Starting phenix.real_space_refine on Sun Jul 21 21:42:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zol_14847/07_2024/7zol_14847_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zol_14847/07_2024/7zol_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zol_14847/07_2024/7zol_14847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zol_14847/07_2024/7zol_14847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zol_14847/07_2024/7zol_14847_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zol_14847/07_2024/7zol_14847_neut.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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 Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ASP 334": "OD1" <-> "OD2" Residue "B ASP 523": "OD1" <-> "OD2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 756": "OD1" <-> "OD2" Residue "B PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1277": "OD1" <-> "OD2" Residue "B GLU 1397": "OE1" <-> "OE2" Residue "B GLU 1518": "OE1" <-> "OE2" Residue "B PHE 1607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1775": "OE1" <-> "OE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 8} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 8} 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: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 4, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 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: 15.73, per 1000 atoms: 1.02 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 - 3.50 Amino acid : False - 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: 6.29 Conformation dependent library (CDL) restraints added in 5.7 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: 5.14 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: 5.86 Time building geometry restraints manager: 6.89 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 1.50e-02 4.44e+03 7.42e+00 bond pdb=" O3' A C 25 " pdb=" P A C 26 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.50e-02 4.44e+03 6.34e+00 bond pdb=" O3' U C 24 " pdb=" P A C 25 " ideal model delta sigma weight residual 1.607 1.577 0.030 1.50e-02 4.44e+03 4.10e+00 bond pdb=" CA LEU B1520 " pdb=" C LEU B1520 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.34e-02 5.57e+03 3.96e+00 bond pdb=" O3' U C 27 " pdb=" P U C 28 " ideal model delta sigma weight residual 1.607 1.578 0.029 1.50e-02 4.44e+03 3.85e+00 ... (remaining 15819 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.66: 445 105.66 - 112.74: 8473 112.74 - 119.82: 5119 119.82 - 126.91: 7220 126.91 - 133.99: 268 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 - 35.71: 9421 35.71 - 71.42: 266 71.42 - 107.13: 22 107.13 - 142.84: 2 142.84 - 178.56: 8 Dihedral angle restraints: 9719 sinusoidal: 4340 harmonic: 5379 Sorted by residual: dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual 200.00 21.44 178.56 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U C 16 " pdb=" C1' U C 16 " pdb=" N1 U C 16 " pdb=" C2 U C 16 " ideal model delta sinusoidal sigma weight residual 200.00 29.08 170.92 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U C 24 " pdb=" C1' U C 24 " pdb=" N1 U C 24 " pdb=" C2 U C 24 " ideal model delta sinusoidal sigma weight residual 200.00 36.74 163.26 1 1.50e+01 4.44e-03 8.35e+01 ... (remaining 9716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2153 0.078 - 0.156: 209 0.156 - 0.234: 20 0.234 - 0.312: 2 0.312 - 0.389: 2 Chirality restraints: 2386 Sorted by residual: chirality pdb=" C1' C C 15 " pdb=" O4' C C 15 " pdb=" C2' C C 15 " pdb=" N1 C C 15 " both_signs ideal model delta sigma weight residual False 2.45 2.06 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" C1' U C 27 " pdb=" O4' U C 27 " pdb=" C2' U C 27 " pdb=" N1 U C 27 " both_signs ideal model delta sigma weight residual False 2.45 2.12 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA PRO B1345 " pdb=" N PRO B1345 " pdb=" C PRO B1345 " pdb=" CB PRO B1345 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.83e+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 2.440 nonbonded pdb=" OE2 GLU B 935 " pdb=" NZ LYS B1703 " model vdw 2.233 2.520 nonbonded pdb=" OD1 ASN A 78 " pdb=" NH2 ARG A 81 " model vdw 2.255 2.520 nonbonded pdb=" O LEU B 317 " pdb=" OG1 THR B 321 " model vdw 2.297 2.440 nonbonded pdb=" O LYS B1449 " pdb=" NZ LYS B1452 " model vdw 2.308 2.520 ... (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 ========== 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: 1.030 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 60.440 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 15824 Z= 0.167 Angle : 0.642 9.524 21525 Z= 0.382 Chirality : 0.047 0.389 2386 Planarity : 0.005 0.088 2643 Dihedral : 17.391 178.556 6227 