Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 15:32:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c06_16355/10_2023/8c06_16355.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c06_16355/10_2023/8c06_16355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c06_16355/10_2023/8c06_16355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c06_16355/10_2023/8c06_16355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c06_16355/10_2023/8c06_16355.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c06_16355/10_2023/8c06_16355.pdb" } resolution = 2.7 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= 0.001 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 178 5.16 5 C 16044 2.51 5 N 4426 2.21 5 O 4670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 872": "OE1" <-> "OE2" Residue "A GLU 1134": "OE1" <-> "OE2" Residue "A GLU 1273": "OE1" <-> "OE2" Residue "A GLU 1367": "OE1" <-> "OE2" Residue "A GLU 1420": "OE1" <-> "OE2" Residue "B GLU 2194": "OE1" <-> "OE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D GLU 563": "OE1" <-> "OE2" Residue "D GLU 796": "OE1" <-> "OE2" Residue "D GLU 872": "OE1" <-> "OE2" Residue "D GLU 1134": "OE1" <-> "OE2" Residue "D GLU 1273": "OE1" <-> "OE2" Residue "D GLU 1367": "OE1" <-> "OE2" Residue "D GLU 1420": "OE1" <-> "OE2" Residue "E GLU 2194": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 25324 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 7080 Classifications: {'peptide': 925} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 874} Chain breaks: 7 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5353 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 43, 'TRANS': 650} Chain breaks: 6 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 13, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "D" Number of atoms: 7080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 7080 Classifications: {'peptide': 925} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 874} Chain breaks: 7 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 106 Chain: "E" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5353 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 43, 'TRANS': 650} Chain breaks: 6 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 13, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 226 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 226 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4617 SG CYS A1179 51.698 175.327 56.938 1.00 39.20 S ATOM 4834 SG CYS A1208 52.784 171.719 57.038 1.00 42.40 S ATOM 4856 SG CYS A1211 55.390 174.337 57.153 1.00 41.44 S ATOM 5013 SG CYS A1232 53.091 173.864 60.106 1.00 42.16 S ATOM 4856 SG CYS A1211 55.390 174.337 57.153 1.00 41.44 S ATOM 4885 SG CYS A1215 57.502 177.074 55.489 1.00 43.83 S ATOM 5024 SG CYS A1234 56.990 177.047 59.257 1.00 44.19 S ATOM 5069 SG CYS A1240 54.141 177.934 56.948 1.00 40.89 S ATOM 4753 SG CYS A1196 65.433 175.584 60.106 1.00 48.12 S ATOM 4777 SG CYS A1199 63.671 178.924 60.234 1.00 47.50 S ATOM 17050 SG CYS D1179 96.465 69.895 56.934 1.00 39.78 S ATOM 17267 SG CYS D1208 95.379 73.503 57.032 1.00 42.20 S ATOM 17289 SG CYS D1211 92.772 70.884 57.149 1.00 41.60 S ATOM 17446 SG CYS D1232 95.072 71.360 60.101 1.00 40.65 S ATOM 17289 SG CYS D1211 92.772 70.884 57.149 1.00 41.60 S ATOM 17318 SG CYS D1215 90.661 68.146 55.487 1.00 43.47 S ATOM 17457 SG CYS D1234 91.173 68.176 59.255 1.00 42.15 S ATOM 17502 SG CYS D1240 94.023 67.287 56.946 1.00 39.13 S ATOM 17186 SG CYS D1196 82.730 69.638 60.102 1.00 45.26 S ATOM 17210 SG CYS D1199 84.493 66.299 60.233 1.00 44.64 S Time building chain proxies: 12.35, per 1000 atoms: 0.49 Number of scatterers: 25324 At special positions: 0 Unit cell: (149.811, 245.997, 106.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 178 16.00 O 4670 8.00 N 4426 7.00 C 16044 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: 8.87 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2801 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1208 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1232 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1211 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1179 " pdb=" ZN A2802 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1240 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1234 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1215 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1211 " pdb=" ZN A2803 " pdb="ZN ZN A2803 " - pdb=" ND1 HIS A1216 " pdb="ZN ZN A2803 " - pdb=" ND1 HIS A1219 " pdb="ZN ZN A2803 " - pdb=" SG CYS A1196 " pdb="ZN ZN A2803 " - pdb=" SG CYS A1199 " pdb=" ZN D2801 " pdb="ZN ZN D2801 " - pdb=" SG CYS D1179 " pdb="ZN ZN D2801 " - pdb=" SG CYS D1232 " pdb="ZN ZN D2801 " - pdb=" SG CYS D1211 " pdb="ZN ZN D2801 " - pdb=" SG CYS D1208 " pdb=" ZN D2802 " pdb="ZN ZN D2802 " - pdb=" SG CYS D1240 " pdb="ZN ZN D2802 " - pdb=" SG CYS D1234 " pdb="ZN ZN D2802 " - pdb=" SG CYS D1215 " pdb="ZN ZN D2802 " - pdb=" SG CYS D1211 " pdb=" ZN D2803 " pdb="ZN ZN D2803 " - pdb=" ND1 HIS D1216 " pdb="ZN ZN D2803 " - pdb=" ND1 HIS D1219 " pdb="ZN ZN D2803 " - pdb=" SG CYS D1196 " pdb="ZN ZN D2803 " - pdb=" SG CYS D1199 " Number of angles added : 28 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6276 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 28 sheets defined 47.