Starting phenix.real_space_refine on Fri Aug 7 19:33:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q85_52886/08_2026/9q85_52886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q85_52886/08_2026/9q85_52886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q85_52886/08_2026/9q85_52886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q85_52886/08_2026/9q85_52886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q85_52886/08_2026/9q85_52886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q85_52886/08_2026/9q85_52886.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.008 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 Ca 1 9.91 5 P 182 5.49 5 S 43 5.16 5 C 14161 2.51 5 N 4044 2.21 5 O 4675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23106 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 10096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1354, 10096 Classifications: {'peptide': 1354} Incomplete info: {'truncation_to_alanine': 298} Link IDs: {'PTRANS': 33, 'TRANS': 1320} Chain breaks: 4 Unresolved non-hydrogen bonds: 1045 Unresolved non-hydrogen angles: 1284 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'ASN:plan1': 26, 'ASP:plan': 56, 'GLN:plan1': 10, 'ARG:plan': 9, 'GLU:plan': 51, 'PHE:plan': 12, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 645 Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 624 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 27} Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1474 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 35, 'rna3p_pyr': 23} Link IDs: {'rna2p': 10, 'rna3p': 58} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 869 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain: "E" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 888 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain: "F" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2035 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 6, 'TRANS': 281} Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 11, 'ARG:plan': 7, 'HIS:plan': 4, 'GLU:plan': 14, 'GLN:plan1': 5, 'TYR:plan': 4, 'PHE:plan': 7, 'ASN:plan1': 8} Unresolved non-hydrogen planarities: 258 Chain: "G" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2171 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 6, 'TRANS': 281} Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 8, 'TYR:plan': 1, 'HIS:plan': 4, 'GLU:plan': 15, 'ASP:plan': 6, 'PHE:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 160 Chain: "I" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1487 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 4, 'TRANS': 213} Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 16, 'ASN:plan1': 2, 'GLN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 6, 'HIS:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 178 Chain: "L" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1605 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 4, 'TRANS': 214} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 100 Chain: "N" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 818 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 668 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 11, 'PHE:plan': 8, 'GLN:plan1': 6, 'TYR:plan': 8, 'ASN:plan1': 4, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 261 Chain: "M" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 965 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 8, 'PHE:plan': 8, 'GLN:plan1': 5, 'TYR:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 212 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.21 Number of scatterers: 23106 At special positions: 0 Unit cell: (108.9, 162.8, 182.6, 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) Ca 1 19.99 S 43 16.00 P 182 15.00 O 4675 8.00 N 4044 7.00 C 14161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5200 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 25 sheets defined 53.0% alpha, 10.3% beta 71 base pairs and 126 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 60 through 94 removed outlier: 5.193A pdb=" N THR A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.970A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 195 removed outlier: 3.823A pdb=" N ASP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.635A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 270 through 283 removed outlier: 3.718A pdb=" N TYR A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.948A pdb=" N GLY A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.542A pdb=" N SER A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.861A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.140A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 