Starting phenix.real_space_refine on Sat Sep 12 12:19:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zol_14847/09_2026/7zol_14847.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zol_14847/09_2026/7zol_14847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zol_14847/09_2026/7zol_14847.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zol_14847/09_2026/7zol_14847.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zol_14847/09_2026/7zol_14847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zol_14847/09_2026/7zol_14847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zol_14847/09_2026/7zol_14847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zol_14847/09_2026/7zol_14847.map" } resolution = 3.03 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= 0.041 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 38 5.49 5 S 52 5.16 5 C 9648 2.51 5 N 2736 2.21 5 O 2962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 15440 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 13412 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1702, 13403 Classifications: {'peptide': 1702} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 84, 'TRANS': 1617} Chain breaks: 7 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 551 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 12, 'ARG:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 10, 'GLN:plan1': 3, 'PHE:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 259 Conformer: "B" Number of residues, atoms: 1702, 13403 Classifications: {'peptide': 1702} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 84, 'TRANS': 1617} Chain breaks: 7 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 551 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 12, 'ARG:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 10, 'GLN:plan1': 3, 'PHE:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 259 bond proxies already assigned to first conformer: 13670 Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 813 Classifications: {'RNAv2': 39} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 4, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 17} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1211 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 6, 'TRANS': 143} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7424 SG CYS B 997 52.572 64.921 95.672 1.00 11.39 S ATOM 11124 SG CYS B1515 55.183 64.566 98.350 1.00 11.39 S ATOM 11373 SG CYS B1545 53.764 68.043 97.285 1.00 11.39 S ATOM 11391 SG CYS B1548 51.704 65.738 99.370 1.00 32.20 S ATOM 679 SG CYS B 97 36.980 36.901 188.081 1.00 29.10 S ATOM 954 SG CYS B 131 36.283 33.384 189.576 1.00 42.45 S ATOM 1004 SG CYS B 137 34.131 34.812 186.698 1.00 26.04 S ATOM 1028 SG CYS B 140 37.685 33.867 186.068 1.00 19.90 S ATOM 3726 SG CYS B 498 47.565 57.863 160.556 1.00 18.78 S ATOM 3803 SG CYS B 508 48.651 56.011 163.614 1.00 32.36 S ATOM 3815 SG CYS B 510 46.302 58.939 163.979 1.00 17.63 S ATOM 3835 SG CYS B 513 45.053 55.676 162.419 1.00 11.39 S ATOM 5519 SG CYS B 757 59.105 70.623 133.930 1.00 23.99 S ATOM 5531 SG CYS B 759 55.824 72.415 133.124 1.00 11.39 S ATOM 5552 SG CYS B 762 55.751 68.741 134.169 1.00 11.39 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS B1526 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B1526 " occ=0.50 Time building chain proxies: 5.56, per 1000 atoms: 0.36 Number of scatterers: 15440 At special positions: 0 Unit cell: (94.4906, 105.983, 203.027, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 52 16.00 P 38 15.00 O 2962 8.00 N 2736 7.00 C 9648 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: 1.36 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B1545 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 997 " pdb="ZN ZN B1801 " - pdb=" SG CYS B1548 " pdb="ZN ZN B1801 " - pdb=" SG CYS B1515 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 140 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 97 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 137 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 131 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 508 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 498 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 510 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 513 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" ND1 HIS B 754 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 759 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 757 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 762 " Number of angles added : 21 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 21 sheets defined 34.7% alpha, 13.4% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 68 through 87 removed outlier: 4.078A pdb=" N VAL B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 145 through 148 removed outlier: 