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 14 through 31 removed outlier: 3.613A pdb=" N LEU A 18 " --> pdb=" O THR A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.835A pdb=" N GLN A 45 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 46 " --> pdb=" O LEU A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 46' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.709A pdb=" N MET A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 555 Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.834A pdb=" N ASN A 798 " --> pdb=" O ASN A 795 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 795 through 799' Processing helix chain 'A' and resid 874 through 882 Processing helix chain 'A' and resid 884 through 903 removed outlier: 3.875A pdb=" N CYS A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 913 removed outlier: 3.980A pdb=" N SER A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 930 Processing helix chain 'A' and resid 935 through 942 removed outlier: 3.770A pdb=" N GLU A 942 " --> pdb=" O THR A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1094 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1101 through 1107 Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1125 through 1141 removed outlier: 3.736A pdb=" N LYS A1141 " --> pdb=" O GLN A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1159 Processing helix chain 'A' and resid 1164 through 1167 Processing helix chain 'A' and resid 1168 through 1175 Processing helix chain 'A' and resid 1208 through 1214 Processing helix chain 'A' and resid 1247 through 1260 removed outlier: 3.622A pdb=" N THR A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1290 removed outlier: 3.793A pdb=" N VAL A1288 " --> pdb=" O ALA A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1293 No H-bonds generated for 'chain 'A' and resid 1291 through 1293' Processing helix chain 'A' and resid 1324 through 1333 Processing helix chain 'A' and resid 1337 through 1344 Processing helix chain 'A' and resid 1364 through 1374 removed outlier: 4.394A pdb=" N GLN A1374 " --> pdb=" O TYR A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1389 Processing helix chain 'A' and resid 1395 through 1410 Processing helix chain 'A' and resid 1416 through 1443 removed outlier: 3.648A pdb=" N GLU A1420 " --> pdb=" O GLY A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1467 Processing helix chain 'A' and resid 1467 through 1488 removed outlier: 4.283A pdb=" N GLU A1473 " --> pdb=" O PRO A1469 " (cutoff:3.500A) Proline residue: A1485 - end of helix Processing helix chain 'A' and resid 1503 through 1515 removed outlier: 3.728A pdb=" N GLU A1512 " --> pdb=" O GLN A1508 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A1513 " --> pdb=" O GLY A1509 " (cutoff:3.500A) Processing helix chain 'B' and resid 1776 through 1800 removed outlier: 3.760A pdb=" N SER B1780 " --> pdb=" O SER B1776 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1809 Processing helix chain 'B' and resid 1820 through 1835 removed outlier: 3.635A pdb=" N ALA B1824 " --> pdb=" O THR B1820 " (cutoff:3.500A) Processing helix chain 'B' and resid 1836 through 1861 removed outlier: 3.684A pdb=" N SER B1861 " --> pdb=" O SER B1857 " (cutoff:3.500A) Processing helix chain 'B' and resid 1873 through 1876 Processing helix chain 'B' and resid 1877 through 1884 Processing helix chain 'B' and resid 1912 through 1927 removed outlier: 3.548A pdb=" N PHE B1917 " --> pdb=" O ALA B1913 " (cutoff:3.500A) Processing helix chain 'B' and resid 1940 through 1943 removed outlier: 3.540A pdb=" N SER B1943 " --> pdb=" O ASP B1940 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1940 through 1943' Processing helix chain 'B' and resid 1944 through 1964 removed outlier: 3.725A pdb=" N ALA B1948 " --> pdb=" O LEU B1944 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B1949 " --> pdb=" O LYS B1945 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B1950 " --> pdb=" O HIS B1946 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) Processing helix chain 'B' and resid 2048 through 2053 removed outlier: 3.725A pdb=" N ASP B2052 " --> pdb=" O ILE B2048 " (cutoff:3.500A) Processing helix chain 'B' and resid 2054 through 2057 removed outlier: 3.927A pdb=" N LEU B2057 " --> pdb=" O PRO B2054 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2054 through 2057' Processing helix chain 'B' and resid 2063 through 2068 Processing helix chain 'B' and resid 2093 through 2097 Processing helix chain 'B' and resid 2103 through 2116 Processing helix chain 'B' and resid 2165 through 2169 removed outlier: 3.521A pdb=" N PHE B2169 " --> pdb=" O LEU B2166 " (cutoff:3.500A) Processing helix chain 'B' and resid 2181 through 2189 removed outlier: 3.614A pdb=" N LEU B2185 " --> pdb=" O SER B2181 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP B2189 " --> pdb=" O LEU B2185 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2200 Processing helix chain 'B' and resid 2203 through 2207 removed outlier: 3.556A pdb=" N GLU B2207 " --> pdb=" O VAL B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2210 through 2215 removed outlier: 3.524A pdb=" N GLU B2214 " --> pdb=" O SER B2210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2217 through 2236 removed outlier: 3.728A pdb=" N LYS B2221 " --> pdb=" O GLY