446 removed outlier: 5.458A pdb=" N GLU A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.392A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 removed outlier: 4.564A pdb=" N LYS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 572 removed outlier: 3.544A pdb=" N ILE A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 601 Processing helix chain 'A' and resid 602 through 608 removed outlier: 3.819A pdb=" N LEU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 625 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 643 through 652 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 677 through 684 Processing helix chain 'A' and resid 691 through 697 Processing helix chain 'A' and resid 702 through 719 Processing helix chain 'A' and resid 720 through 727 Processing helix chain 'A' and resid 731 through 752 Processing helix chain 'A' and resid 778 through 793 removed outlier: 3.551A pdb=" N LYS A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 815 through 824 Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.513A pdb=" N ARG A 871 " --> pdb=" O ALA A 868 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 872 " --> pdb=" O SER A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 896 removed outlier: 5.702A pdb=" N THR A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N PHE A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 896 " --> pdb=" O GLN A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 Processing helix chain 'A' and resid 916 through 929 Processing helix chain 'A' and resid 932 through 947 removed outlier: 3.562A pdb=" N LYS A 936 " --> pdb=" O ARG A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 978 removed outlier: 4.185A pdb=" N VAL A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1008 removed outlier: 4.022A pdb=" N ALA A 991 " --> pdb=" O ASP A 987 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 994 " --> pdb=" O HIS A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1016 removed outlier: 4.362A pdb=" N PHE A1015 " --> pdb=" O LEU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1033 Processing helix chain 'A' and resid 1041 through 1046 Processing helix chain 'A' and resid 1076 through 1088 Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1188 through 1195 Processing helix chain 'A' and resid 1245 through 1257 Processing helix chain 'A' and resid 1264 through 1273 Processing helix chain 'A' and resid 1275 through 1291 removed outlier: 4.147A pdb=" N GLU A1279 " --> pdb=" O LYS A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1306 Processing helix chain 'A' and resid 1312 through 1321 Processing helix chain 'A' and resid 1357 through 1362 Processing helix chain 'F' and resid 52 through 61 Processing helix chain 'F' and resid 86 through 96 removed outlier: 3.637A pdb=" N ALA F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 123 removed outlier: 3.768A pdb=" N LYS F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 139 Processing helix chain 'F' and resid 147 through 162 Processing helix chain 'F' and resid 171 through 195 Processing helix chain 'F' and resid 212 through 220 Processing helix chain 'F' and resid 223 through 233 removed outlier: 4.251A pdb=" N ILE F 229 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 246 Processing helix chain 'F' and resid 247 through 250 Processing helix chain 'F' and resid 262 through 279 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 87 through 96 removed outlier: 3.974A pdb=" N ILE G 91 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA G 92 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 124 Processing helix chain 'G' and resid 126 through 139 Processing helix chain 'G' and resid 147 through 161 Processing helix chain 'G' and resid 171 through 195 Processing helix chain 'G' and resid 212 through 220 Processing helix chain 'G' and resid 222 through 233 removed outlier: 3.995A pdb=" N ILE G 226 " --> pdb=" O PHE G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 246 Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 262 through 280 Processing helix chain 'O' and resid 24 through 37 Processing helix chain 'O' and resid 55 through 57 No H-bonds generated for 'chain 'O' and resid 55 through 57' Processing helix chain 'O' and resid 72 through 89 Processing helix chain 'O' and resid 90 through 115 Processing helix chain 'O' and resid 125 through 133 Processing helix chain 'O' and resid 143 through 158 Processing helix chain 'O' and resid 174 through 188 Processing helix chain 'L' and resid 24 through 37 removed outlier: 3.556A pdb=" N PHE L 28 " --> pdb=" O ASP L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 90 removed outlier: 3.630A pdb=" N