3.801A pdb=" N LYS B 148 " --> pdb=" O ARG B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 145 through 148' Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.559A pdb=" N VAL B 181 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 245 Processing helix chain 'B' and resid 291 through 309 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 314 through 329 removed outlier: 4.264A pdb=" N ARG B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 377 removed outlier: 3.530A pdb=" N PHE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 401 Processing helix chain 'B' and resid 478 through 495 removed outlier: 3.540A pdb=" N LEU B 482 " --> pdb=" O PRO B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 517 removed outlier: 4.024A pdb=" N CYS B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 592 removed outlier: 3.543A pdb=" N GLN B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 630 removed outlier: 3.968A pdb=" N THR B 629 " --> pdb=" O LYS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 731 through 748 Processing helix chain 'B' and resid 759 through 765 Processing helix chain 'B' and resid 834 through 851 Processing helix chain 'B' and resid 858 through 862 removed outlier: 3.578A pdb=" N GLY B 862 " --> pdb=" O GLY B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 873 removed outlier: 3.924A pdb=" N HIS B 873 " --> pdb=" O PRO B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 Processing helix chain 'B' and resid 978 through 995 removed outlier: 4.184A pdb=" N ILE B 982 " --> pdb=" O PRO B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1065 removed outlier: 3.698A pdb=" N ASN B1062 " --> pdb=" O ASN B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1084 removed outlier: 3.720A pdb=" N GLU B1080 " --> pdb=" O ASP B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1100 Proline residue: B1097 - end of helix Processing helix chain 'B' and resid 1107 through 1120 Processing helix chain 'B' and resid 1125 through 1133 removed outlier: 3.543A pdb=" N ILE B1129 " --> pdb=" O ASN B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.857A pdb=" N LEU B1145 " --> pdb=" O THR B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1165 removed outlier: 4.021A pdb=" N LEU B1165 " --> pdb=" O GLN B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1184 removed outlier: 3.507A pdb=" N VAL B1184 " --> pdb=" O LEU B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1196 removed outlier: 3.506A pdb=" N LEU B1196 " --> pdb=" O ILE B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1199 No H-bonds generated for 'chain 'B' and resid 1197 through 1199' Processing helix chain 'B' and resid 1206 through 1216 Processing helix chain 'B' and resid 1219 through 1229 removed outlier: 3.796A pdb=" N VAL B1223 " --> pdb=" O PRO B1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 1237 through 1259 removed outlier: 3.774A pdb=" N HIS B1259 " --> pdb=" O LEU B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1274 through 1283 removed outlier: 3.584A pdb=" N LEU B1283 " --> pdb=" O MET B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1431 through 1452 removed outlier: 3.900A pdb=" N GLU B1435 " --> pdb=" O PRO B1431 " (cutoff:3.500A) Processing helix chain 'B' and resid 1500 through 1504 Processing helix chain 'B' and resid 1518 through 1522 removed outlier: 3.952A pdb=" N ASP B1521 " --> pdb=" O GLU B1518 " (cutoff:3.500A) Processing helix chain 'B' and resid 1524 through 1532 Processing helix chain 'B' and resid 1545 through 1552 Processing helix chain 'B' and resid 1574 through 1579 removed outlier: 3.883A pdb=" N ASN B1577 " --> pdb=" O LEU B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1613 through 1621 Processing helix chain 'B' and resid 1659 through 1671 Processing helix chain 'B' and resid 1683 through 1687 Processing helix chain 'B' and resid 1706 through 1723 Processing helix chain 'B' and resid 1726 through 1736 Processing helix chain 'B' and resid 1763 through 1771 removed outlier: 3.606A pdb=" N GLU B1770 " --> pdb=" O GLU B1766 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 33 removed outlier: 3.549A pdb=" N LEU A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 79 removed outlier: 4.209A pdb=" N LYS A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 114 removed outlier: 3.608A pdb=" N LYS A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 123 through 151 removed outlier: 3.553A pdb=" N ILE A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.521A pdb=" N PHE B 29 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG B 189 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 187 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN B 202 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG B 185 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TRP B 204 