B2217 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B2223 " --> pdb=" O GLU B2219 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B2224 " --> pdb=" O VAL B2220 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN B2236 " --> pdb=" O LEU B2232 " (cutoff:3.500A) Processing helix chain 'B' and resid 2248 through 2262 Processing helix chain 'B' and resid 2289 through 2305 removed outlier: 3.713A pdb=" N ARG B2293 " --> pdb=" O SER B2289 " (cutoff:3.500A) Processing helix chain 'B' and resid 2522 through 2542 removed outlier: 3.550A pdb=" N LEU B2526 " --> pdb=" O THR B2522 " (cutoff:3.500A) Processing helix chain 'B' and resid 2551 through 2560 Processing helix chain 'B' and resid 2564 through 2571 removed outlier: 3.501A pdb=" N ALA B2569 " --> pdb=" O HIS B2566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2572 through 2586 Processing helix chain 'B' and resid 2591 through 2596 removed outlier: 3.611A pdb=" N PHE B2595 " --> pdb=" O ALA B2591 " (cutoff:3.500A) Processing helix chain 'B' and resid 2620 through 2624 removed outlier: 4.053A pdb=" N ASN B2623 " --> pdb=" O ASN B2620 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B2624 " --> pdb=" O GLY B2621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2620 through 2624' Processing helix chain 'B' and resid 2630 through 2645 Processing helix chain 'B' and resid 2647 through 2662 removed outlier: 4.060A pdb=" N VAL B2661 " --> pdb=" O GLY B2657 " (cutoff:3.500A) Processing helix chain 'B' and resid 2671 through 2680 Processing helix chain 'B' and resid 2686 through 2694 removed outlier: 3.945A pdb=" N LEU B2690 " --> pdb=" O ASN B2686 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B2694 " --> pdb=" O LEU B2690 " (cutoff:3.500A) Processing helix chain 'B' and resid 2709 through 2720 Processing helix chain 'B' and resid 2722 through 2735 Processing helix chain 'B' and resid 2742 through 2746 removed outlier: 3.503A pdb=" N GLY B2745 " --> pdb=" O SER B2742 " (cutoff:3.500A) Processing helix chain 'B' and resid 2779 through 2793 removed outlier: 3.860A pdb=" N LYS B2792 " --> pdb=" O LEU B2788 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B2793 " --> pdb=" O LEU B2789 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 31 removed outlier: 3.613A pdb=" N LEU D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.834A pdb=" N GLN D 45 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 46 " --> pdb=" O LEU D 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 42 through 46' Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 449 through 452 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 498 through 500 No H-bonds generated for 'chain 'D' and resid 498 through 500' Processing helix chain 'D' and resid 501 through 506 removed outlier: 3.708A pdb=" N MET D 505 " --> pdb=" O GLN D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 555 Processing helix chain 'D' and resid 787 through 793 Processing helix chain 'D' and resid 795 through 799 removed outlier: 3.834A pdb=" N ASN D 798 " --> pdb=" O ASN D 795 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 799 " --> pdb=" O GLU D 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 795 through 799' Processing helix chain 'D' and resid 874 through 882 Processing helix chain 'D' and resid 884 through 903 removed outlier: 3.874A pdb=" N CYS D 888 " --> pdb=" O ASP D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 913 removed outlier: 3.979A pdb=" N SER D 913 " --> pdb=" O GLN D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 930 Processing helix chain 'D' and resid 935 through 942 removed outlier: 3.771A pdb=" N GLU D 942 " --> pdb=" O THR D 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 1080 through 1094 Processing helix chain 'D' and resid 1098 through 1100 No H-bonds generated for 'chain 'D' and resid 1098 through 1100' Processing helix chain 'D' and resid 1101 through 1107 Processing helix chain 'D' and resid 1115 through 1123 Processing helix chain 'D' and resid 1125 through 1141 removed outlier: 3.736A pdb=" N LYS D1141 " --> pdb=" O GLN D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1149 through 1159 Processing helix chain 'D' and resid 1164 through 1167 Processing helix chain 'D' and resid 1168 through 1175 Processing helix chain 'D' and resid 1208 through 1214 Processing helix chain 'D' and resid 1247 through 1260 removed outlier: 3.621A pdb=" N THR D1260 " --> pdb=" O TYR D1256 " (cutoff:3.500A) Processing helix chain 'D' and resid 1274 through 1290 removed outlier: 3.793A pdb=" N VAL D1288 " --> pdb=" O ALA D1284 " (cutoff:3.500A) Processing helix chain 'D' and resid 1291 through 1293 No H-bonds generated for 'chain 'D' and resid 1291 through 1293' Processing helix chain 'D' and resid 1324 through 1333 Processing helix chain 'D' and resid 1337 through 1344 Processing helix chain 'D' and resid 1364 through 1374 removed outlier: 4.395A pdb=" N GLN D1374 " --> pdb=" O TYR D1370 " (cutoff:3.500A) Processing helix chain 'D' and resid 1377 through 1389 Processing helix chain 'D' and resid 1395 through 1410 Processing helix chain 'D' and resid 1416 through 1443 removed outlier: 3.648A pdb=" N GLU D1420 " --> pdb=" O GLY D1416 " (cutoff:3.500A) Processing helix chain 'D' and resid 1454 through 1467 Processing helix chain 'D' and resid 1467 through 1488 