LYS L 90 " --> pdb=" O GLN L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 114 removed outlier: 4.067A pdb=" N GLU L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 134 Processing helix chain 'L' and resid 143 through 158 Processing helix chain 'L' and resid 169 through 173 removed outlier: 3.701A pdb=" N PHE L 173 " --> pdb=" O LEU L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 188 Processing helix chain 'N' and resid 24 through 37 Processing helix chain 'N' and resid 72 through 90 removed outlier: 3.507A pdb=" N LYS N 90 " --> pdb=" O GLN N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 115 removed outlier: 3.552A pdb=" N ASN N 115 " --> pdb=" O GLU N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 133 Processing helix chain 'N' and resid 143 through 158 Processing helix chain 'N' and resid 169 through 173 removed outlier: 3.840A pdb=" N TYR N 172 " --> pdb=" O SER N 169 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE N 173 " --> pdb=" O LEU N 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 169 through 173' Processing helix chain 'N' and resid 174 through 189 Processing helix chain 'M' and resid 24 through 37 Processing helix chain 'M' and resid 72 through 90 removed outlier: 3.594A pdb=" N LYS M 90 " --> pdb=" O GLN M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 115 removed outlier: 3.926A pdb=" N GLU M 111 " --> pdb=" O ILE M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 133 Processing helix chain 'M' and resid 143 through 158 Processing helix chain 'M' and resid 174 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 961 through 964 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.397A pdb=" N LEU A 661 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'A' and resid 844 through 847 Processing sheet with id=AA6, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id=AA8, first strand: chain 'A' and resid 1104 through 1106 Processing sheet with id=AA9, first strand: chain 'A' and resid 1131 through 1132 Processing sheet with id=AB1, first strand: chain 'A' and resid 1167 through 1178 removed outlier: 7.062A pdb=" N THR A1159 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE A1201 " --> pdb=" O THR A1159 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLU A1161 " --> pdb=" O LYS A1199 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LYS A1199 " --> pdb=" O GLU A1161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1234 through 1238 removed outlier: 6.495A pdb=" N HIS A1237 " --> pdb=" O LEU A1223 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU A1223 " --> pdb=" O HIS A1237 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A1211 " --> pdb=" O LEU A1223 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A1212 " --> pdb=" O ILE A1368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1343 through 1345 Processing sheet with id=AB4, first strand: chain 'F' and resid 64 through 66 removed outlier: 5.815A pdb=" N ARG F 5 " --> pdb=" O ILE F 38 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE F 40 " --> pdb=" O ARG F 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AB6, first strand: chain 'F' and resid 49 through 51 removed outlier: 6.022A pdb=" N SER G 13 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR G 51 " --> pdb=" O SER G 13 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU G 15 " --> pdb=" O THR G 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 80 removed outlier: 3.610A pdb=" N PHE F 77 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR F 79 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE G 67 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE G 77 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL G 65 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU G 64 " --> pdb=" O ASP G 39 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG G 5 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE G 40 " --> pdb=" O ARG G 5 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 252 through 253 Processing sheet with id=AB9, first strand: chain 'G' and resid 252 through 255 Processing sheet with id=AC1, first strand: chain 'O' and resid 12 through 13 Processing sheet with id=AC2, first strand: chain 'O' and resid 59 through 62 removed outlier: 6.270A pdb=" N LEU O 164 " --> pdb=" O LEU O 193 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU O 195 " --> pdb=" O LEU O 164 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE O 166 " --> pdb=" O LEU O 195 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR O 18 " --> pdb=" O PHE O 194 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU O 196 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU O 20 " --> pdb=" O GLU O 196 