt0) cc_final: 0.7856 (pt0) REVERT: A 199 ASP cc_start: 0.7976 (m-30) cc_final: 0.7672 (m-30) REVERT: B 93 GLN cc_start: 0.7977 (mm110) cc_final: 0.7632 (mm-40) REVERT: C 47 TYR cc_start: 0.6421 (OUTLIER) cc_final: 0.5696 (p90) REVERT: C 405 PHE cc_start: 0.7881 (t80) cc_final: 0.7370 (t80) REVERT: C 517 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7639 (tp40) REVERT: C 523 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7577 (mt-10) REVERT: C 541 GLU cc_start: 0.7151 (tp30) cc_final: 0.6711 (tp30) REVERT: C 583 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6235 (tm-30) REVERT: C 680 LEU cc_start: 0.9232 (tt) cc_final: 0.8991 (tt) REVERT: C 789 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.8767 (p) REVERT: C 862 LEU cc_start: 0.8406 (mp) cc_final: 0.8122 (tt) REVERT: C 900 LYS cc_start: 0.6351 (OUTLIER) cc_final: 0.5770 (mttt) REVERT: C 948 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7894 (tp) REVERT: C 1157 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8645 (pt0) REVERT: C 1289 GLU cc_start: 0.7978 (pp20) cc_final: 0.7707 (pt0) REVERT: C 1315 MET cc_start: 0.7639 (mmp) cc_final: 0.7337 (mmm) REVERT: D 102 MET cc_start: 0.5214 (OUTLIER) cc_final: 0.3385 (mmt) REVERT: D 301 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6601 (pt0) REVERT: D 330 MET cc_start: 0.7907 (tpt) cc_final: 0.7558 (tpp) REVERT: D 346 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8069 (mtt-85) REVERT: D 629 PHE cc_start: 0.9029 (m-10) cc_final: 0.8722 (m-80) REVERT: D 680 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8584 (t0) REVERT: D 707 ILE cc_start: 0.8846 (mt) cc_final: 0.8635 (mm) REVERT: D 736 GLN cc_start: 0.8457 (mt0) cc_final: 0.8236 (mt0) REVERT: D 772 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: D 835 LEU cc_start: 0.7857 (pp) cc_final: 0.7603 (pp) REVERT: D 1040 MET cc_start: 0.3673 (tpt) cc_final: 0.3236 (tpt) REVERT: D 1367 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.6966 (pm20) REVERT: M 125 MET cc_start: 0.7770 (tpp) cc_final: 0.6780 (mmp) REVERT: M 199 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7885 (tt) REVERT: M 259 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7191 (ptp90) REVERT: M 265 GLN cc_start: 0.4329 (OUTLIER) cc_final: 0.3818 (mt0) REVERT: M 270 GLU cc_start: 0.7574 (tp30) cc_final: 0.5992 (tp30) outliers start: 133 outliers final: 65 residues processed: 472 average time/residue: 0.1766 time to fit residues: 136.5498 Evaluate side-chains 414 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 334 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 719 LYS Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 789 THR 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 1082 ILE Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1187 PHE Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 259 ARG Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 91 optimal weight: 8.9990 chunk 363 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 304 optimal weight: 40.0000 chunk 197 optimal weight: 0.9980 chunk 354 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 725 GLN C1108 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS D1244 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.090851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067429 restraints weight = 115763.526| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 4.39 r_work: 0.3196 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 1.0753 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= 0.166 Angle : 0.757 13.706 40250 Z= 0.382 Chirality : 0.045 0.274 4788 Planarity : 0.005 0.063 4929 Dihedral : 16.584 163.610 5044 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.81 % Favored : 93.13 % Rotamer: Outliers : 3.11 % Allowed : 33.90 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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 are not related in a simple way. whole: -0.90 (0.14), residues: 3612 helix: 0.51 (0.14), residues: 1335 sheet: -0.21 (0.27), residues: 377 loop : -1.52 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 431 TYR 0.033 0.002 TYR M 112 PHE 0.028 0.002 PHE C 506 TRP 0.023 0.002 TRP D 580 HIS 0.027 0.002 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (29301) covalent geometry : angle 0.75662 / 0.38 (40250) hydrogen bonds : bond 0.03900 / 3.93 ( 1237) hydrogen bonds : angle 4.60102 / 5.85 ( 3427) metal coordination : bond 0.00307 / 0.13 ( 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 431 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 350 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8373 (ppp) cc_final: 0.8038 (ppp) REVERT: A 147 GLN cc_start: 0.8186 (pt0) cc_final: 