Starting phenix.real_space_refine on Mon Sep 14 02:40:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p19_20234/09_2026/6p19_20234.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p19_20234/09_2026/6p19_20234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p19_20234/09_2026/6p19_20234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p19_20234/09_2026/6p19_20234.map" model { file = "/net/cci-nas-00/data/ceres_data/6p19_20234/09_2026/6p19_20234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p19_20234/09_2026/6p19_20234.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6p19_20234/09_2026/6p19_20234.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p19_20234/09_2026/6p19_20234.cif" } resolution = 3.8 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= 0.007 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 66 5.49 5 Mg 1 5.21 5 S 114 5.16 5 C 16968 2.51 5 N 4853 2.21 5 O 5412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27416 Number of models: 1 Model: "" Number of chains: 10 Chain: "1" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 478 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "2" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 542 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1324, 10437 Classifications: {'peptide': 1324} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1268} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10319 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1271} Chain breaks: 2 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Q" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1129 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 1 Chain: "R" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 355 Classifications: {'RNAv2': 16} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 13} 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 15468 SG CYS D 70 43.245 119.165 62.351 1.00103.34 S ATOM 15482 SG CYS D 72 44.915 122.455 61.689 1.00 94.59 S ATOM 21302 SG CYS D 814 41.460 52.961 47.558 1.00 74.88 S ATOM 21867 SG CYS D 888 43.473 56.080 48.436 1.00 69.19 S ATOM 21918 SG CYS D 895 41.008 54.351 50.914 1.00 60.42 S ATOM 21939 SG CYS D 898 43.952 51.936 49.962 1.00 58.11 S Time building chain proxies: 5.89, per 1000 atoms: 0.21 Number of scatterers: 27416 At special positions: 0 Unit cell: (141.312, 137.216, 146.432, 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 114 16.00 P 66 15.00 Mg 1 11.99 O 5412 8.00 N 4853 7.00 C 16968 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " Number of angles added : 6 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6140 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 45 sheets defined 40.2% alpha, 15.0% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.262A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 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 154 through 162 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.450A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.534A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.719A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.550A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.879A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.797A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 4.086A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.736A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 614 removed outlier: 4.310A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 609 through 614' Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.281A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.506A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 861 through 865 removed outlier: 3.860A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 993 through 997 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.643A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.941A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1334 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.671A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.636A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 4.483A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.538A pdb=" N ARG D 250 " --> pdb=" O PRO D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.090A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.844A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.709A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.006A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.622A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.055A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1316 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1361 through 1375 removed outlier: 4.457A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 39 through 48 Processing helix chain 'Q' and resid 60 through 74 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 3.986A pdb=" N PHE Q 81 " --> pdb=" O ASP Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 103 Processing helix chain 'Q' and resid 123 through 151 Proline residue: Q 143 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.510A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY A 149 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.627A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.509A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.835A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 105 removed outlier: 3.686A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.661A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 removed outlier: 