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL O 19 " --> pdb=" O PHE O 206 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU O 208 " --> pdb=" O VAL O 19 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL O 21 " --> pdb=" O LEU O 208 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE O 207 " --> pdb=" O MET O 215 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET O 215 " --> pdb=" O ILE O 207 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AC4, first strand: chain 'L' and resid 59 through 62 removed outlier: 5.952A pdb=" N LEU L 60 " --> pdb=" O VAL L 165 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL L 167 " --> pdb=" O LEU L 60 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE L 62 " --> pdb=" O VAL L 167 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU L 164 " --> pdb=" O LEU L 193 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU L 195 " --> pdb=" O LEU L 164 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE L 166 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL L 19 " --> pdb=" O PHE L 206 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU L 208 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL L 21 " --> pdb=" O LEU L 208 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 119 through 120 Processing sheet with id=AC6, first strand: chain 'N' and resid 19 through 21 removed outlier: 6.785A pdb=" N LEU N 164 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU N 195 " --> pdb=" O LEU N 164 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE N 166 " --> pdb=" O LEU N 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 18 through 21 removed outlier: 3.739A pdb=" N PHE M 194 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU M 20 " --> pdb=" O PHE M 194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU M 196 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU M 60 " --> pdb=" O VAL M 165 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL M 167 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE M 62 " --> pdb=" O VAL M 167 " (cutoff:3.500A) 1122 hydrogen bonds defined for protein. 3252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 174 hydrogen bonds 336 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 126 stacking parallelities Total time for adding SS restraints: 7.01 Time building geometry restraints manager: 2.59 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: 4057 1.33 - 1.45: 6727 1.45 - 1.57: 12658 1.57 - 1.70: 362 1.70 - 1.82: 74 Bond restraints: 23878 Sorted by residual: bond pdb=" O4' DA E 6 " pdb=" C1' DA E 6 " ideal model delta sigma weight residual 1.420 1.379 0.041 1.10e-02 8.26e+03 1.41e+01 bond pdb=" C1' DT D 33 " pdb=" N1 DT D 33 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" C1' DT D 14 " pdb=" N1 DT D 14 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.53e+00 bond pdb=" C4' DA E 6 " pdb=" O4' DA E 6 " ideal model delta sigma weight residual 1.446 1.474 -0.028 1.00e-02 1.00e+04 7.93e+00 bond pdb=" C3' DT D 44 " pdb=" C2' DT D 44 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.79e+00 ... (remaining 23873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 32323 1.99 - 3.98: 909 3.98 - 5.97: 73 5.97 - 7.96: 28 7.96 - 9.95: 9 Bond angle restraints: 33342 Sorted by residual: angle pdb=" CA GLU L 40 " pdb=" CB GLU L 40 " pdb=" CG GLU L 40 " ideal model delta sigma weight residual 114.10 123.30 -9.20 2.00e+00 2.50e-01 2.12e+01 angle pdb=" N3 DT D 33 " pdb=" C4 DT D 33 " pdb=" O4 DT D 33 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT E 34 " pdb=" C4 DT E 34 " pdb=" O4 DT E 34 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT E 4 " pdb=" C4 DT E 4 " pdb=" O4 DT E 4 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT E 31 " pdb=" C4 DT E 31 " pdb=" O4 DT E 31 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 ... (remaining 33337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.68: 11912 18.68 - 37.36: 1367 37.36 - 56.04: 656 56.04 - 74.73: 189 74.73 - 93.41: 13 Dihedral angle restraints: 14137 sinusoidal: 6142 harmonic: 7995 Sorted by residual: dihedral pdb=" CA TYR A1039 " pdb=" C TYR A1039 " pdb=" N SER A1040 " pdb=" CA SER A1040 " ideal model delta harmonic sigma weight residual 180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA PRO A 117 " pdb=" C PRO A 117 " pdb=" N ILE A 118 " pdb=" CA ILE A 118 " ideal model delta harmonic sigma weight residual -180.00 -156.11 -23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA TYR A 843 " pdb=" C TYR A 843 " pdb=" N ASP A 844 " pdb=" CA ASP A 844 " ideal model delta harmonic sigma weight residual -180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 14134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3801 