0.7906 (pt0) REVERT: A 199 ASP cc_start: 0.7982 (m-30) cc_final: 0.7734 (m-30) REVERT: B 37 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.7481 (t-90) REVERT: B 93 GLN cc_start: 0.7914 (mm110) cc_final: 0.7524 (mm-40) REVERT: C 47 TYR cc_start: 0.6354 (OUTLIER) cc_final: 0.5777 (p90) REVERT: C 517 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7801 (tp40) REVERT: C 523 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7818 (mt-10) REVERT: C 541 GLU cc_start: 0.7124 (tp30) cc_final: 0.6708 (tp30) REVERT: C 680 LEU cc_start: 0.9255 (tt) cc_final: 0.9022 (tt) REVERT: C 704 MET cc_start: 0.7365 (mtm) cc_final: 0.7140 (mtm) REVERT: C 741 MET cc_start: 0.7653 (mmt) cc_final: 0.7362 (ppp) REVERT: C 862 LEU cc_start: 0.8499 (mp) cc_final: 0.8163 (tt) REVERT: C 900 LYS cc_start: 0.6371 (OUTLIER) cc_final: 0.5768 (mttt) REVERT: C 1157 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8791 (pt0) REVERT: C 1216 ARG cc_start: 0.7675 (mtm180) cc_final: 0.6979 (mtm-85) REVERT: C 1289 GLU cc_start: 0.8020 (pp20) cc_final: 0.7709 (pt0) REVERT: C 1315 MET cc_start: 0.7654 (mmp) cc_final: 0.6892 (mmm) REVERT: D 102 MET cc_start: 0.5303 (OUTLIER) cc_final: 0.3988 (mmt) REVERT: D 301 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6757 (pt0) REVERT: D 314 ARG cc_start: 0.6743 (mmp80) cc_final: 0.6364 (mmp80) REVERT: D 330 MET cc_start: 0.7914 (tpt) cc_final: 0.7543 (tpp) REVERT: D 489 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8595 (p0) REVERT: D 562 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6595 (tp30) REVERT: D 680 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8589 (t0) REVERT: D 772 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: D 835 LEU cc_start: 0.8012 (pp) cc_final: 0.7700 (pp) REVERT: D 1040 MET cc_start: 0.3160 (tpt) cc_final: 0.2630 (tpt) REVERT: D 1206 ARG cc_start: 0.7200 (ttp80) cc_final: 0.6648 (tmm160) REVERT: D 1244 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8318 (tp40) REVERT: D 1345 ARG cc_start: 0.8697 (tpp80) cc_final: 0.8430 (tpp80) REVERT: M 125 MET cc_start: 0.7769 (tpp) cc_final: 0.6794 (mmp) REVERT: M 154 LEU cc_start: 0.7489 (mt) cc_final: 0.6144 (tt) REVERT: M 172 LEU cc_start: 0.8616 (tt) cc_final: 0.8246 (pp) REVERT: M 199 LEU cc_start: 0.8215 (mm) cc_final: 0.7882 (tt) REVERT: M 270 GLU cc_start: 0.7549 (tp30) cc_final: 0.6043 (tp30) outliers start: 81 outliers final: 54 residues processed: 415 average time/residue: 0.1655 time to fit residues: 113.9257 Evaluate side-chains 390 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 326 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 282 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 B residue 153 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 719 LYS Chi-restraints excluded: chain C residue 724 VAL 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 1047 LEU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1187 PHE Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1323 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain M residue 210 THR 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: 10.0000 chunk 283 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 234 optimal weight: 8.9990 chunk 308 optimal weight: 40.0000 chunk 121 optimal weight: 5.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 519 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.086712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.062750 restraints weight = 114440.477| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.22 r_work: 0.3063 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 1.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.238 29305 Z= 0.329 Angle : 0.985 27.034 40250 Z= 0.514 Chirality : 0.054 0.723 4788 Planarity : 0.008 0.133 4929 Dihedral : 16.830 163.559 5044 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.44 % Favored : 91.47 % Rotamer: Outliers : 3.87 % Allowed : 33.63 % Favored : 62.50 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 3612 helix: 0.02 (0.14), residues: 1328 sheet: -0.67 (0.26), residues: 362 loop : -1.69 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG M 259 TYR 0.028 0.003 TYR D1241 PHE 0.037 0.004 PHE C1323 TRP 0.062 0.005 TRP D 115 HIS 0.027 0.002 HIS D 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.33 (29301) covalent geometry : angle 0.98535 / 0.51 (40250) hydrogen bonds : bond 0.05288 / 5.30 ( 1237) hydrogen bonds : angle 5.02372 / 6.42 ( 3427) metal coordination : bond 0.00660 / 0.58 ( 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 436 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 335 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8849 (pt0) cc_final: 