7.259A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.556A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.847A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.708A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C 106 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL C 114 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.234A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'C' and resid 158 through 160 removed outlier: 3.830A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AC1, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.843A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.589A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.510A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.510A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 615 through 617 Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.940A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 7.675A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.668A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.987A pdb=" N LYS C 914 " --> pdb=" O THR C 888 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1269 through 1270 removed outlier: 3.591A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1341 Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.319A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.132A 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 removed outlier: 4.238A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 350 through 357 removed outlier: 7.612A pdb=" N ALA D 446 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.555A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) 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 958 through 961 removed outlier: 3.551A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 966 removed outlier: 4.302A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1025 through 1026 removed outlier: 3.615A pdb=" N ILE D1124 " --> pdb=" O MET D1025 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.756A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.950A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1174 through 1178 removed outlier: 6.520A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1280 through 1281 removed outlier: 3.575A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL D1267 " --> pdb=" O THR D1301 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 8.02 Time building geometry restraints manager: 3.24 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: 7017 1.33 - 1.45: 5218 1.45 - 1.57: 15411 1.57 - 1.69: 127 1.69 - 1.82: 198 Bond restraints: 27971 Sorted by residual: bond pdb=" C3' DT 1 100 " pdb=" C2' DT 1 100 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.67e+01 bond pdb=" C1' DT 2 15 " pdb=" N1 DT 2 15 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" N ILE B 211 " pdb=" CA ILE B 211 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.07e-02 8.73e+03 1.35e+01 bond pdb=" C4' DC 2 17 " pdb=" C3' DC 2 17 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.00e-02 1.00e+04 1.26e+01 bond pdb=" C3' DC 2 17 " pdb=" O3' DC 2 17 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.12e+01 ... (remaining 27966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 36532 2.13 - 4.27: 1363 4.27 - 6.40: 123 6.40 - 8.53: 38 8.53 - 10.66: 10 Bond angle restraints: 38066 Sorted by residual: angle pdb=" O4' DC 1 111 " pdb=" C4' DC 1 111 " pdb=" C3' DC 1 111 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.75e+01 angle pdb=" O4' DG 1 96 " pdb=" C4' DG 1 96 " pdb=" C3' DG 1 96 " ideal model delta sigma weight residual 106.00 102.93 3.07 6.00e-01 2.78e+00 2.62e+01 angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" N ILE B 130 " pdb=" CA ILE B 130 " pdb=" C ILE B 130 " ideal model delta sigma weight residual 111.48 106.92 4.56 9.40e-01 1.13e+00 2.35e+01 angle pdb=" O4' DC 2 18 " pdb=" C4' DC 2 18 " pdb=" C3' DC 2 18 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.34e+01 ... (remaining 38061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 14728 17.83 - 35.67: 1714 35.67 - 53.50: 431 53.50 - 71.33: 106 71.33 - 89.16: 30 Dihedral angle restraints: 17009 sinusoidal: 7464 harmonic: 9545 Sorted by residual: dihedral pdb=" C4' G R 55 " pdb=" C3' G R 55 " pdb=" C2' G R 55 " pdb=" C1' G R 55 " ideal model delta sinusoidal sigma weight residual 36.34 -33.50 69.85 1 3.10e+00 1.04e-01 6.55e+02 dihedral pdb=" C4' A R 56 " pdb=" C3' A R 56 " pdb=" C2' A R 56 " pdb=" C1' A R 56 " ideal model delta sinusoidal sigma weight residual 36.34 -33.47 69.82 1 3.10e+00 1.04e-01 6.54e+02 dihedral pdb=" O4' A R 56 " pdb=" C4' A R 56 " pdb=" C3' A R 56 " pdb=" C2' A R 56 " ideal model delta sinusoidal sigma weight residual -35.15 24.21 -59.35 1 4.00e+00 6.25e-02 2.94e+02 ... (remaining 17006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3195 0.060 - 0.120: 934 0.120 - 0.180: 159 0.180 - 0.240: 39 0.240 - 0.300: 10 Chirality restraints: 4337 Sorted by residual: chirality pdb=" CB ILE D1177 " pdb=" CA ILE D1177 " pdb=" CG1 ILE D1177 " pdb=" CG2 ILE D1177 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB VAL C1094 " pdb=" CA VAL C1094 " pdb=" CG1 VAL C1094 " pdb=" CG2 VAL C1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" P U R 69 " pdb=" OP1 U R 69 " pdb=" OP2 U R 69 " pdb=" O5' U R 69 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 4334 not shown) Planarity restraints: 4749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 504 " -0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLN D 504 " 0.085 2.00e-02 2.50e+03 pdb=" O GLN D 504 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP D 505 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 450 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO D 451 