0.097 - 0.194: 275 0.194 - 0.291: 3 0.291 - 0.388: 0 0.388 - 0.485: 1 Chirality restraints: 4080 Sorted by residual: chirality pdb=" CB ILE M 124 " pdb=" CA ILE M 124 " pdb=" CG1 ILE M 124 " pdb=" CG2 ILE M 124 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA MET L 109 " pdb=" N MET L 109 " pdb=" C MET L 109 " pdb=" CB MET L 109 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE L 203 " pdb=" N ILE L 203 " pdb=" C ILE L 203 " pdb=" CB ILE L 203 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 4077 not shown) Planarity restraints: 3582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU L 196 " -0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO L 197 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO L 197 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO L 197 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 555 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" CG ASP A 555 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP A 555 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP A 555 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1109 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.24e+00 pdb=" N PRO A1110 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A1110 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1110 " -0.034 5.00e-02 4.00e+02 ... (remaining 3579 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3970 2.76 - 3.30: 22254 3.30 - 3.83: 41981 3.83 - 4.37: 46445 4.37 - 4.90: 75470 Nonbonded interactions: 190120 Sorted by model distance: nonbonded pdb=" O ARG A 784 " pdb=" OG SER A 788 " model vdw 2.227 3.040 nonbonded pdb=" NH2 ARG A 70 " pdb=" OP1 A B -6 " model vdw 2.227 3.120 nonbonded pdb=" NH1 ARG A 62 " pdb=" OP1 U C 38 " model vdw 2.232 3.120 nonbonded pdb=" N2 G B 6 " pdb=" OP2 U C 18 " model vdw 2.233 3.120 nonbonded pdb=" O VAL L 101 " pdb=" OG1 THR L 105 " model vdw 2.234 3.040 ... (remaining 190115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 2 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 26 or (resid 27 through 29 and (nam \ e N or name CA or name C or name O or name CB )) or resid 30 through 33 or (resi \ d 34 and (name N or name CA or name C or name O or name CB )) or resid 35 throug \ h 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or re \ sid 38 or (resid 39 and (name N or name CA or name C or name O or name CB )) or \ resid 40 through 55 or (resid 56 and (name N or name CA or name C or name O or n \ ame CB )) or resid 57 through 59 or (resid 60 and (name N or name CA or name C o \ r name O or name CB )) or resid 61 through 99 or (resid 100 and (name N or name \ CA or name C or name O or name CB )) or resid 101 through 103 or (resid 104 and \ (name N or name CA or name C or name O or name CB )) or resid 105 through 185 or \ (resid 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 196 or (resid 197 and (name N or name CA or name C or name O or name C \ B )) or resid 198 through 212 or (resid 213 and (name N or name CA or name C or \ name O or name CB )) or resid 214 through 246 or (resid 247 and (name N or name \ CA or name C or name O or name CB )) or resid 248 through 249 or (resid 250 thro \ ugh 251 and (name N or name CA or name C or name O or name CB )) or resid 252 th \ rough 277 or (resid 278 through 280 and (name N or name CA or name C or name O o \ r name CB )) or resid 281 through 289)) selection = (chain 'G' and (resid 2 through 46 or (resid 47 and (name N or name CA or name C \ or name O or name CB )) or resid 48 through 68 or (resid 69 through 71 and (nam \ e N or name CA or name C or name O or name CB )) or resid 72 through 83 or (resi \ d 84 through 86 and (name N or name CA or name C or name O or name CB )) or resi \ d 87 through 111 or (resid 112 and (name N or name CA or name C or name O or nam \ e CB )) or resid 113 through 118 or (resid 119 through 120 and (name N or name C \ A or name C or name O or name CB )) or resid 121 through 122 or (resid 123 throu \ gh 129 and (name N or name CA or name C or name O or name CB )) or resid 130 or \ (resid 131 through 132 and (name N or name CA or name C or name O or name CB )) \ or resid 133 through 135 or (resid 136 through 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 or (resid 140 through 144 and (name N o \ r name CA or name C or name O or name CB )) or resid 145 or (resid 146 through 1 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 150 through \ 155 or (resid 156 through 158 and (name N or name CA or name C or name O or nam \ e CB )) or resid 159 or (resid 160 through 161 and (name N or name CA or name C \ or name O or name CB )) or (resid 162 through 172 and (name N or name CA or name \ C or name O