0.8451 (pt0) REVERT: A 181 GLU cc_start: 0.8751 (pp20) cc_final: 0.8467 (pp20) REVERT: A 199 ASP cc_start: 0.8460 (m-30) cc_final: 0.8073 (m-30) REVERT: B 37 HIS cc_start: 0.9317 (OUTLIER) cc_final: 0.7961 (t-90) REVERT: B 95 LYS cc_start: 0.8615 (tptp) cc_final: 0.8300 (tptp) REVERT: C 47 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.7053 (p90) REVERT: C 183 TRP cc_start: 0.7808 (OUTLIER) cc_final: 0.6885 (m-90) REVERT: C 336 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7429 (tt) REVERT: C 370 MET cc_start: 0.7092 (mmm) cc_final: 0.6846 (tpp) REVERT: C 503 LYS cc_start: 0.8495 (tptm) cc_final: 0.8180 (mptp) REVERT: C 517 GLN cc_start: 0.8570 (mm-40) cc_final: 0.7953 (tp40) REVERT: C 523 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8068 (mt-10) REVERT: C 541 GLU cc_start: 0.7588 (tp30) cc_final: 0.7293 (tm-30) REVERT: C 680 LEU cc_start: 0.9477 (tt) cc_final: 0.9236 (tt) REVERT: C 826 ASP cc_start: 0.8582 (m-30) cc_final: 0.8354 (t0) REVERT: C 862 LEU cc_start: 0.8968 (mp) cc_final: 0.8709 (tt) REVERT: C 900 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6027 (mttt) REVERT: C 957 LYS cc_start: 0.9373 (pptt) cc_final: 0.9018 (pttt) REVERT: C 1108 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8918 (p0) REVERT: C 1216 ARG cc_start: 0.8573 (mtm180) cc_final: 0.8004 (mtm-85) REVERT: C 1238 LEU cc_start: 0.8862 (mm) cc_final: 0.8505 (mt) REVERT: D 102 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.6114 (mmm) REVERT: D 301 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: D 680 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8769 (t0) REVERT: D 772 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: D 788 LEU cc_start: 0.9195 (pp) cc_final: 0.8952 (mt) REVERT: D 1040 MET cc_start: 0.3604 (tpt) cc_final: 0.3043 (tpt) REVERT: D 1230 THR cc_start: 0.9497 (m) cc_final: 0.9262 (p) REVERT: D 1305 ASP cc_start: 0.8321 (t0) cc_final: 0.7968 (m-30) REVERT: D 1345 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8710 (tpp80) REVERT: M 125 MET cc_start: 0.8619 (tpp) cc_final: 0.8293 (tpp) REVERT: M 172 LEU cc_start: 0.8859 (tt) cc_final: 0.8497 (pp) REVERT: M 199 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8159 (tt) REVERT: M 259 ARG cc_start: 0.8780 (ptp90) cc_final: 0.8270 (ptp90) REVERT: M 270 GLU cc_start: 0.7915 (tp30) cc_final: 0.6421 (tp30) outliers start: 101 outliers final: 56 residues processed: 416 average time/residue: 0.1561 time to fit residues: 105.9009 Evaluate side-chains 351 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 284 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS 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 222 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 100 LEU 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 335 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1187 PHE Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1323 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 332 LYS 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 407 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 781 LYS Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 210 THR 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: 7.9990 chunk 180 optimal weight: 8.9990 chunk 363 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 chunk 292 optimal weight: 0.9980 chunk 325 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 301 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** M 377 HIS ** 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 = 0.3871 r_free = 0.3871 target = 0.088792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.064945 restraints weight = 113763.214| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 4.32 r_work: 0.3123 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 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 = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 1.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29305 Z= 0.159 Angle : 0.817 14.963 40250 Z= 0.410 Chirality : 0.047 0.338 4788 Planarity : 0.005 0.070 4929 Dihedral : 16.736 162.342 5044 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.62 % Favored : 93.33 % Rotamer: Outliers : 2.07 % Allowed : 35.70 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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 are not related in a simple way. whole: -1.06 (0.14), residues: 3612 helix: 0.37 (0.14), residues: 1324 sheet: -0.49 (0.26), residues: 367 loop : -1.55 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 678 TYR 0.037 0.002 TYR M 112 PHE 0.030 0.002 PHE C1323 TRP 0.028 0.002 TRP D 580 HIS 0.011 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (29301) covalent