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 451 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 451 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 209 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C GLY B 209 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY B 209 " 0.017 2.00e-02 2.50e+03 pdb=" N THR B 210 " 0.015 2.00e-02 2.50e+03 ... (remaining 4746 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 452 2.63 - 3.20: 23145 3.20 - 3.76: 44219 3.76 - 4.33: 57163 4.33 - 4.90: 93319 Nonbonded interactions: 218298 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.061 2.170 nonbonded pdb=" O3' A R 70 " pdb="MG MG D1503 " model vdw 2.075 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.108 2.170 nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1503 " model vdw 2.217 2.170 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1501 " model vdw 2.222 2.310 ... (remaining 218293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.040 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.890 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.009 0.466 27977 Z= 0.406 Angle : 0.951 26.600 38072 Z= 0.542 Chirality : 0.059 0.300 4337 Planarity : 0.007 0.073 4749 Dihedral : 16.632 89.163 10869 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.46 % Allowed : 9.93 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.11), residues: 3303 helix: -2.40 (0.10), residues: 1223 sheet: -2.64 (0.24), residues: 352 loop : -2.78 (0.12), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 44 TYR 0.030 0.002 TYR C1281 PHE 0.025 0.002 PHE Q 43 TRP 0.019 0.002 TRP D 580 HIS 0.015 0.002 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00822 / 0.39 (27971) covalent geometry : angle 0.93663 / 0.54 (38066) hydrogen bonds : bond 0.14593 / 16.02 ( 1165) hydrogen bonds : angle 6.97642 / 6.79 ( 3283) metal coordination : bond 0.22267 / 13.71 ( 6) metal coordination : angle 13.30794 / 23.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 401 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8881 (mppt) cc_final: 0.8599 (mmtt) REVERT: A 58 GLU cc_start: 0.7765 (mp0) cc_final: 0.7474 (mt-10) REVERT: A 117 HIS cc_start: 0.8606 (p-80) cc_final: 0.8351 (p-80) REVERT: B 104 LYS cc_start: 0.7986 (tptp) cc_final: 0.7645 (tptp) REVERT: B 128 HIS cc_start: 0.8810 (t70) cc_final: 0.8425 (t-90) REVERT: C 409 LEU cc_start: 0.9156 (mt) cc_final: 0.8779 (tp) REVERT: C 432 LEU cc_start: 0.9002 (tp) cc_final: 0.8800 (tp) REVERT: C 1131 MET cc_start: 0.8502 (mtm) cc_final: 0.8206 (mtp) REVERT: C 1273 MET cc_start: 0.8511 (mtt) cc_final: 0.8198 (mtt) REVERT: C 1329 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7921 (mt-10) REVERT: D 196 GLN cc_start: 0.8992 (tp40) cc_final: 0.8384 (tp-100) REVERT: D 197 GLU cc_start: 0.8568 (mp0) cc_final: 0.8020 (mp0) REVERT: D 458 ASN cc_start: 0.8842 (m110) cc_final: 0.8148 (t0) REVERT: D 892 PHE cc_start: 0.7641 (m-80) cc_final: 0.6597 (t80) REVERT: D 999 TYR cc_start: 0.6809 (t80) cc_final: 0.6556 (t80) REVERT: D 1241 TYR cc_start: 0.8481 (m-80) cc_final: 0.8240 (m-80) REVERT: E 63 ILE cc_start: 0.8601 (mt) cc_final: 0.8311 (mt) outliers start: 13 outliers final: 8 residues processed: 414 average time/residue: 0.2008 time to fit residues: 127.6520 Evaluate side-chains 290 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 282 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 1176 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 23 HIS A 66 HIS B 93 GLN B 194 GLN B 208 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 314 ASN C 517 GLN C 618 GLN C 659 GLN C 766 ASN C 767 GLN C 832 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 200 GLN D 450 HIS D 667 GLN D 861 ASN D 962 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1114 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1259 GLN E 29 GLN Q 17 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.139860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102690 restraints weight = 54345.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.099798 restraints weight = 46637.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.100965 restraints weight = 50682.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101212 restraints weight = 33850.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102046 restraints weight = 30033.093| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27977 Z= 0.156 Angle : 0.689 16.854 38072 Z= 0.353 Chirality : 0.050 0.940 4337 Planarity : 0.005 0.061 4749 Dihedral : 13.528 89.629 4377 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.98 % Allowed : 14.41 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.13), residues: 3303 helix: -0.70 (0.13), residues: 1233 sheet: -1.95 (0.26), residues: 335 loop : -2.38 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 478 TYR 0.060 0.001 TYR C 62 PHE 0.018 0.001 PHE C1025 TRP 0.018 0.001 TRP D1193 HIS 0.009 0.001 HIS Q 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (27971) covalent geometry : angle 0.68736 / 0.35 (38066) hydrogen bonds : bond 0.05059 / 5.45 ( 1165) hydrogen bonds : angle 5.55460 / 5.40 ( 3283) metal coordination : bond 0.00674 / 0.70 ( 6) metal coordination : angle 3.63570 / 6.