or name CB )) or resid 173 or (resid 174 through 176 and (name N or \ name CA or name C or name O or name CB )) or resid 177 or (resid 178 and (name \ N or name CA or name C or name O or name CB )) or resid 179 through 198 or (resi \ d 199 and (name N or name CA or name C or name O or name CB )) or resid 200 or ( \ resid 201 and (name N or name CA or name C or name O or name CB )) or resid 202 \ through 209 or (resid 210 and (name N or name CA or name C or name O or name CB \ )) or resid 211 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 or (resid 219 through 220 and (name N or name CA \ or name C or name O or name CB )) or resid 221 through 222 or (resid 223 and (n \ ame N or name CA or name C or name O or name CB )) or resid 224 through 231 or ( \ resid 232 and (name N or name CA or name C or name O or name CB )) or resid 233 \ through 239 or (resid 240 and (name N or name CA or name C or name O or name CB \ )) or resid 241 through 242 or (resid 243 through 244 and (name N or name CA or \ name C or name O or name CB )) or resid 245 through 253 or (resid 254 and (name \ N or name CA or name C or name O or name CB )) or resid 255 or (resid 256 and (n \ ame N or name CA or name C or name O or name CB )) or resid 257 through 270 or ( \ resid 271 through 272 and (name N or name CA or name C or name O or name CB )) o \ r resid 273 through 287 or (resid 288 through 289 and (name N or name CA or name \ C or name O or name CB )))) } ncs_group { reference = (chain 'L' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 5 or (resid 6 through 7 and (name N or name CA or \ name C or name O or name CB )) or resid 8 or (resid 9 through 10 and (name N or \ name CA or name C or name O or name CB )) or resid 11 through 14 or (resid 15 t \ hrough 16 and (name N or name CA or name C or name O or name CB )) or resid 17 t \ hrough 39 or (resid 40 through 41 and (name N or name CA or name C or name O or \ name CB )) or resid 42 through 46 or (resid 47 through 52 and (name N or name CA \ or name C or name O or name CB )) or resid 53 through 56 or (resid 57 through 5 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 59 through 6 \ 8 or (resid 69 and (name N or name CA or name C or name O or name CB )) or resid \ 70 through 74 or (resid 75 and (name N or name CA or name C or name O or name C \ B )) or resid 76 through 78 or (resid 79 through 98 and (name N or name CA or na \ me C or name O or name CB )) or resid 99 through 101 or (resid 102 through 104 a \ nd (name N or name CA or name C or name O or name CB )) or resid 105 through 107 \ or (resid 108 and (name N or name CA or name C or name O or name CB )) or resid \ 109 through 118 or (resid 119 through 121 and (name N or name CA or name C or n \ ame O or name CB )) or resid 122 or (resid 123 through 124 and (name N or name C \ A or name C or name O or name CB )) or resid 125 through 128 or (resid 129 throu \ gh 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thr \ ough 134 or (resid 135 through 136 and (name N or name CA or name C or name O or \ name CB )) or resid 137 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 158 or (resid 159 through 160 a \ nd (name N or name CA or name C or name O or name CB )) or resid 161 or (resid 1 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 163 through \ 176 or (resid 177 and (name N or name CA or name C or name O or name CB )) or r \ esid 178 through 186 or (resid 187 and (name N or name CA or name C or name O or \ name CB )) or resid 188 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 197 or (resid 198 through 199 and (name N o \ r name CA or name C or name O or name CB )) or resid 200 or (resid 201 and (name \ N or name CA or name C or name O or name CB )) or resid 202 through 208 or (res \ id 209 through 211 and (name N or name CA or name C or name O or name CB )) or r \ esid 212 or (resid 213 through 215 and (name N or name CA or name C or name O or \ name CB )) or resid 216 through 218)) selection = (chain 'O' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 48 or (resid 49 through 52 and (name N or name CA \ or name C or name O or name CB )) or resid 53 through 90 or (resid 91 through 9 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 99 or (resid \ 100 and (name N or name CA or name C or name O or name CB )) or resid 101 throu \ gh 103 or (resid 104 and (name N or name CA or name C or name O or name CB )) or \ resid 105 through 106 or (resid 107 through 108 and (name N or name CA or name \ C or name O or name CB )) or resid 109 through 110 or (resid 111 and (name N or \ name CA or name C or name O or name CB )) or resid 112 through 114 or (resid 115 \ through 121 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 