removed outlier: 4.282A pdb=" N GLU D1473 " --> pdb=" O PRO D1469 " (cutoff:3.500A) Proline residue: D1485 - end of helix Processing helix chain 'D' and resid 1503 through 1515 removed outlier: 3.729A pdb=" N GLU D1512 " --> pdb=" O GLN D1508 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D1513 " --> pdb=" O GLY D1509 " (cutoff:3.500A) Processing helix chain 'E' and resid 1776 through 1800 removed outlier: 3.760A pdb=" N SER E1780 " --> pdb=" O SER E1776 " (cutoff:3.500A) Processing helix chain 'E' and resid 1804 through 1809 Processing helix chain 'E' and resid 1820 through 1835 removed outlier: 3.634A pdb=" N ALA E1824 " --> pdb=" O THR E1820 " (cutoff:3.500A) Processing helix chain 'E' and resid 1836 through 1861 removed outlier: 3.683A pdb=" N SER E1861 " --> pdb=" O SER E1857 " (cutoff:3.500A) Processing helix chain 'E' and resid 1873 through 1876 Processing helix chain 'E' and resid 1877 through 1884 Processing helix chain 'E' and resid 1912 through 1927 removed outlier: 3.548A pdb=" N PHE E1917 " --> pdb=" O ALA E1913 " (cutoff:3.500A) Processing helix chain 'E' and resid 1940 through 1943 removed outlier: 3.541A pdb=" N SER E1943 " --> pdb=" O ASP E1940 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1940 through 1943' Processing helix chain 'E' and resid 1944 through 1964 removed outlier: 3.724A pdb=" N ALA E1948 " --> pdb=" O LEU E1944 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR E1949 " --> pdb=" O LYS E1945 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E1950 " --> pdb=" O HIS E1946 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E1964 " --> pdb=" O ALA E1960 " (cutoff:3.500A) Processing helix chain 'E' and resid 2048 through 2053 removed outlier: 3.725A pdb=" N ASP E2052 " --> pdb=" O ILE E2048 " (cutoff:3.500A) Processing helix chain 'E' and resid 2054 through 2057 removed outlier: 3.927A pdb=" N LEU E2057 " --> pdb=" O PRO E2054 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2054 through 2057' Processing helix chain 'E' and resid 2063 through 2068 Processing helix chain 'E' and resid 2093 through 2097 Processing helix chain 'E' and resid 2103 through 2116 Processing helix chain 'E' and resid 2165 through 2169 removed outlier: 3.521A pdb=" N PHE E2169 " --> pdb=" O LEU E2166 " (cutoff:3.500A) Processing helix chain 'E' and resid 2181 through 2189 removed outlier: 3.613A pdb=" N LEU E2185 " --> pdb=" O SER E2181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP E2189 " --> pdb=" O LEU E2185 " (cutoff:3.500A) Processing helix chain 'E' and resid 2189 through 2200 Processing helix chain 'E' and resid 2203 through 2207 removed outlier: 3.556A pdb=" N GLU E2207 " --> pdb=" O VAL E2204 " (cutoff:3.500A) Processing helix chain 'E' and resid 2210 through 2215 removed outlier: 3.524A pdb=" N GLU E2214 " --> pdb=" O SER E2210 " (cutoff:3.500A) Processing helix chain 'E' and resid 2217 through 2236 removed outlier: 3.729A pdb=" N LYS E2221 " --> pdb=" O GLY E2217 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER E2223 " --> pdb=" O GLU E2219 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS E2224 " --> pdb=" O VAL E2220 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN E2236 " --> pdb=" O LEU E2232 " (cutoff:3.500A) Processing helix chain 'E' and resid 2248 through 2262 Processing helix chain 'E' and resid 2289 through 2305 removed outlier: 3.714A pdb=" N ARG E2293 " --> pdb=" O SER E2289 " (cutoff:3.500A) Processing helix chain 'E' and resid 2522 through 2542 removed outlier: 3.550A pdb=" N LEU E2526 " --> pdb=" O THR E2522 " (cutoff:3.500A) Processing helix chain 'E' and resid 2551 through 2560 Processing helix chain 'E' and resid 2564 through 2571 removed outlier: 3.501A pdb=" N ALA E2569 " --> pdb=" O HIS E2566 " (cutoff:3.500A) Processing helix chain 'E' and resid 2572 through 2586 Processing helix chain 'E' and resid 2591 through 2596 removed outlier: 3.611A pdb=" N PHE E2595 " --> pdb=" O ALA E2591 " (cutoff:3.500A) Processing helix chain 'E' and resid 2620 through 2624 removed outlier: 4.053A pdb=" N ASN E2623 " --> pdb=" O ASN E2620 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE E2624 " --> pdb=" O GLY E2621 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2620 through 2624' Processing helix chain 'E' and resid 2630 through 2645 Processing helix chain 'E' and resid 2647 through 2662 removed outlier: 4.060A pdb=" N VAL E2661 " --> pdb=" O GLY E2657 " (cutoff:3.500A) Processing helix chain 'E' and resid 2671 through 2680 Processing helix chain 'E' and resid 2686 through 2694 removed outlier: 3.945A pdb=" N LEU E2690 " --> pdb=" O ASN E2686 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E2694 " --> pdb=" O LEU E2690 " (cutoff:3.500A) Processing helix chain 'E' and resid 2709 through 2720 Processing helix chain 'E' and resid 2722 through 2735 Processing helix chain 'E' and resid 2742 through 2746 removed outlier: 3.503A pdb=" N GLY E2745 " --> pdb=" O SER E2742 " (cutoff:3.500A) Processing helix chain 'E' and resid 2779 through 2793 removed outlier: 3.860A pdb=" N LYS E2792 " --> pdb=" O LEU E2788 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR E2793 " --> pdb=" O LEU E2789 " (cutoff:3.500A) Processing helix chain 'F' and resid 1706 through 1710 Processing helix chain 'G' and resid 1706 through 1710 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 