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 HIS cc_start: 0.8398 (p-80) cc_final: 0.8142 (p-80) REVERT: B 86 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8349 (ttpt) REVERT: B 104 LYS cc_start: 0.8234 (tptp) cc_final: 0.7885 (tptp) REVERT: B 128 HIS cc_start: 0.8689 (t70) cc_final: 0.8285 (t-90) REVERT: B 145 LYS cc_start: 0.9009 (tptp) cc_final: 0.8796 (tptp) REVERT: C 124 MET cc_start: 0.8144 (ptp) cc_final: 0.7664 (ptp) REVERT: C 1014 LEU cc_start: 0.1909 (OUTLIER) cc_final: 0.1562 (tt) REVERT: C 1131 MET cc_start: 0.8413 (mtm) cc_final: 0.8171 (mtp) REVERT: C 1171 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7427 (ttp-170) REVERT: C 1290 MET cc_start: 0.8756 (ttm) cc_final: 0.8508 (ttm) REVERT: D 136 GLU cc_start: 0.8108 (tp30) cc_final: 0.7854 (tp30) REVERT: D 196 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8332 (tp-100) REVERT: D 458 ASN cc_start: 0.8739 (m110) cc_final: 0.8144 (t0) REVERT: D 785 ASP cc_start: 0.7398 (t0) cc_final: 0.7178 (t70) REVERT: D 892 PHE cc_start: 0.7620 (m-80) cc_final: 0.6604 (t80) REVERT: D 1040 MET cc_start: 0.2812 (ptp) cc_final: 0.2271 (pmm) REVERT: D 1241 TYR cc_start: 0.8214 (m-80) cc_final: 0.7880 (m-80) outliers start: 56 outliers final: 25 residues processed: 358 average time/residue: 0.1740 time to fit residues: 100.3039 Evaluate side-chains 296 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 87 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 198 optimal weight: 0.0030 chunk 42 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 268 optimal weight: 9.9990 chunk 273 optimal weight: 50.0000 chunk 59 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 218 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 HIS D 667 GLN D 777 HIS D1044 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.140222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103453 restraints weight = 53894.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100222 restraints weight = 47169.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102063 restraints weight = 47633.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101809 restraints weight = 32810.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102405 restraints weight = 29829.343| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27977 Z= 0.140 Angle : 0.630 11.696 38072 Z= 0.324 Chirality : 0.045 0.367 4337 Planarity : 0.005 0.057 4749 Dihedral : 13.509 106.454 4374 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.91 % Allowed : 16.35 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.14), residues: 3303 helix: 0.06 (0.14), residues: 1232 sheet: -1.92 (0.27), residues: 330 loop : -2.18 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 275 TYR 0.027 0.001 TYR Q 28 PHE 0.019 0.001 PHE D 172 TRP 0.016 0.001 TRP D 115 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (27971) covalent geometry : angle 0.62908 / 0.32 (38066) hydrogen bonds : bond 0.04488 / 4.88 ( 1165) hydrogen bonds : angle 5.22919 / 5.11 ( 3283) metal coordination : bond 0.00293 / 0.30 ( 6) metal coordination : angle 2.49570 / 4.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 303 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8418 (mmtp) REVERT: A 185 TYR cc_start: 0.8729 (p90) cc_final: 0.8465 (p90) REVERT: B 104 LYS cc_start: 0.8237 (tptp) cc_final: 0.8007 (tptp) REVERT: B 128 HIS cc_start: 0.8601 (t70) cc_final: 0.8214 (t-90) REVERT: C 369 MET cc_start: 0.8093 (tmm) cc_final: 0.7134 (tmm) REVERT: C 1014 LEU cc_start: 0.1456 (OUTLIER) cc_final: 0.1106 (tt) REVERT: D 151 MET cc_start: 0.7707 (pmm) cc_final: 0.7447 (pmm) REVERT: D 196 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8363 (tp-100) REVERT: D 458 ASN cc_start: 0.8763 (m110) cc_final: 0.8311 (t0) REVERT: D 785 ASP cc_start: 0.7324 (t0) cc_final: 0.7100 (t70) REVERT: D 892 PHE cc_start: 0.7584 (m-80) cc_final: 0.6574 (t80) REVERT: D 982 LEU cc_start: 0.8347 (pp) cc_final: 0.7966 (pt) REVERT: D 1040 MET cc_start: 0.2855 (ptp) cc_final: 0.2034 (pmm) REVERT: D 1241 TYR cc_start: 0.8164 (m-80) cc_final: 0.7880 (m-80) outliers start: 54 outliers final: 35 residues processed: 341 average time/residue: 0.1606 time to fit residues: 90.0093 Evaluate side-chains 310 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 20 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 208 optimal weight: 20.0000 chunk 285 optimal weight: 40.0000 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 282 optimal weight: 50.0000 chunk 33 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 23 optimal weight: 9.9990 chunk 293 optimal weight: 20.0000 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN C 314 ASN C 673 HIS ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1023 HIS ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.136983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099955 restraints weight = 54040.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096920 restraints weight = 46915.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.098367 restraints weight = 51297.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098296 restraints weight = 32764.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099001 restraints weight = 29669.898| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 27977 Z= 0.297 Angle : 0.731 9.822 38072 Z= 0.373 Chirality : 0.047 0.358 4337 Planarity : 0.005 0.058 4749 Dihedral : 13.585 110.126 4374 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.29 % Allowed : 17.06 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.14), residues: 3303 helix: 0.13 (0.14), residues: 1239 sheet: -1.98 (0.26), residues: 351 loop : -2.14 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1174 TYR 0.019 0.002 TYR C 105 PHE 0.022 0.002 PHE D 172 TRP 0.028 0.002 TRP Q 15 HIS 0.012 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.30 (27971) covalent geometry : angle 0.73060 / 0.37 (38066) hydrogen bonds : bond 0.04977 / 5.35 ( 1165) hydrogen bonds : angle 5.30103 / 5.29 ( 3283) metal coordination : bond 0.01058 / 1.02 ( 6) metal coordination : angle 2.80974 / 5.