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP B 183 " --> pdb=" O TRP B 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 123 removed outlier: 5.736A pdb=" N THR B 122 " --> pdb=" O ALA B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 519 through 521 removed outlier: 4.823A pdb=" N GLU B 442 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ASN B 611 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL B 444 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B 609 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.979A pdb=" N LYS B 466 " --> pdb=" O TRP B 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 476 through 477 removed outlier: 3.774A pdb=" N SER B 524 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 534 through 538 Processing sheet with id=AA9, first strand: chain 'B' and resid 653 through 662 removed outlier: 4.828A pdb=" N LYS B 822 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR B 728 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 727 " --> pdb=" O THR B 688 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 653 through 662 Processing sheet with id=AB2, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB3, first strand: chain 'B' and resid 1745 through 1746 removed outlier: 4.781A pdb=" N LYS B1745 " --> pdb=" O LYS B 902 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY B1789 " --> pdb=" O ILE B 903 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 907 through 910 Processing sheet with id=AB5, first strand: chain 'B' and resid 976 through 977 Processing sheet with id=AB6, first strand: chain 'B' and resid 976 through 977 removed outlier: 5.830A pdb=" N TYR B 937 " --> pdb=" O ASN B1657 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU B1697 " --> pdb=" O VAL B 942 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR B 944 " --> pdb=" O VAL B1695 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL B1695 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLU B 946 " --> pdb=" O ILE B1693 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE B1693 " --> pdb=" O GLU B 946 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 954 through 959 removed outlier: 6.747A pdb=" N GLU B 957 " --> pdb=" O ASP B 967 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP B 967 " --> pdb=" O GLU B 957 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 965 " --> pdb=" O GLN B 959 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 3.723A pdb=" N ARG B1476 " --> pdb=" O ASP B1486 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP B1486 " --> pdb=" O ARG B1476 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1044 through 1047 Processing sheet with id=AC1, first strand: chain 'B' and resid 1169 through 1170 removed outlier: 3.633A pdb=" N VAL B1138 " --> pdb=" O TYR B1170 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ARG B1135 " --> pdb=" O ARG B1204 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG B1204 " --> pdb=" O ARG B1135 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LYS B1137 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B1139 " --> pdb=" O ASP B1200 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASP B1200 " --> pdb=" O ARG B1139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1378 through 1379 Processing sheet with id=AC3, first strand: chain 'B' and resid 1581 through 1583 removed outlier: 4.343A pdb=" N ARG B1638 " --> pdb=" O LEU B1583 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 1.84 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: 4452 1.33 - 1.46: 2894 1.46 - 1.58: 8330 1.58 - 1.70: 73 1.70 - 1.82: 75 Bond restraints: 15824 Sorted by residual: bond pdb=" O3' G C 11 " pdb=" P A C 12 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.20e-02 6.94e+03 1.16e+01 bond pdb=" O3' A C 25 " pdb=" P A C 26 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.20e-02 6.94e+03 9.91e+00 bond pdb=" O3' U C 24 " pdb=" P A C 25 " ideal model delta sigma weight residual 1.607 1.577 0.030 1.20e-02 6.94e+03 6.40e+00 bond pdb=" O3' U C 27 " pdb=" P U C 28 " ideal model delta sigma weight residual 1.607 1.578 0.029 1.20e-02 6.94e+03 6.01e+00 bond pdb=" O3' G C 22 " pdb=" P A C 23 " ideal model delta sigma weight residual 1.607 1.578 0.029 1.20e-02 6.94e+03 5.81e+00 ... (remaining 15819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 21051 2.22 - 4.45: 387 4.45 - 6.67: 62 6.67 - 8.90: 21 8.90 - 11.12: 4 Bond angle restraints: 21525 Sorted by residual: angle pdb=" N PRO B 289 " pdb=" CA PRO B 289 " pdb=" CB PRO B 289 " ideal model delta sigma weight residual 103.08 111.52 -8.44 9.70e-01 1.06e+00 7.57e+01 angle pdb=" N PRO B1049 " pdb=" CA PRO B1049 " pdb=" CB PRO B1049 " ideal model delta sigma weight residual 103.25 111.77 -8.52 1.05e+00 9.07e-01 6.58e+01 angle pdb=" N PRO B 277 " pdb=" CA PRO B 277 " pdb=" CB PRO B 277 " ideal model delta sigma weight residual 