3.806A pdb=" N SER A 843 " --> pdb=" O ALA A 870 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU A 872 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 841 " --> pdb=" O GLU A 872 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 53 removed outlier: 3.717A pdb=" N ARG A 69 " --> pdb=" O GLN A 361 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A 361 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 376 removed outlier: 6.573A pdb=" N VAL A 384 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE A 374 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 382 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA A 376 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 429 Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 478 removed outlier: 5.506A pdb=" N GLY A 495 " --> pdb=" O THR A 734 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A 734 " --> pdb=" O GLY A 495 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 649 through 652 removed outlier: 6.807A pdb=" N PHE A 549 " --> pdb=" O PHE A 658 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE A 658 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 751 removed outlier: 6.583A pdb=" N VAL A 759 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 749 " --> pdb=" O HIS A 757 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS A 757 " --> pdb=" O VAL A 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.437A pdb=" N LEU A 812 " --> pdb=" O TYR A 820 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1194 through 1196 Processing sheet with id=AB2, first strand: chain 'B' and resid 2238 through 2244 removed outlier: 6.917A pdb=" N ARG B2238 " --> pdb=" O HIS B2275 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B2277 " --> pdb=" O ARG B2238 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B2240 " --> pdb=" O VAL B2277 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL B2279 " --> pdb=" O LEU B2240 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B2242 " --> pdb=" O VAL B2279 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE B2281 " --> pdb=" O LEU B2242 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B2244 " --> pdb=" O PHE B2281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 2505 through 2506 Processing sheet with id=AB4, first strand: chain 'B' and resid 2603 through 2604 Processing sheet with id=AB5, first strand: chain 'B' and resid 2751 through 2755 Processing sheet with id=AB6, first strand: chain 'D' and resid 2 through 10 removed outlier: 3.805A pdb=" N SER D 843 " --> pdb=" O ALA D 870 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU D 872 " --> pdb=" O ILE D 841 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE D 841 " --> pdb=" O GLU D 872 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 53 Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 53 removed outlier: 3.717A pdb=" N ARG D 69 " --> pdb=" O GLN D 361 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN D 361 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 371 through 376 removed outlier: 6.573A pdb=" N VAL D 384 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE D 374 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU D 382 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA D 376 " --> pdb=" O GLU D 380 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 424 through 429 Processing sheet with id=AC2, first strand: chain 'D' and resid 475 through 478 removed outlier: 5.505A pdb=" N GLY D 495 " --> pdb=" O THR D 734 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR D 734 " --> pdb=" O GLY D 495 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 649 through 652 removed outlier: 6.806A pdb=" N PHE D 549 " --> pdb=" O PHE D 658 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE D 658 " --> pdb=" O PHE D 549 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 745 through 751 removed outlier: 6.584A pdb=" N VAL D 759 " --> pdb=" O LEU D 747 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL D 749 " --> pdb=" O HIS D 757 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS D 757 " --> pdb=" O VAL D 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 800 through 802 removed outlier: 4.437A pdb=" N LEU D 812 " --> pdb=" O TYR D 820 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1194 through 1196 Processing sheet with id=AC7, first strand: chain 'E' and resid 2238 through 2244 removed outlier: 6.918A pdb=" N ARG E2238 " --> pdb=" O HIS E2275 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL E2277 " --> pdb=" O ARG E2238 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU E2240 " --> pdb=" O VAL E2277 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL E2279 " --> pdb=" O LEU E2240 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU E2242 " --> pdb=" O VAL E2279 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHE E2281 " --> pdb=" O LEU E2242 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E2244 " --> pdb=" O PHE E2281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 2505 through 2506 Processing sheet with id=AC9, first strand: chain 'E' and resid 2603 through 2604 Processing sheet with id=AD1, first strand: chain 'E' and resid 2751 through 2755 1126 hydrogen bonds defined for protein. 