geometry : angle 0.81693 / 0.41 (40250) hydrogen bonds : bond 0.03930 / 4.06 ( 1237) hydrogen bonds : angle 4.66091 / 5.95 ( 3427) metal coordination : bond 0.00311 / 0.14 ( 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 361 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8948 (ppp) cc_final: 0.8502 (ptm) REVERT: A 147 GLN cc_start: 0.8720 (pt0) cc_final: 0.8420 (pt0) REVERT: A 181 GLU cc_start: 0.8697 (pp20) cc_final: 0.8419 (pp20) REVERT: A 199 ASP cc_start: 0.8268 (m-30) cc_final: 0.7930 (m-30) REVERT: B 37 HIS cc_start: 0.9116 (OUTLIER) cc_final: 0.7793 (t-90) REVERT: B 93 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7250 (mm-40) REVERT: B 95 LYS cc_start: 0.8602 (tptp) cc_final: 0.8274 (tptp) REVERT: B 185 TYR cc_start: 0.9111 (p90) cc_final: 0.8685 (p90) REVERT: B 200 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8744 (tmtt) REVERT: C 370 MET cc_start: 0.7152 (mmm) cc_final: 0.6906 (tpp) REVERT: C 503 LYS cc_start: 0.8513 (tptm) cc_final: 0.8190 (mttp) REVERT: C 517 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8190 (tp40) REVERT: C 541 GLU cc_start: 0.7462 (tp30) cc_final: 0.7116 (tm-30) REVERT: C 862 LEU cc_start: 0.8887 (mp) cc_final: 0.8599 (tt) REVERT: C 1216 ARG cc_start: 0.8421 (mtm180) cc_final: 0.7927 (mtm-85) REVERT: D 330 MET cc_start: 0.8109 (tpt) cc_final: 0.7880 (tpt) REVERT: D 680 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8723 (t0) REVERT: D 731 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.7938 (ttm110) REVERT: D 772 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: D 788 LEU cc_start: 0.9212 (pp) cc_final: 0.8965 (mt) REVERT: D 1040 MET cc_start: 0.3757 (tpt) cc_final: 0.3336 (tpt) REVERT: D 1219 ASP cc_start: 0.8369 (t0) cc_final: 0.7825 (m-30) REVERT: D 1230 THR cc_start: 0.9465 (m) cc_final: 0.9242 (p) REVERT: E 7 GLN cc_start: 0.7748 (pm20) cc_final: 0.6975 (pm20) REVERT: M 125 MET cc_start: 0.8599 (tpp) cc_final: 0.8300 (tpp) REVERT: M 172 LEU cc_start: 0.8870 (tt) cc_final: 0.8542 (pp) REVERT: M 199 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8180 (tt) REVERT: M 270 GLU cc_start: 0.7912 (tp30) cc_final: 0.6027 (tm-30) REVERT: M 363 LYS cc_start: 0.7018 (mtmm) cc_final: 0.6365 (mmmt) outliers start: 54 outliers final: 38 residues processed: 349 average time/residue: 0.1675 time to fit residues: 95.1403 Evaluate side-chains 330 residues out of total 3113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET 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 93 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 1187 PHE Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1323 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 332 LYS 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 407 VAL Chi-restraints excluded: chain D residue 412 LEU 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 820 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 210 THR 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 45 optimal weight: 0.5980 chunk 313 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 4 optimal weight: 50.0000 chunk 205 optimal weight: 0.9980 chunk 266 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** M 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.088673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.064799 restraints weight = 114149.365| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.30 r_work: 0.3123 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 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 = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 1.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.327 29305 Z= 0.251 Angle : 0.908 59.191 40250 Z= 0.479 Chirality : 0.047 0.422 4788 Planarity : 0.005 0.071 4929 Dihedral : 16.732 162.352 5044 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.59 % Favored : 93.38 % Rotamer: Outliers : 2.22 % Allowed : 35.70 % Favored : 62.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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 are not related in a simple way. whole: -1.06 (0.14), residues: 3612 helix: 0.36 (0.14), residues: 1324 sheet: -0.47 (0.26), residues: 367 loop : -1.55 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 478 TYR 0.052 0.002 TYR D 382 PHE 0.029 0.002 PHE C1323 TRP 0.025 0.002 TRP D 580 HIS 0.009 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 (29301) covalent geometry : angle 0.90812 / 0.48 (40250) hydrogen bonds : bond 0.03927 / 4.05 ( 1237) hydrogen bonds : angle 4.65863 / 5.94 ( 3427) metal coordination : bond 0.00363 / 0.16 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7819.03 seconds wall clock time: 134 minutes 21.48 seconds (8061.48 seconds total)