101.88 109.98 -8.10 1.01e+00 9.80e-01 6.43e+01 angle pdb=" N PRO B1356 " pdb=" CA PRO B1356 " pdb=" CB PRO B1356 " ideal model delta sigma weight residual 103.25 111.65 -8.40 1.05e+00 9.07e-01 6.41e+01 angle pdb=" N PRO B1031 " pdb=" CA PRO B1031 " pdb=" CB PRO B1031 " ideal model delta sigma weight residual 103.25 111.48 -8.23 1.05e+00 9.07e-01 6.14e+01 ... (remaining 21520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 9194 33.71 - 67.42: 349 67.42 - 101.13: 39 101.13 - 134.83: 0 134.83 - 168.54: 1 Dihedral angle restraints: 9583 sinusoidal: 4204 harmonic: 5379 Sorted by residual: dihedral pdb=" C4' G C 10 " pdb=" C3' G C 10 " pdb=" C2' G C 10 " pdb=" C1' G C 10 " ideal model delta sinusoidal sigma weight residual 36.34 -44.01 80.35 1 3.10e+00 1.04e-01 8.32e+02 dihedral pdb=" C4' U C 30 " pdb=" C3' U C 30 " pdb=" C2' U C 30 " pdb=" C1' U C 30 " ideal model delta sinusoidal sigma weight residual 36.34 -39.99 76.34 1 3.10e+00 1.04e-01 7.63e+02 dihedral pdb=" C4' A C 12 " pdb=" C3' A C 12 " pdb=" C2' A C 12 " pdb=" C1' A C 12 " ideal model delta sinusoidal sigma weight residual 36.34 -38.62 74.97 1 3.10e+00 1.04e-01 7.40e+02 ... (remaining 9580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2124 0.085 - 0.171: 174 0.171 - 0.256: 59 0.256 - 0.341: 23 0.341 - 0.427: 6 Chirality restraints: 2386 Sorted by residual: chirality pdb=" P G C 11 " pdb=" OP1 G C 11 " pdb=" OP2 G C 11 " pdb=" O5' G C 11 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" P G C 21 " pdb=" OP1 G C 21 " pdb=" OP2 G C 21 " pdb=" O5' G C 21 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C3' U C 27 " pdb=" C4' U C 27 " pdb=" O3' U C 27 " pdb=" C2' U C 27 " both_signs ideal model delta sigma weight residual False -2.50 -2.92 0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 2383 not shown) Planarity restraints: 2643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B1468 " 0.057 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO B1469 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B1469 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B1469 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 345 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO B 346 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 346 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 346 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 816 " 0.040 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO B 817 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 817 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 817 " 0.034 5.00e-02 4.00e+02 ... (remaining 2640 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1814 2.75 - 3.29: 14328 3.29 - 3.83: 23569 3.83 - 4.36: 28037 4.36 - 4.90: 48551 Nonbonded interactions: 116299 Sorted by model distance: nonbonded pdb=" O PRO B 923 " pdb=" OH TYR B1556 " model vdw 2.216 3.040 nonbonded pdb=" OE2 GLU B 935 " pdb=" NZ LYS B1703 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASN A 78 " pdb=" NH2 ARG A 81 " model vdw 2.255 3.120 nonbonded pdb=" O LEU B 317 " pdb=" OG1 THR B 321 " model vdw 2.297 3.040 nonbonded pdb=" O LYS B1449 " pdb=" NZ LYS B1452 " model vdw 2.308 3.120 ... (remaining 116294 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.750 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 : 0.003 0.041 15840 Z= 0.148 Angle : 0.715 11.124 21546 Z= 0.375 Chirality : 0.064 0.427 2386 Planarity : 0.005 0.088 2643 Dihedral : 17.096 168.543 6091 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.54 % Favored : 92.64 % Rotamer: Outliers : 0.20 % Allowed : 0.26 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.20), residues: 1837 helix: 1.48 (0.22), residues: 593 sheet: 0.81 (0.38), residues: 202 loop : -1.73 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1588 TYR 0.018 0.001 TYR B1444 PHE 0.009 0.001 PHE B 808 TRP 0.009 0.001 TRP B1788 HIS 0.002 0.001 HIS B 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (15824) covalent geometry : angle 0.71218 / 0.38 (21525) hydrogen bonds : bond 0.21720 / 14.51 ( 514) hydrogen bonds : angle 6.55994 / 4.57 ( 1485) metal coordination : bond 0.00488 / 0.27 ( 16) metal coordination : angle 2.28087 / 1.60 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.584 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1321 time to fit residues: 25.1286 Evaluate side-chains 94 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 GLN ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 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 = 0.4273 r_free = 0.4273 target = 0.184713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132759 restraints weight = 42274.353| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.79 r_work: 0.3514 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 15840 Z= 0.297 Angle : 1.114 19.370 21546 Z= 0.492 Chirality : 0.105 1.582 2386 