3186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.20 Time building geometry restraints manager: 9.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8398 1.35 - 1.47: 5923 1.47 - 1.60: 11277 1.60 - 1.72: 0 1.72 - 1.85: 260 Bond restraints: 25858 Sorted by residual: bond pdb=" C GLN D 75 " pdb=" N PRO D 76 " ideal model delta sigma weight residual 1.334 1.382 -0.049 2.34e-02 1.83e+03 4.31e+00 bond pdb=" C GLN A 75 " pdb=" N PRO A 76 " ideal model delta sigma weight residual 1.334 1.382 -0.049 2.34e-02 1.83e+03 4.30e+00 bond pdb=" C PRO D 38 " pdb=" N PRO D 39 " ideal model delta sigma weight residual 1.337 1.355 -0.019 1.06e-02 8.90e+03 3.09e+00 bond pdb=" C PRO A 38 " pdb=" N PRO A 39 " ideal model delta sigma weight residual 1.337 1.355 -0.019 1.06e-02 8.90e+03 3.09e+00 bond pdb=" C ILE E1836 " pdb=" N PRO E1837 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.23e-02 6.61e+03 2.70e+00 ... (remaining 25853 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.38: 632 105.38 - 112.58: 13320 112.58 - 119.78: 8937 119.78 - 126.99: 11896 126.99 - 134.19: 359 Bond angle restraints: 35144 Sorted by residual: angle pdb=" CA GLU D1480 " pdb=" CB GLU D1480 " pdb=" CG GLU D1480 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA GLU A1480 " pdb=" CB GLU A1480 " pdb=" CG GLU A1480 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" N GLU D 27 " pdb=" CA GLU D 27 " pdb=" CB GLU D 27 " ideal model delta sigma weight residual 110.39 117.86 -7.47 1.66e+00 3.63e-01 2.03e+01 angle pdb=" N GLU A 27 " pdb=" CA GLU A 27 " pdb=" CB GLU A 27 " ideal model delta sigma weight residual 110.39 117.86 -7.47 1.66e+00 3.63e-01 2.03e+01 angle pdb=" C PRO E2619 " pdb=" N ASN E2620 " pdb=" CA ASN E2620 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 ... (remaining 35139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14258 17.97 - 35.95: 1198 35.95 - 53.92: 150 53.92 - 71.90: 48 71.90 - 89.87: 24 Dihedral angle restraints: 15678 sinusoidal: 6050 harmonic: 9628 Sorted by residual: dihedral pdb=" CA GLN E2747 " pdb=" C GLN E2747 " pdb=" N PRO E2748 " pdb=" CA PRO E2748 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA GLN B2747 " pdb=" C GLN B2747 " pdb=" N PRO B2748 " pdb=" CA PRO B2748 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA GLN D 75 " pdb=" C GLN D 75 " pdb=" N PRO D 76 " pdb=" CA PRO D 76 " ideal model delta harmonic sigma weight residual 180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 15675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3702 0.088 - 0.177: 300 0.177 - 0.265: 10 0.265 - 0.354: 4 0.354 - 0.442: 2 Chirality restraints: 4018 Sorted by residual: chirality pdb=" CB ILE B2752 " pdb=" CA ILE B2752 " pdb=" CG1 ILE B2752 " pdb=" CG2 ILE B2752 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CB ILE E2752 " pdb=" CA ILE E2752 " pdb=" CG1 ILE E2752 " pdb=" CG2 ILE E2752 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CB VAL D 436 " pdb=" CA VAL D 436 " pdb=" CG1 VAL D 436 " pdb=" CG2 VAL D 436 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 4015 not shown) Planarity restraints: 4550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B2627 " -0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO B2628 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B2628 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B2628 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E2627 " 0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO E2628 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO E2628 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E2628 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E2618 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO E2619 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO E2619 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E2619 " 0.040 5.00e-02 4.00e+02 ... (remaining 4547 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 8180 2.85 - 3.36: 21336 3.36 - 3.87: 40522 3.87 - 4.39: 44024 4.39 - 4.90: 78752 Nonbonded interactions: 192814 Sorted by model distance: nonbonded pdb=" OD1 ASN E2531 " pdb=" NH2 ARG E2534 " model vdw 2.333 2.520 nonbonded pdb=" OD1 ASN B2531 " pdb=" NH2 ARG B2534 " model vdw 2.334 2.520 nonbonded pdb=" O ASP A1352 " pdb=" OG SER A1358 " model vdw 2.338 2.440 nonbonded pdb=" O ASP D1352 " pdb=" OG SER D1358 " model vdw 2.338 2.440 nonbonded pdb=" O SER D1180 " pdb=" OG1 THR D1184 " model vdw 2.347 2.440 ... (remaining 192809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.670 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 65.090 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.160 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 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 0.050 25858 Z= 0.232 Angle : 0.762 9.705 35144 Z= 0.405 Chirality : 0.049 0.442 4018 Planarity : 0.007 0.081 4550 Dihedral : 13.594 89.873 9402 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: -1.51 (0.13), residues: 3234 helix: -0.92 (0.12), residues: 1348 sheet: 0.91 (0.27), residues: 322 loop : -1.43 (0.14), residues: 1564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 1.5552 time to fit residues: 811.5358 Evaluate side-chains 271 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 191 optimal weight: 0.6980 chunk 297 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 849 HIS A 878 GLN A 890 GLN