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (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 TRP 0.009 0.001 TRP B1788 HIS 0.002 0.001 HIS B 754 PHE 0.009 0.001 PHE B 808 TYR 0.018 0.001 TYR B1444 ARG 0.005 0.000 ARG B1588 *********************** 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 fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.696 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2820 time to fit residues: 53.4871 Evaluate side-chains 94 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 0.2980 chunk 76 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 GLN ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15824 Z= 0.154 Angle : 0.586 11.060 21525 Z= 0.294 Chirality : 0.043 0.285 2386 Planarity : 0.005 0.075 2643 Dihedral : 16.074 179.418 2600 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.49 % Favored : 92.86 % Rotamer: Outliers : 0.79 % Allowed : 3.94 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1837 helix: 1.67 (0.22), residues: 595 sheet: 0.67 (0.38), residues: 205 loop : -1.72 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 382 HIS 0.003 0.001 HIS B 754 PHE 0.010 0.001 PHE B 350 TYR 0.010 0.001 TYR B1375 ARG 0.004 0.000 ARG B1588 *********************** 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 117 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.871 Fit side-chains REVERT: B 1239 LYS cc_start: 0.5614 (OUTLIER) cc_final: 0.5364 (ptpp) outliers start: 10 outliers final: 8 residues processed: 111 average time/residue: 0.2686 time to fit residues: 47.3635 Evaluate side-chains 103 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 1.933 ------------------------------------------------------------------------------- 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 386 CYS 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 A residue 23 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 47 optimal weight: 0.4980 chunk 171 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 GLN B1126 GLN ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1445 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15824 Z= 0.273 Angle : 0.655 10.001 21525 Z= 0.331 Chirality : 0.047 0.395 2386 Planarity : 0.005 0.065 2643 Dihedral : 16.215 179.929 2600 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.52 % Favored : 91.82 % Rotamer: Outliers : 0.85 % Allowed : 6.96 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.19), residues: 1837 helix: 1.50 (0.22), residues: 591 sheet: 0.42 (0.37), residues: 205 loop : -1.91 (0.17), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1788 HIS 0.004 0.001 HIS B 754 PHE 0.017 0.002 PHE B 735 TYR 0.012 0.002 TYR B 435 ARG 0.006 0.001 ARG B1588 *********************** 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 116 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: B 1128 MET cc_start: 0.6373 (pmm) cc_final: 0.6138 (pmm) outliers start: 11 outliers final: 9 residues processed: 109 average time/residue: 0.2594 time to fit residues: 44.1643 Evaluate side-chains 105 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 991 GLU Chi-restraints excluded: chain B residue 1279 MET Chi-restraints excluded: chain A residue 23 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1126 GLN ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15824 Z= 0.235 Angle : 0.622 10.527 21525 Z= 0.313 Chirality : 0.045 0.345 2386 Planarity : 0.005 0.057 2643 Dihedral : 16.162 179.810 2600 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.42 % Favored : 91.93 % Rotamer: Outliers : 1.18 % Allowed : 8.66 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1837 helix: 1.51 (0.22), residues: 592 sheet: 0.30 (0.36), residues: 205 loop : -1.95 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1788 HIS 0.004 0.001 HIS B 907 PHE 0.013 0.002 PHE B 855 TYR 0.010 0.001 TYR B1409 ARG 0.006 0.001 ARG B1588 *********************** 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 116 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: B 516 MET cc_start: 0.8274 (mmm) cc_final: 0.7925 (mmm) REVERT: B 1128 MET cc_start: 0.6309 (pmm) cc_final: 0.5961 (pmm) REVERT: B 1715 MET cc_start: 0.7831 (tpt) cc_final: 0.7571 (mmt) outliers start: 16 outliers final: 13 residues processed: 106 average time/residue: 0.2517 time to fit residues: 42.3502 Evaluate side-chains 108 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 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 657 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 GLN B1126 GLN B1220 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15824 Z= 0.160 Angle : 0.592 12.764 21525 Z= 0.293 Chirality : 0.043 0.292 2386 Planarity : 0.005 0.055 2643 Dihedral : 16.038 178.795 2600 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.52 % Favored : 91.88 % Rotamer: Outliers : 1.18 % Allowed : 9.71 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.19), residues: 1837 helix: 1.69 (0.23), residues: 592 sheet: 0.38 (0.37), residues: 202 loop : -1.91 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 437 HIS 0.002 0.001 HIS B 907 PHE 0.009 0.001 PHE B 806 TYR 0.010 0.001 TYR B1409 ARG 0.006 0.000 ARG B1588 *********************** 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 118 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: B 1239 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5663 (ptpp) REVERT: B 1269 ARG cc_start: 0.4305 (mtp180) cc_final: 0.4045 (mtp180) REVERT: B 1715 MET cc_start: 0.7881 (tpt) cc_final: 0.7603 (mmt) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.2598 time to fit residues: 44.3543 Evaluate side-chains 108 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 375 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 985 MET Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1239 LYS Chi-restraints excluded: chain B residue 1279 MET Chi-restraints excluded: chain B residue 1619 LYS Chi-restraints excluded: chain A residue 28 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 150 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 15 optimal weight: 0.0570 chunk 60 optimal weight: 0.0030 chunk 95 optimal weight: 2.9990 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 ASN B1126 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15824 Z= 0.127 Angle : 0.555 12.346 21525 Z= 0.272 Chirality : 0.041 0.216 2386 Planarity : 0.004 0.059 2643 Dihedral : 15.857 178.266 2600 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.71 % Favored : 92.69 % Rotamer: Outliers : 1.18 % Allowed : 10.17 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1837 helix: 1.74 (0.22), residues: 607 sheet: 1.04 (0.40), residues: 176 loop : -1.81 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 437 HIS 0.002 0.000 HIS B1610 PHE 0.008 0.001 PHE B 350 TYR 0.010 0.001 TYR B1409 ARG 0.006 0.000 ARG B1588 *********************** 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 123 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.734 Fit side-chains REVERT: B 516 MET cc_start: 0.8071 (mmm) cc_final: 0.7855 (mmm) REVERT: B 1128 MET cc_start: 0.6391 (pmm) cc_final: 0.5935 (pmm) REVERT: B 1411 MET cc_start: 0.5950 (ttt) cc_final: 0.5733 (ttt) outliers start: 16 outliers final: 11 residues processed: 114 average time/residue: 0.2613 time to fit residues: 46.6078 Evaluate side-chains 107 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 248 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 985 MET Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1279 MET Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 54 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 0.0020 chunk 103 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 0.0020 chunk 101 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 83 optimal weight: 0.0010 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 GLN B1126 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1580 HIS A 133 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15824 Z= 0.222 Angle : 0.612 11.766 21525 Z= 0.305 Chirality : 0.044 0.338 2386 Planarity : 0.005 0.057 2643 Dihedral : 15.963 179.927 2600 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.69 % Favored : 91.71 % Rotamer: Outliers : 1.05 % Allowed : 10.63 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1837 helix: 1.70 (0.22), residues: 600 sheet: 0.45 (0.38), residues: 201 loop : -1.88 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 437 HIS 0.003 0.001 HIS B 907 PHE 0.013 0.001 PHE B 735 TYR 0.012 0.001 TYR B1409 ARG 0.004 0.000 ARG B 983 *********************** 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 105 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.733 Fit side-chains REVERT: B 1128 MET cc_start: 0.6380 (pmm) cc_final: 0.5874 (pmm) REVERT: B 1715 MET cc_start: 0.7784 (tpt) cc_final: 0.7513 (mmt) outliers start: 14 outliers final: 13 residues processed: 95 average time/residue: 0.2606 time to fit residues: 39.1439 Evaluate side-chains 99 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 375 ASP Chi-restraints excluded: chain B residue 985 MET Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1279 MET Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 54 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 123 optimal weight: 30.0000 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1126 GLN B1198 ASN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15824 Z= 0.324 Angle : 0.696 11.779 21525 Z= 0.350 Chirality : 0.048 0.406 2386 Planarity : 0.005 0.058 2643 Dihedral : 16.177 179.473 2600 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.51 % Favored : 90.89 % Rotamer: Outliers : 0.98 % Allowed : 11.09 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1837 helix: 1.39 (0.22), residues: 593 sheet: 0.11 (0.37), residues: 199 loop : -2.03 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 437 HIS 0.005 0.001 HIS B 907 PHE 0.017 0.002 PHE B 735 TYR 0.015 0.002 TYR B1409 ARG 0.007 0.001 ARG B 983 *********************** 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 108 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.841 Fit side-chains REVERT: B 1225 MET cc_start: 0.3738 (mpt) cc_final: 0.3511 (mpp) REVERT: B 1715 MET cc_start: 0.7833 (tpt) cc_final: 0.7621 (mmt) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.2579 time to fit residues: 41.7875 Evaluate side-chains 96 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 375 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1453 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 23 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15824 Z= 0.196 Angle : 0.619 11.961 21525 Z= 0.308 Chirality : 0.044 0.318 2386 Planarity : 0.005 0.054 2643 Dihedral : 15.961 179.989 2600 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.58 % Favored : 91.77 % Rotamer: Outliers : 0.92 % Allowed : 11.75 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1837 helix: 1.51 (0.22), residues: 600 sheet: 0.16 (0.37), residues: 203 loop : -1.99 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 437 HIS 0.004 0.001 HIS B 907 PHE 0.027 0.001 PHE B 808 TYR 0.011 0.001 TYR B1409 ARG 0.003 0.000 ARG B 983 *********************** 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 102 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.748 Fit side-chains REVERT: B 1225 MET cc_start: 0.4267 (mpt) cc_final: 0.4020 (mpp) REVERT: B 1715 MET cc_start: 0.7785 (tpt) cc_final: 0.7506 (mmt) outliers start: 12 outliers final: 10 residues processed: 95 average time/residue: 0.2666 time to fit residues: 39.9022 Evaluate side-chains 98 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.759 ------------------------------------------------------------------------------- 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 657 THR Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 124 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 782 GLN ** B1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 15824 Z= 0.468 Angle : 0.808 13.494 21525 Z= 0.409 Chirality : 0.053 0.524 2386 Planarity : 0.007 0.062 2643 Dihedral : 16.354 179.608 2600 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.27 % Favored : 89.91 % Rotamer: Outliers : 0.79 % Allowed : 11.88 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.19), residues: 1837 helix: 1.04 (0.22), residues: 595 sheet: 0.00 (0.37), residues: 196 loop : -2.31 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 437 HIS 0.007 0.002 HIS B1611 PHE 0.052 0.003 PHE B 808 TYR 0.017 0.002 TYR B 435 ARG 0.011 0.001 ARG B 983 ********************** 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 103 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.755 Fit side-chains REVERT: B 1225 MET cc_start: 0.4176 (mpt) cc_final: 0.3911 (mpp) REVERT: B 1715 MET cc_start: 0.7852 (tpt) cc_final: 0.7645 (mmt) outliers start: 10 outliers final: 8 residues processed: 98 average time/residue: 0.2511 time to fit residues: 39.3764 Evaluate side-chains 93 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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 375 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 991 GLU Chi-restraints excluded: chain B residue 1467 LEU Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.8980 chunk 137 optimal weight: 0.0020 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 153 optimal weight: 0.0000 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 GLN ** B1447 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 = 0.4287 r_free = 0.4287 target = 0.185965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.134326 restraints weight = 47697.443| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.69 r_work: 0.3544 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15824 Z= 0.155 Angle : 0.612 12.321 21525 Z= 0.306 Chirality : 0.044 0.258 2386 Planarity : 0.005 0.056 2643 Dihedral : 15.972 179.826 2600 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.03 % Favored : 92.26 % Rotamer: Outliers : 0.52 % Allowed : 12.40 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1837 helix: 1.46 (0.22), residues: 599 sheet: -0.01 (0.37), residues: 203 loop : -2.07 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 437 HIS 0.002 0.001 HIS B 907 PHE 0.044 0.001 PHE B 808 TYR 0.011 0.001 TYR B1375 ARG 0.003 0.000 ARG B1414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.74 seconds wall clock time: 54 minutes 26.29 seconds (3266.29 seconds total)