Planarity : 0.007 0.077 2643 Dihedral : 12.684 149.511 2464 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.52 % Favored : 91.77 % Rotamer: Outliers : 0.98 % Allowed : 6.30 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.19), residues: 1837 helix: 1.08 (0.22), residues: 588 sheet: 0.17 (0.37), residues: 198 loop : -2.02 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 983 TYR 0.017 0.002 TYR B 435 PHE 0.027 0.003 PHE B 855 TRP 0.016 0.002 TRP B 588 HIS 0.007 0.002 HIS B1611 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.30 (15824) covalent geometry : angle 1.11152 / 0.49 (21525) hydrogen bonds : bond 0.06183 / 4.14 ( 514) hydrogen bonds : angle 5.20651 / 3.66 ( 1485) metal coordination : bond 0.01308 / 0.73 ( 16) metal coordination : angle 2.82090 / 1.83 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.622 Fit side-chains REVERT: B 901 ASP cc_start: 0.8183 (t0) cc_final: 0.7932 (t0) REVERT: B 1109 GLU cc_start: 0.6087 (mp0) cc_final: 0.5594 (tt0) REVERT: B 1715 MET cc_start: 0.8501 (mmm) cc_final: 0.8257 (tpt) REVERT: A 28 LEU cc_start: 0.7829 (mt) cc_final: 0.7576 (mm) outliers start: 13 outliers final: 11 residues processed: 111 average time/residue: 0.1241 time to fit residues: 21.6130 Evaluate side-chains 98 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1279 MET Chi-restraints excluded: chain B residue 1379 ILE Chi-restraints excluded: chain A residue 23 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 118 optimal weight: 7.9990 chunk 153 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.190008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144646 restraints weight = 47844.235| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 4.60 r_work: 0.3569 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15840 Z= 0.137 Angle : 0.791 11.835 21546 Z= 0.356 Chirality : 0.073 1.243 2386 Planarity : 0.005 0.065 2643 Dihedral : 12.712 151.340 2464 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.65 % Favored : 92.69 % Rotamer: Outliers : 0.92 % Allowed : 8.20 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.19), residues: 1837 helix: 1.45 (0.22), residues: 591 sheet: 0.45 (0.37), residues: 200 loop : -1.92 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.011 0.001 TYR B1772 PHE 0.015 0.001 PHE B1475 TRP 0.011 0.001 TRP B1788 HIS 0.002 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (15824) covalent geometry : angle 0.78861 / 0.36 (21525) hydrogen bonds : bond 0.04159 / 2.80 ( 514) hydrogen bonds : angle 4.58621 / 3.25 ( 1485) metal coordination : bond 0.00414 / 0.26 ( 16) metal coordination : angle 2.12780 / 1.40 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.567 Fit side-chains REVERT: B 871 LEU cc_start: 0.7681 (mp) cc_final: 0.7472 (mt) REVERT: B 901 ASP cc_start: 0.8266 (t0) cc_final: 0.7984 (t0) REVERT: B 1109 GLU cc_start: 0.5968 (mp0) cc_final: 0.5640 (tt0) REVERT: B 1239 LYS cc_start: 0.4435 (OUTLIER) cc_final: 0.3892 (pttp) REVERT: B 1409 TYR cc_start: 0.5203 (m-10) cc_final: 0.4670 (m-10) REVERT: B 1520 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5196 (mt) REVERT: B 1715 MET cc_start: 0.8501 (mmm) cc_final: 0.8234 (tpt) REVERT: B 1769 LYS cc_start: 0.8426 (mmtp) cc_final: 0.8071 (mmmt) outliers start: 12 outliers final: 6 residues processed: 110 average time/residue: 0.1335 time to fit residues: 22.4759 Evaluate side-chains 102 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1239 LYS Chi-restraints excluded: chain B residue 1520 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 72 optimal weight: 0.0010 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 ASN ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1220 GLN ** B1271 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 = 0.4337 r_free = 0.4337 target = 0.191127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144920 restraints weight = 44897.804| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 4.27 r_work: 0.3590 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15840 Z= 0.122 Angle : 0.728 11.588 21546 Z= 0.330 Chirality : 0.065 1.061 2386 Planarity : 0.005 0.062 2643 Dihedral : 12.457 153.214 2464 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.76 % Favored : 92.58 % Rotamer: Outliers : 1.12 % Allowed : 9.06 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.19), residues: 1837 helix: 1.63 (0.22), residues: 598 sheet: 0.58 (0.38), residues: 199 loop : -1.88 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 483 TYR 0.011 0.001 TYR B1409 PHE 0.011 0.001 PHE B 806 TRP 0.014 0.001 TRP B 437 HIS 0.002 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (15824) covalent geometry : angle 0.72476 / 0.33 (21525) hydrogen bonds : bond 0.03615 / 2.43 ( 514) hydrogen bonds : angle 4.29161 / 3.05 ( 1485) metal coordination : bond 0.00418 / 0.25 ( 16) metal coordination : angle 2.39364 / 1.54 