A1290 HIS A1385 HIS A1455 GLN B2019 ASN B2110 ASN B2113 ASN ** B2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2275 HIS B2543 ASN B2564 ASN B2652 HIS D 57 HIS D 849 HIS D 878 GLN D 879 HIS D1290 HIS D1385 HIS D1455 GLN E2019 ASN E2110 ASN ** E2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2564 ASN E2652 HIS E2781 GLN F1720 ASN G1720 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 25858 Z= 0.357 Angle : 0.698 7.563 35144 Z= 0.362 Chirality : 0.047 0.256 4018 Planarity : 0.006 0.064 4550 Dihedral : 4.560 23.579 3524 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.81 % Allowed : 9.36 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: -0.49 (0.14), residues: 3234 helix: 0.40 (0.14), residues: 1378 sheet: 0.90 (0.27), residues: 338 loop : -1.29 (0.15), residues: 1518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 293 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 32 residues processed: 333 average time/residue: 1.3997 time to fit residues: 539.4295 Evaluate side-chains 274 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 242 time to evaluate : 2.798 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 20 residues processed: 13 average time/residue: 0.6709 time to fit residues: 15.3601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 247 optimal weight: 0.7980 chunk 202 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 chunk 322 optimal weight: 10.0000 chunk 265 optimal weight: 0.6980 chunk 295 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 ASN B2019 ASN ** B2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2301 GLN D 849 HIS E2116 ASN ** E2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2652 HIS E2781 GLN F1720 ASN G1720 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25858 Z= 0.201 Angle : 0.546 6.938 35144 Z= 0.285 Chirality : 0.041 0.185 4018 Planarity : 0.005 0.060 4550 Dihedral : 4.241 24.008 3524 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.74 % Allowed : 11.58 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 0.05 (0.15), residues: 3234 helix: 1.07 (0.14), residues: 1386 sheet: 0.99 (0.27), residues: 338 loop : -1.21 (0.15), residues: 1510 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 256 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 32 residues processed: 298 average time/residue: 1.2982 time to fit residues: 454.8430 Evaluate side-chains 268 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 3.043 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 22 residues processed: 12 average time/residue: 0.5419 time to fit residues: 13.4140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 4.9990 chunk 224 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 200 optimal weight: 0.2980 chunk 299 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 283 optimal weight: 0.6980 chunk 85 optimal weight: 0.0060 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2019 ASN ** B2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 783 ASN D 849 HIS E2116 ASN ** E2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2652 HIS E2781 GLN F1720 ASN G1720 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25858 Z= 0.171 Angle : 0.516 7.037 35144 Z= 0.268 Chirality : 0.040 0.168 4018 Planarity : 0.004 0.066 4550 Dihedral : 4.029 23.803 3524 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.70 % Allowed : 12.94 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 0.45 (0.15), residues: 3234 helix: 1.51 (0.14), residues: 1370 sheet: 1.08 (0.28), residues: 338 loop : -1.05 (0.15), residues: 1526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 251 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 33 residues processed: 300 average time/residue: 1.2252 time to fit residues: 435.4096 Evaluate side-chains 259 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 226 time to evaluate : 2.676 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 23 residues processed: 12 average time/residue: 0.6514 time to fit residues: 13.9189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 9.9990 chunk 179 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 270 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1828 GLN B2116 ASN ** B2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2697 ASN E1828 GLN E1962 ASN E2116 ASN E2258 GLN E2301 GLN ** E2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2652 HIS E2697 ASN E2781 GLN F1720 ASN G1720 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 25858 Z= 0.436 Angle : 0.726 8.028 35144 Z= 0.378 Chirality : 0.048 0.255 4018 Planarity : 0.006 0.063 4550 Dihedral : 4.689 24.561 3524 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 3.51 % Allowed : 13.87 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: -0.12 (0.14), residues: 3234 helix: 0.96 (0.14), residues: 1382 sheet: 0.63 (0.27), residues: 348 loop : -1.25 (0.15), residues: 1504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 245 time to evaluate : 2.643 Fit side-chains revert: symmetry clash outliers start: 95 outliers final: 53 residues processed: 309 average time/residue: 1.3717 time to fit residues: 496.3396 Evaluate side-chains 285 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 232 time to evaluate : 2.801 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 39 residues processed: 16 average