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 282 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8299 (mmmm) REVERT: A 185 TYR cc_start: 0.8830 (p90) cc_final: 0.8547 (p90) REVERT: B 93 GLN cc_start: 0.7843 (mp10) cc_final: 0.7526 (mp10) REVERT: B 104 LYS cc_start: 0.8270 (tptp) cc_final: 0.7995 (tptp) REVERT: B 128 HIS cc_start: 0.8643 (t70) cc_final: 0.8253 (t-90) REVERT: C 351 LEU cc_start: 0.9291 (tp) cc_final: 0.9090 (tt) REVERT: C 1014 LEU cc_start: 0.1407 (OUTLIER) cc_final: 0.1042 (tt) REVERT: C 1171 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7434 (ttp-170) REVERT: D 29 MET cc_start: 0.8266 (tpp) cc_final: 0.8033 (tpp) REVERT: D 136 GLU cc_start: 0.8191 (tp30) cc_final: 0.7985 (tp30) REVERT: D 196 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8358 (tp-100) REVERT: D 308 ASP cc_start: 0.8283 (t0) cc_final: 0.7929 (t0) REVERT: D 458 ASN cc_start: 0.8853 (m110) cc_final: 0.8127 (t0) REVERT: D 785 ASP cc_start: 0.7632 (t0) cc_final: 0.7406 (t70) REVERT: D 892 PHE cc_start: 0.7619 (m-80) cc_final: 0.6594 (t80) REVERT: D 1040 MET cc_start: 0.3111 (ptp) cc_final: 0.2466 (pmm) REVERT: D 1241 TYR cc_start: 0.8404 (m-80) cc_final: 0.8112 (m-80) REVERT: Q 74 MET cc_start: 0.7620 (mpp) cc_final: 0.6368 (mpp) REVERT: Q 94 LYS cc_start: 0.8238 (tppt) cc_final: 0.7685 (mmtt) outliers start: 93 outliers final: 69 residues processed: 357 average time/residue: 0.1597 time to fit residues: 94.1082 Evaluate side-chains 340 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 15 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1083 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 110 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 203 optimal weight: 0.2980 chunk 80 optimal weight: 20.0000 chunk 333 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102731 restraints weight = 54003.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.099974 restraints weight = 45836.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101343 restraints weight = 48032.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101403 restraints weight = 33476.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102075 restraints weight = 29725.433| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27977 Z= 0.128 Angle : 0.617 12.720 38072 Z= 0.316 Chirality : 0.044 0.336 4337 Planarity : 0.004 0.056 4749 Dihedral : 13.481 118.876 4374 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.83 % Allowed : 18.51 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3303 helix: 0.47 (0.15), residues: 1231 sheet: -1.59 (0.27), residues: 336 loop : -1.98 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 275 TYR 0.036 0.001 TYR Q 88 PHE 0.021 0.001 PHE C1025 TRP 0.025 0.002 TRP C 997 HIS 0.004 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (27971) covalent geometry : angle 0.61674 / 0.32 (38066) hydrogen bonds : bond 0.04241 / 4.64 ( 1165) hydrogen bonds : angle 5.03660 / 5.00 ( 3283) metal coordination : bond 0.00190 / 0.21 ( 6) metal coordination : angle 2.23078 / 4.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 290 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8237 (mmtp) REVERT: A 51 MET cc_start: 0.8218 (tpp) cc_final: 0.7991 (mmm) REVERT: A 185 TYR cc_start: 0.8757 (p90) cc_final: 0.8494 (p90) REVERT: B 104 LYS cc_start: 0.8208 (tptp) cc_final: 0.7963 (tptp) REVERT: B 128 HIS cc_start: 0.8566 (t70) cc_final: 0.8173 (t-90) REVERT: C 124 MET cc_start: 0.7953 (ptp) cc_final: 0.7663 (ptp) REVERT: C 1014 LEU cc_start: 0.1392 (OUTLIER) cc_final: 0.0918 (tt) REVERT: D 29 MET cc_start: 0.8211 (tpp) cc_final: 0.7958 (tpp) REVERT: D 196 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8262 (tp-100) REVERT: D 458 ASN cc_start: 0.8667 (m110) cc_final: 0.8171 (t0) REVERT: D 892 PHE cc_start: 0.7528 (m-80) cc_final: 0.6528 (t80) REVERT: D 982 LEU cc_start: 0.8295 (pp) cc_final: 0.7994 (pt) REVERT: D 1040 MET cc_start: 0.2978 (ptp) cc_final: 0.2071 (pmm) REVERT: D 1241 TYR cc_start: 0.8126 (m-80) cc_final: 0.7816 (m-80) REVERT: E 28 ARG cc_start: 0.8510 (mmt90) cc_final: 0.7760 (mmt90) REVERT: Q 15 TRP cc_start: 0.7718 (t60) cc_final: 0.7438 (t-100) REVERT: Q 19 TRP cc_start: 0.7207 (m100) cc_final: 0.6775 (t-100) REVERT: Q 81 PHE cc_start: 0.8094 (m-80) cc_final: 0.7547 (m-10) outliers start: 80 outliers final: 55 residues processed: 356 average time/residue: 0.1539 time to fit residues: 91.5749 Evaluate side-chains 329 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 273 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 15 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 26 optimal weight: 8.9990 chunk 275 optimal weight: 30.0000 chunk 328 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 279 optimal weight: 50.0000 chunk 71 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN B 147 GLN B 194 GLN C 314 ASN C 856 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** 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 = 0.3905 r_free = 0.3905 target = 0.138243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100106 restraints weight = 54412.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.097871 restraints weight = 46765.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098938 restraints weight = 48407.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099162 restraints weight = 32755.