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.625 Fit side-chains REVERT: B 199 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7458 (p0) REVERT: B 334 ASP cc_start: 0.8528 (t70) cc_final: 0.8269 (t0) REVERT: B 829 ILE cc_start: 0.8588 (pt) cc_final: 0.8284 (mt) REVERT: B 901 ASP cc_start: 0.8296 (t0) cc_final: 0.8059 (t0) REVERT: B 1109 GLU cc_start: 0.5976 (mp0) cc_final: 0.5600 (tt0) REVERT: B 1409 TYR cc_start: 0.5458 (m-10) cc_final: 0.4949 (m-10) REVERT: B 1715 MET cc_start: 0.8531 (mmm) cc_final: 0.8246 (tpt) REVERT: B 1769 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7923 (mmmt) REVERT: A 35 GLU cc_start: 0.7577 (pm20) cc_final: 0.7237 (pm20) REVERT: A 63 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7356 (tp40) outliers start: 15 outliers final: 9 residues processed: 109 average time/residue: 0.1329 time to fit residues: 22.1814 Evaluate side-chains 108 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 176 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 181 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1580 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.190026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143603 restraints weight = 43763.386| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 4.17 r_work: 0.3582 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15840 Z= 0.131 Angle : 0.735 11.725 21546 Z= 0.333 Chirality : 0.064 0.978 2386 Planarity : 0.005 0.059 2643 Dihedral : 12.510 151.732 2464 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.03 % Favored : 92.37 % Rotamer: Outliers : 1.12 % Allowed : 10.30 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.20), residues: 1837 helix: 1.67 (0.22), residues: 598 sheet: 0.67 (0.37), residues: 206 loop : -1.91 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 483 TYR 0.009 0.001 TYR B1772 PHE 0.010 0.001 PHE B1651 TRP 0.011 0.001 TRP B1788 HIS 0.003 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15824) covalent geometry : angle 0.73231 / 0.33 (21525) hydrogen bonds : bond 0.03667 / 2.47 ( 514) hydrogen bonds : angle 4.27110 / 3.03 ( 1485) metal coordination : bond 0.00467 / 0.29 ( 16) metal coordination : angle 2.27936 / 1.47 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.578 Fit side-chains REVERT: B 199 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7259 (p0) REVERT: B 325 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7069 (mt) REVERT: B 334 ASP cc_start: 0.8545 (t70) cc_final: 0.8249 (t0) REVERT: B 829 ILE cc_start: 0.8572 (pt) cc_final: 0.8236 (mt) REVERT: B 901 ASP cc_start: 0.8326 (t0) cc_final: 0.8051 (t0) REVERT: B 1109 GLU cc_start: 0.5968 (mp0) cc_final: 0.5645 (tt0) REVERT: B 1409 TYR cc_start: 0.5461 (m-10) cc_final: 0.4897 (m-10) REVERT: B 1715 MET cc_start: 0.8425 (mmm) cc_final: 0.8145 (tpt) REVERT: B 1769 LYS cc_start: 0.7974 (mmtp) cc_final: 0.7749 (mmmt) REVERT: A 35 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6977 (pm20) REVERT: A 63 GLN cc_start: 0.7444 (tp40) cc_final: 0.7119 (tp40) outliers start: 15 outliers final: 12 residues processed: 108 average time/residue: 0.1352 time to fit residues: 22.6073 Evaluate side-chains 112 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1279 MET Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 54 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 105 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1198 ASN ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.186672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140801 restraints weight = 48765.076| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 4.45 r_work: 0.3536 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15840 Z= 0.172 Angle : 0.794 12.608 21546 Z= 0.361 Chirality : 0.069 1.045 2386 Planarity : 0.005 0.056 2643 Dihedral : 12.836 153.216 2464 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.63 % Favored : 91.77 % Rotamer: Outliers : 1.25 % Allowed : 11.15 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.19), residues: 1837 helix: 1.52 (0.22), residues: 598 sheet: 0.45 (0.37), residues: 208 loop : -1.97 (0.17), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 118 TYR 0.010 0.001 TYR B1772 PHE 0.015 0.002 PHE B 735 TRP 0.015 0.001 TRP B1788 HIS 0.003 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (15824) covalent geometry : angle 0.79049 / 0.36 (21525) hydrogen bonds : bond 0.04253 / 2.85 ( 514) hydrogen bonds : angle 4.42856 / 3.13 ( 1485) metal coordination : bond 0.00759 / 0.44 ( 16) metal coordination : angle 2.49305 / 1.63 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.500 Fit side-chains REVERT: B 325 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7163 (mt) REVERT: B 829 ILE cc_start: 0.8560 (pt) cc_final: 0.8278 (mt) REVERT: B 901 ASP cc_start: 0.8345 (t0) cc_final: 0.8085 (t0) REVERT: B 1409 TYR cc_start: 0.5581 (m-10) cc_final: 0.4881 (m-10) REVERT: B 1715 MET cc_start: 0.8468 (mmm) cc_final: 0.8252 (tpt) REVERT: A 35 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: A 63 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7170 (tp40) outliers start: 17 outliers final: 14 residues processed: 106 average time/residue: 0.1313 time to fit residues: 21.4529 Evaluate side-chains 106 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1619 LYS Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 181 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 400 GLN ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.184254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141047 restraints weight = 52681.334| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.66 r_work: 0.3485 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15840 Z= 0.211 Angle : 0.842 13.609 21546 Z= 0.385 Chirality : 0.073 1.213 2386 Planarity : 0.006 0.057 2643 Dihedral : 12.976 156.306 2464 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.18 % Favored : 91.11 % Rotamer: Outliers : 1.57 % Allowed : 11.29 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.19), residues: 1837 helix: 1.33 (0.22), residues: 596 sheet: 0.20 (0.37), residues: 206 loop : -2.08 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 483 TYR 0.011 0.002 TYR B1409 PHE 0.017 0.002 PHE B 735 TRP 0.019 0.002 TRP B 292 HIS 0.005 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (15824) covalent geometry : angle 0.83750 / 0.39 (21525) hydrogen bonds : bond 0.04688 / 3.16 ( 514) hydrogen bonds : angle 4.62480 / 3.26 ( 1485) metal coordination : bond 0.00814 / 0.47 ( 16) metal coordination : angle 2.80372 / 1.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.624 Fit side-chains REVERT: B 325 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7378 (mt) REVERT: B 813 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8280 (mp) REVERT: B 901 ASP cc_start: 0.8402 (t0) cc_final: 0.8101 (t0) REVERT: A 63 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6877 (tp40) outliers start: 22 outliers final: 11 residues processed: 106 average time/residue: 0.1252 time to fit residues: 20.6998 Evaluate side-chains 103 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1619 LYS Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 63 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 187 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 chunk 170 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 154 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.186261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141643 restraints weight = 49192.512| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 4.50 r_work: 0.3529 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15840 Z= 0.151 Angle : 0.770 12.240 21546 Z= 0.350 Chirality : 0.067 1.132 2386 Planarity : 0.005 0.056 2643 Dihedral : 12.881 152.331 2464 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.52 % Favored : 91.82 % Rotamer: Outliers : 1.44 % Allowed : 11.75 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.19), residues: 1837 helix: 1.43 (0.22), residues: 599 sheet: 0.27 (0.37), residues: 208 loop : -2.06 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 483 TYR 0.011 0.001 TYR B1409 PHE 0.013 0.001 PHE B 968 TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15824) covalent geometry : angle 0.76651 / 0.35 (21525) hydrogen bonds : bond 0.04013 / 2.71 ( 514) hydrogen bonds : angle 4.45158 / 3.15 ( 1485) metal coordination : bond 0.00602 / 0.35 ( 16) metal coordination : angle 2.54370 / 1.69 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.594 Fit side-chains REVERT: B 118 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8041 (mtt90) REVERT: B 325 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7391 (mt) REVERT: B 550 LYS cc_start: 0.8111 (tppt) cc_final: 0.7869 (tppt) REVERT: B 813 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 901 ASP cc_start: 0.8381 (t0) cc_final: 0.8095 (t0) REVERT: A 63 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7039 (tp40) outliers start: 20 outliers final: 15 residues processed: 106 average time/residue: 0.1315 time to fit residues: 21.3918 Evaluate side-chains 104 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1279 MET Chi-restraints excluded: chain B residue 1619 LYS Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 63 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 35 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1372 ASN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.186283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141506 restraints weight = 48819.338| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 4.58 r_work: 0.3527 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15840 Z= 0.157 Angle : 0.768 12.249 21546 Z= 0.350 Chirality : 0.066 1.090 