time/residue: 0.5766 time to fit residues: 16.4950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 317 optimal weight: 4.9990 chunk 263 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 104 optimal weight: 0.5980 chunk 166 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2018 GLN B2116 ASN ** B2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2652 HIS ** E1962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2116 ASN ** E2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2652 HIS F1720 ASN G1720 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25858 Z= 0.163 Angle : 0.528 8.922 35144 Z= 0.275 Chirality : 0.040 0.166 4018 Planarity : 0.004 0.058 4550 Dihedral : 4.218 23.744 3524 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.74 % Allowed : 15.50 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 0.42 (0.15), residues: 3234 helix: 1.57 (0.14), residues: 1376 sheet: 0.91 (0.27), residues: 338 loop : -1.12 (0.16), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 233 time to evaluate : 2.924 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 45 residues processed: 289 average time/residue: 1.2473 time to fit residues: 424.6117 Evaluate side-chains 263 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 218 time to evaluate : 2.845 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 39 residues processed: 7 average time/residue: 0.6867 time to fit residues: 10.1305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 267 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 316 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2116 ASN ** B2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1099 GLN ** E1962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2116 ASN ** E2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2652 HIS E2781 GLN F1720 ASN G1720 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25858 Z= 0.374 Angle : 0.684 8.105 35144 Z= 0.355 Chirality : 0.046 0.227 4018 Planarity : 0.006 0.069 4550 Dihedral : 4.624 24.335 3524 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.46 % Favored : 93.48 % Rotamer: Outliers : 3.22 % Allowed : 15.46 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 0.02 (0.15), residues: 3234 helix: 1.15 (0.14), residues: 1384 sheet: 0.53 (0.27), residues: 348 loop : -1.23 (0.16), residues: 1502 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 233 time to evaluate : 2.860 Fit side-chains outliers start: 87 outliers final: 50 residues processed: 297 average time/residue: 1.2635 time to fit residues: 443.6781 Evaluate side-chains 274 residues out of total 2894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 224 time to evaluate : 2.736 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 43 residues processed: 8 average time/residue: 0.5639 time to fit residues: 10.0047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2038 > 50: distance: 45 - 136: 35.702 distance: 48 - 133: 14.311 distance: 85 - 88: 10.997 distance: 88 - 89: 7.674 distance: 89 - 90: 5.359 distance: 89 - 92: 4.351 distance: 90 - 91: 30.818 distance: 90 - 99: 11.832 distance: 92 - 93: 7.702 distance: 93 - 94: 3.034 distance: 93 - 95: 11.014 distance: 94 - 96: 4.541 distance: 95 - 97: 4.558 distance: 96 - 98: 9.793 distance: 97 - 98: 6.712 distance: 99 - 100: 10.146 distance: 100 - 101: 11.996 distance: 100 - 103: 9.329 distance: 101 - 102: 35.480 distance: 101 - 108: 26.564 distance: 103 - 104: 9.477 distance: 104 - 105: 11.947 distance: 105 - 106: 9.307 distance: 105 - 107: 6.679 distance: 108 - 109: 17.151 distance: 109 - 110: 21.359 distance: 109 - 112: 7.247 distance: 110 - 111: 49.400 distance: 110 - 119: 10.538 distance: 112 - 113: 22.535 distance: 113 - 114: 10.008 distance: 114 - 115: 12.261 distance: 115 - 116: 19.684 distance: 116 - 117: 12.786 distance: 116 - 118: 15.426 distance: 119 - 120: 4.287 distance: 120 - 121: 27.121 distance: 120 - 123: 15.407 distance: 121 - 122: 16.353 distance: 121 - 126: 15.648 distance: 123 - 124: 32.859 distance: 123 - 125: 18.993 distance: 126 - 127: 21.444 distance: 126 - 132: 38.521 distance: 127 - 128: 3.651 distance: 127 - 130: 27.608 distance: 128 - 129: 31.492 distance: 128 - 133: 16.582 distance: 130 - 131: 13.205 distance: 131 - 132: 30.624 distance: 133 - 134: 16.329 distance: 134 - 135: 12.969 distance: 134 - 137: 10.887 distance: 135 - 136: 35.640 distance: 135 - 142: 18.462 distance: 137 - 138: 15.608 distance: 138 - 139: 13.457 distance: 139 - 140: 12.553 distance: 140 - 141: 7.420 distance: 142 - 143: 14.067 distance: 143 - 144: 33.039 distance: 143 - 146: 7.620 distance: 144 - 145: 30.542 distance: 144 - 151: 3.789 distance: 146 - 147: 19.906 distance: 147 - 148: 21.690 distance: 148 - 149: 15.684 distance: 149 - 150: 15.046 distance: 151 - 152: 16.669 distance: 152 - 153: 23.429 distance: 152 - 155: 25.607 distance: 153 - 154: 21.826 distance: 153 - 159: 24.358 distance: 155 - 156: 23.905 distance: 156 - 157: 42.279 distance: 156 - 158: 14.996 distance: 159 - 160: 7.820 distance: 160 - 161: 10.193 distance: 161 - 162: 17.624 distance: 161 - 165: 26.259 distance: 163 - 164: 45.617 distance: 165 - 166: 20.855 distance: 166 - 167: 5.618 distance: 166 - 169: 14.414 distance: 167 - 168: 4.298 distance: 167 - 173: 6.117 distance: 169 - 170: 10.015 distance: 169 - 171: 8.042 distance: 170 - 172: 8.796