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099854 restraints weight = 28747.165| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27977 Z= 0.230 Angle : 0.672 12.601 38072 Z= 0.342 Chirality : 0.045 0.311 4337 Planarity : 0.005 0.055 4749 Dihedral : 13.515 125.086 4374 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.86 % Allowed : 19.39 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3303 helix: 0.44 (0.15), residues: 1236 sheet: -1.59 (0.27), residues: 343 loop : -1.94 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 275 TYR 0.016 0.002 TYR C 62 PHE 0.030 0.002 PHE D1145 TRP 0.033 0.002 TRP C 997 HIS 0.009 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (27971) covalent geometry : angle 0.67159 / 0.34 (38066) hydrogen bonds : bond 0.04548 / 4.89 ( 1165) hydrogen bonds : angle 5.09249 / 5.10 ( 3283) metal coordination : bond 0.00767 / 0.76 ( 6) metal coordination : angle 2.26037 / 4.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 281 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8309 (mmmm) REVERT: A 185 TYR cc_start: 0.8828 (p90) cc_final: 0.8542 (p90) REVERT: B 104 LYS cc_start: 0.8263 (tptp) cc_final: 0.8006 (tptp) REVERT: B 128 HIS cc_start: 0.8591 (t70) cc_final: 0.8178 (t-90) REVERT: C 124 MET cc_start: 0.8035 (ptp) cc_final: 0.7748 (ptp) REVERT: C 1171 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7572 (ttp-170) REVERT: D 196 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8299 (tp-100) REVERT: D 308 ASP cc_start: 0.8199 (t0) cc_final: 0.7901 (t0) REVERT: D 892 PHE cc_start: 0.7584 (m-80) cc_final: 0.6511 (t80) REVERT: D 982 LEU cc_start: 0.8397 (pp) cc_final: 0.8158 (pt) REVERT: D 1241 TYR cc_start: 0.8326 (m-80) cc_final: 0.7989 (m-80) REVERT: Q 15 TRP cc_start: 0.7736 (t60) cc_final: 0.7533 (t-100) REVERT: Q 19 TRP cc_start: 0.7258 (m100) cc_final: 0.6708 (t-100) REVERT: Q 81 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7743 (m-80) outliers start: 81 outliers final: 67 residues processed: 346 average time/residue: 0.1595 time to fit residues: 92.1269 Evaluate side-chains 333 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 265 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 15 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 81 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 23 optimal weight: 4.9990 chunk 139 optimal weight: 0.0670 chunk 15 optimal weight: 0.0270 chunk 232 optimal weight: 0.5980 chunk 287 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 308 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 GLN B 194 GLN C 554 HIS ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.141376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103765 restraints weight = 53028.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101040 restraints weight = 43475.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102007 restraints weight = 48853.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.102302 restraints weight = 33571.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102972 restraints weight = 29454.044| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27977 Z= 0.115 Angle : 0.625 19.075 38072 Z= 0.314 Chirality : 0.043 0.280 4337 Planarity : 0.004 0.057 4749 Dihedral : 13.404 129.257 4374 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.33 % Allowed : 20.42 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3303 helix: 0.67 (0.15), residues: 1226 sheet: -1.27 (0.27), residues: 341 loop : -1.80 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 275 TYR 0.015 0.001 TYR Q 87 PHE 0.021 0.001 PHE C1025 TRP 0.041 0.002 TRP C 997 HIS 0.004 0.001 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (27971) covalent geometry : angle 0.62490 / 0.31 (38066) hydrogen bonds : bond 0.03946 / 4.28 ( 1165) hydrogen bonds : angle 4.85403 / 4.81 ( 3283) metal coordination : bond 0.00166 / 0.17 ( 6) metal coordination : angle 1.82725 / 3.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 294 time to evaluate : 1.011 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 10 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8245 (mmtm) REVERT: A 185 TYR cc_start: 0.8728 (p90) cc_final: 0.8450 (p90) REVERT: B 104 LYS cc_start: 0.8224 (tptp) cc_final: 0.8003 (tptp) REVERT: C 805 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8018 (ptp) REVERT: C 856 ASN cc_start: 0.6565 (OUTLIER) cc_final: 0.5700 (t0) REVERT: C 1014 LEU cc_start: 0.1076 (OUTLIER) cc_final: 0.0805 (tt) REVERT: D 29 MET cc_start: 0.8199 (tpp) cc_final: 0.7949 (tpp) REVERT: D 196 GLN cc_start: 0.8728 (tp-100) cc_final: 0.8235 (tp-100) REVERT: D 227 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: D 308 ASP cc_start: 0.7942 (t0) cc_final: 0.7653 (t0) REVERT: D 458 ASN cc_start: 0.8640 (m110) cc_final: 0.8103 (t0) REVERT: D 892 PHE cc_start: 0.7400 (m-80) cc_final: 0.6459 (t80) REVERT: D 982 LEU cc_start: 0.8329 (pp) cc_final: 0.8099 (pt) REVERT: D 1040 MET cc_start: 0.2415 (ptp) cc_final: 0.1790 (pmm) REVERT: D 1241 TYR cc_start: 0.8097 (m-80) cc_final: 0.7819 (m-80) REVERT: E 53 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8147 (mm-30) REVERT: Q 81 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7629 (m-80) outliers start: 66 outliers final: 46 residues processed: 346 average time/residue: 0.1619 time to fit residues: 92.6508 Evaluate side-chains 322 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 15 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 81 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 174 optimal weight: 0.9990 chunk 1 optimal weight: 30.0000 chunk 291 optimal weight: 7.9990 chunk 323 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 321 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 206 optimal weight: 0.2980 chunk 252 optimal weight: 0.0370 chunk 154 optimal weight: 4.9990 overall best weight: 2.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 HIS B 194 GLN C 447 HIS ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.140101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102786 restraints weight = 54351.