2386 Planarity : 0.005 0.057 2643 Dihedral : 12.825 152.923 2464 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.85 % Favored : 91.55 % Rotamer: Outliers : 1.51 % Allowed : 12.07 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.20), residues: 1837 helix: 1.45 (0.22), residues: 599 sheet: 0.21 (0.37), residues: 210 loop : -2.03 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.011 0.001 TYR B1409 PHE 0.013 0.001 PHE B 968 TRP 0.016 0.001 TRP B 437 HIS 0.003 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (15824) covalent geometry : angle 0.76448 / 0.35 (21525) hydrogen bonds : bond 0.03967 / 2.67 ( 514) hydrogen bonds : angle 4.41433 / 3.12 ( 1485) metal coordination : bond 0.00606 / 0.36 ( 16) metal coordination : angle 2.58122 / 1.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: B 118 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7972 (mtt90) REVERT: B 325 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7455 (mt) REVERT: B 813 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8280 (mp) REVERT: B 901 ASP cc_start: 0.8402 (t0) cc_final: 0.8120 (t0) REVERT: A 63 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7086 (tp40) outliers start: 21 outliers final: 16 residues processed: 103 average time/residue: 0.1343 time to fit residues: 21.1196 Evaluate side-chains 108 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1279 MET Chi-restraints excluded: chain B residue 1372 ASN Chi-restraints excluded: chain B residue 1619 LYS Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 63 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 147 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1372 ASN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.186019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138191 restraints weight = 37957.248| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 4.12 r_work: 0.3540 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 15840 Z= 0.218 Angle : 0.943 59.199 21546 Z= 0.487 Chirality : 0.068 1.103 2386 Planarity : 0.005 0.057 2643 Dihedral : 12.837 152.950 2464 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.80 % Favored : 91.55 % Rotamer: Outliers : 1.44 % Allowed : 12.27 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.20), residues: 1837 helix: 1.44 (0.22), residues: 599 sheet: 0.42 (0.38), residues: 200 loop : -2.06 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 118 TYR 0.015 0.002 TYR B1064 PHE 0.012 0.002 PHE B 968 TRP 0.015 0.002 TRP B 437 HIS 0.004 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (15824) covalent geometry : angle 0.93993 / 0.49 (21525) hydrogen bonds : bond 0.04055 / 2.73 ( 514) hydrogen bonds : angle 4.41523 / 3.12 ( 1485) metal coordination : bond 0.00698 / 0.42 ( 16) metal coordination : angle 2.57732 / 1.71 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: B 118 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7959 (mtt90) REVERT: B 325 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7440 (mt) REVERT: B 813 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8265 (mp) REVERT: B 901 ASP cc_start: 0.8370 (t0) cc_final: 0.8094 (t0) REVERT: A 63 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7105 (tp40) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.1266 time to fit residues: 20.3933 Evaluate side-chains 107 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1279 MET Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 63 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 184 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 128 optimal weight: 50.0000 chunk 105 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.186015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140954 restraints weight = 49878.293| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 4.49 r_work: 0.3520 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 15840 Z= 0.218 Angle : 0.943 59.199 21546 Z= 0.487 Chirality : 0.068 1.103 2386 Planarity : 0.005 0.057 2643 Dihedral : 12.837 152.950 2464 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.80 % Favored : 91.55 % Rotamer: Outliers : 1.38 % Allowed : 12.40 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.20), residues: 1837 helix: 1.44 (0.22), residues: 599 sheet: 0.42 (0.38), residues: 200 loop : -2.06 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 118 TYR 0.015 0.002 TYR B1064 PHE 0.012 0.002 PHE B 968 TRP 0.015 0.002 TRP B 437 HIS 0.004 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (15824) covalent geometry : angle 0.93993 / 0.49 (21525) hydrogen bonds : bond 0.04055 / 2.73 ( 514) hydrogen bonds : angle 4.41523 / 3.12 ( 1485) metal coordination : bond 0.00698 / 0.42 ( 16) metal coordination : angle 2.57732 / 1.71 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4564.48 seconds wall clock time: 79 minutes 7.54 seconds (4747.54 seconds total)