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.099904 restraints weight = 49900.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101466 restraints weight = 50464.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101384 restraints weight = 33924.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102325 restraints weight = 30241.495| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27977 Z= 0.160 Angle : 0.642 14.878 38072 Z= 0.322 Chirality : 0.044 0.266 4337 Planarity : 0.004 0.055 4749 Dihedral : 13.395 129.193 4373 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.44 % Allowed : 20.70 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3303 helix: 0.64 (0.15), residues: 1238 sheet: -1.27 (0.27), residues: 351 loop : -1.79 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 275 TYR 0.016 0.001 TYR Q 87 PHE 0.019 0.001 PHE C1025 TRP 0.031 0.002 TRP C 997 HIS 0.012 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (27971) covalent geometry : angle 0.64158 / 0.32 (38066) hydrogen bonds : bond 0.04075 / 4.38 ( 1165) hydrogen bonds : angle 4.86219 / 4.84 ( 3283) metal coordination : bond 0.00443 / 0.47 ( 6) metal coordination : angle 1.67546 / 3.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 275 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8269 (mmmm) REVERT: A 185 TYR cc_start: 0.8742 (p90) cc_final: 0.8491 (p90) REVERT: B 104 LYS cc_start: 0.8230 (tptp) cc_final: 0.7997 (tptp) REVERT: C 805 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8156 (ptp) REVERT: C 856 ASN cc_start: 0.6326 (OUTLIER) cc_final: 0.5313 (t0) REVERT: C 1014 LEU cc_start: 0.1098 (OUTLIER) cc_final: 0.0833 (tt) REVERT: C 1316 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6964 (tm-30) REVERT: D 29 MET cc_start: 0.8153 (tpp) cc_final: 0.7905 (tpp) REVERT: D 196 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8252 (tp-100) REVERT: D 227 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8562 (m-80) REVERT: D 308 ASP cc_start: 0.8034 (t0) cc_final: 0.7745 (t0) REVERT: D 458 ASN cc_start: 0.8689 (m110) cc_final: 0.8129 (t0) REVERT: D 892 PHE cc_start: 0.7507 (m-80) cc_final: 0.6511 (t80) REVERT: D 982 LEU cc_start: 0.8388 (pp) cc_final: 0.8175 (pt) REVERT: D 1040 MET cc_start: 0.2101 (ptp) cc_final: 0.1382 (pmm) REVERT: D 1241 TYR cc_start: 0.8194 (m-80) cc_final: 0.7841 (m-80) REVERT: Q 81 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7651 (m-80) outliers start: 69 outliers final: 58 residues processed: 331 average time/residue: 0.1514 time to fit residues: 84.1539 Evaluate side-chains 328 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 15 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 81 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 195 optimal weight: 20.0000 chunk 204 optimal weight: 0.7980 chunk 311 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 141 optimal weight: 0.0170 chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 255 optimal weight: 8.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS B 194 GLN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** 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 = 0.3948 r_free = 0.3948 target = 0.141548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.102307 restraints weight = 53895.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100131 restraints weight = 43370.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101401 restraints weight = 42504.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101504 restraints weight = 29705.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102062 restraints weight = 27023.301| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27977 Z= 0.117 Angle : 0.632 14.395 38072 Z= 0.316 Chirality : 0.043 0.255 4337 Planarity : 0.004 0.099 4749 Dihedral : 13.339 129.189 4373 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.23 % Allowed : 21.05 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3303 helix: 0.75 (0.15), residues: 1226 sheet: -1.13 (0.28), residues: 331 loop : -1.69 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 293 TYR 0.017 0.001 TYR Q 28 PHE 0.020 0.001 PHE C1025 TRP 0.054 0.003 TRP Q 19 HIS 0.025 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (27971) covalent geometry : angle 0.63212 / 0.32 (38066) hydrogen bonds : bond 0.03888 / 4.18 ( 1165) hydrogen bonds : angle 4.77544 / 4.73 ( 3283) metal coordination : bond 0.00177 / 0.22 ( 6) metal coordination : angle 1.50990 / 2.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 287 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8250 (mmtm) REVERT: A 51 MET cc_start: 0.8215 (mmm) cc_final: 0.7790 (mpp) REVERT: A 185 TYR cc_start: 0.8755 (p90) cc_final: 0.8494 (p90) REVERT: B 104 LYS cc_start: 0.8246 (tptp) cc_final: 0.7953 (tptp) REVERT: B 212 ASP cc_start: 0.7235 (t0) cc_final: 0.6858 (t0) REVERT: C 805 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7980 (ptp) REVERT: C 1014 LEU cc_start: 0.1055 (OUTLIER) cc_final: 0.0797 (tt) REVERT: C 1316 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6960 (tm-30) REVERT: D 29 MET cc_start: 0.8226 (tpp) cc_final: 0.7978 (tpp) REVERT: D 196 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8339 (tp-100) REVERT: D 227 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8627 (m-80) REVERT: D 308 ASP cc_start: 0.8050 (t0) cc_final: 0.7740 (t0) REVERT: D 458 ASN cc_start: 0.8649 (m110) cc_final: 0.8070 (t0) REVERT: D 892 PHE cc_start: 0.7480 (m-80) cc_final: 0.6464 (t80) REVERT: D 982 LEU cc_start: 0.8437 (pp) cc_final: 0.8232 (pt) REVERT: D 1040 MET cc_start: 0.1938 (ptp) cc_final: 0.1317 (pmm) REVERT: D 1241 TYR cc_start: 0.8137 (m-80) cc_final: 0.7837 (m-80) REVERT: E 53 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8218 (mm-30) REVERT: Q 81 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7729 (m-80) outliers start: 63 outliers final: 52 residues processed: 337 average time/residue: 0.1594 time to fit residues: 90.2701 Evaluate side-chains 332 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 15 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 81 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 129 optimal weight: 0.9990 chunk 201 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 86 optimal weight: 0.0000 chunk 128 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 120 optimal weight: 0.0270 chunk 138 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 307 optimal weight: 0.1980 overall best weight: 0.6446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS B 194 GLN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** 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 = 0.3955 r_free = 0.3955 target = 0.142005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103258 restraints weight = 54069.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100079 restraints weight = 42149.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101208 restraints weight = 45023.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101540 restraints weight = 31477.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102111 restraints weight = 27666.586| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27977 Z= 0.115 Angle : 0.630 14.795 38072 Z= 0.315 Chirality : 0.043 0.255 4337 Planarity : 0.004 0.066 4749 Dihedral : 13.292 129.249 4373 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.05 % Allowed : 21.44 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3303 helix: 0.81 (0.15), residues: 1227 sheet: -1.01 (0.28), residues: 336 loop : -1.63 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 293 TYR 0.016 0.001 TYR Q 28 PHE 0.020 0.001 PHE C1025 TRP 0.049 0.003 TRP Q 19 HIS 0.049 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (27971) covalent geometry : angle 0.63016 / 0.32 (38066) hydrogen bonds : bond 0.03811 / 4.08 ( 1165) hydrogen bonds : angle 4.72422 / 4.69 ( 3283) metal coordination : bond 0.00170 / 0.21 ( 6) metal coordination : angle 1.36784 / 2.41 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 283 time to evaluate : 0.907 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 10 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8246 (mmtm) REVERT: A 51 MET cc_start: 0.8159 (mmm) cc_final: 0.7725 (mpp) REVERT: A 185 TYR cc_start: 0.8737 (p90) cc_final: 0.8475 (p90) REVERT: B 104 LYS cc_start: 0.8286 (tptp) cc_final: 0.7986 (tptp) REVERT: C 87 ILE cc_start: 0.8262 (mm) cc_final: 0.7961 (pt) REVERT: C 805 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7975 (ptp) REVERT: C 1014 LEU cc_start: 0.1013 (OUTLIER) cc_final: 0.0765 (tt) REVERT: C 1316 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6957 (tm-30) REVERT: D 29 MET cc_start: 0.8215 (tpp) cc_final: 0.7953 (tpp) REVERT: D 196 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8381 (tp-100) REVERT: D 227 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: D 308 ASP cc_start: 0.8069 (t0) cc_final: 0.7739 (t0) REVERT: D 458 ASN cc_start: 0.8624 (m110) cc_final: 0.8039 (t0) REVERT: D 892 PHE cc_start: 0.7476 (m-80) cc_final: 0.6460 (t80) REVERT: D 982 LEU cc_start: 0.8541 (pp) cc_final: 0.8320 (pt) REVERT: D 1040 MET cc_start: 0.1922 (ptp) cc_final: 0.1254 (pmm) REVERT: D 1241 TYR cc_start: 0.8125 (m-80) cc_final: 0.7817 (m-80) REVERT: D 1244 GLN cc_start: 0.7852 (tp40) cc_final: 0.7562 (mm-40) REVERT: Q 81 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7810 (m-80) outliers start: 58 outliers final: 51 residues processed: 332 average time/residue: 0.1564 time to fit residues: 86.9629 Evaluate side-chains 334 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 279 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 81 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 102 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 209 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 chunk 230 optimal weight: 0.9990 chunk 279 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 HIS B 194 GLN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.141791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.104743 restraints weight = 53068.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102476 restraints weight = 48008.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.103507 restraints weight = 48532.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103801 restraints weight = 33539.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.104594 restraints weight = 29859.174| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27977 Z= 0.119 Angle : 0.635 15.344 38072 Z= 0.316 Chirality : 0.043 0.258 4337 Planarity : 0.004 0.069 4749 Dihedral : 13.266 129.214 4373 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.01 % Allowed : 21.65 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.14), residues: 3303 helix: 0.84 (0.15), residues: 1229 sheet: -0.89 (0.28), residues: 318 loop : -1.59 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 293 TYR 0.017 0.001 TYR Q 28 PHE 0.019 0.001 PHE C1025 TRP 0.050 0.002 TRP D 115 HIS 0.016 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (27971) covalent geometry : angle 0.63463 / 0.32 (38066) hydrogen bonds : bond 0.03791 / 4.06 ( 1165) hydrogen bonds : angle 4.66676 / 4.64 ( 3283) metal coordination : bond 0.00217 / 0.26 ( 6) metal coordination : angle 1.34168 / 2.36 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3994.16 seconds wall clock time: 70 minutes 11.76 seconds (4211.76 seconds total)