22 through 123 or (resid 124 and (name N or name CA or name C or name O or name \ CB )) or resid 125 through 127 or (resid 128 through 132 and (name N or name CA \ or name C or name O or name CB )) or resid 133 through 175 or (resid 176 through \ 177 and (name N or name CA or name C or name O or name CB )) or resid 178 throu \ gh 218)) } ncs_group { reference = (chain 'M' and (resid 18 through 38 or resid 58 through 70 or (resid 71 through \ 85 and (name N or name CA or name C or name O or name CB )) or resid 86 through \ 87 or (resid 88 through 90 and (name N or name CA or name C or name O or name CB \ )) or resid 91 or (resid 92 through 132 and (name N or name CA or name C or nam \ e O or name CB )) or resid 133 through 134 or (resid 135 through 197 and (name N \ or name CA or name C or name O or name CB )))) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.970 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23878 Z= 0.292 Angle : 0.749 9.953 33342 Z= 0.504 Chirality : 0.048 0.485 4080 Planarity : 0.005 0.077 3582 Dihedral : 19.952 93.407 8937 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.88 % Allowed : 27.01 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2674 helix: 0.64 (0.13), residues: 1371 sheet: -0.51 (0.34), residues: 247 loop : -0.66 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 100 TYR 0.041 0.002 TYR A 980 PHE 0.041 0.002 PHE A1038 TRP 0.014 0.002 TRP A 658 HIS 0.008 0.001 HIS A 654 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.29 (23878) covalent geometry : angle 0.74908 / 0.50 (33342) hydrogen bonds : bond 0.12631 / 8.83 ( 1296) hydrogen bonds : angle 5.89415 / 4.17 ( 3588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1277 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.6632 (m-80) REVERT: O 3 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8373 (tp) REVERT: O 31 LEU cc_start: 0.9262 (tp) cc_final: 0.8576 (tt) REVERT: O 35 PHE cc_start: 0.8527 (m-80) cc_final: 0.7984 (m-80) REVERT: O 139 THR cc_start: 0.8340 (p) cc_final: 0.7949 (p) REVERT: O 141 SER cc_start: 0.8716 (p) cc_final: 0.8407 (p) REVERT: L 31 LEU cc_start: 0.8293 (tp) cc_final: 0.7939 (tt) outliers start: 31 outliers final: 7 residues processed: 304 average time/residue: 0.1579 time to fit residues: 77.1061 Evaluate side-chains 174 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1277 PHE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain O residue 3 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS A 654 HIS ** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 ASN F 264 ASN G 21 HIS ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN G 211 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.048092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.033160 restraints weight = 180191.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.034100 restraints weight = 87728.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.034706 restraints weight = 54497.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035110 restraints weight = 39549.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.035322 restraints weight = 31939.359| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23878 Z= 0.247 Angle : 0.665 9.214 33342 Z= 0.359 Chirality : 0.044 0.365 4080 Planarity : 0.005 0.054 3582 Dihedral : 19.740 91.666 5338 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.54 % Allowed : 25.98 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.16), residues: 2674 helix: 1.12 (0.13), residues: 1391 sheet: -0.64 (0.32), residues: 265 loop : -0.53 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 234 TYR 0.019 0.002 TYR F 81 PHE 0.032 0.002 PHE F 77 TRP 0.011 0.001 TRP A 476 HIS 0.006 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.25 (23878) covalent geometry : angle 0.66524 / 0.36 (33342) hydrogen bonds : bond 0.05031 / 3.38 ( 1296) hydrogen bonds : angle 4.87702 / 3.46 ( 3588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 184 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8821 (t) REVERT: A 1100 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8166 (pp20) REVERT: F 4 TRP cc_start: 0.8793 (p-90) cc_final: 0.8583 (p-90) REVERT: F 18 LYS cc_start: 0.9212 (ttpt) cc_final: 0.8908 (tttt) REVERT: F 25 ARG cc_start: 0.9396 (mtt180) cc_final: 0.9043 (mmm-85) REVERT: F 32 MET cc_start: 0.9050 (ptp) cc_final: 0.8453 (ppp) REVERT: F 37 GLU cc_start: 0.9500 (mt-10) cc_final: 0.9001 (tt0) REVERT: F 191 GLU cc_start: 0.9161 (tp30) cc_final: 0.8907 (tp30) REVERT: F 269 TYR cc_start: 0.9603 (t80) cc_final: 0.9112 (t80) REVERT: G 53 MET cc_start: 0.9396 (tpt) cc_final: 0.9104 (tpt) REVERT: G 232 GLN cc_start: 0.9769 (mm110) cc_final: 0.9463 (mp10) REVERT: G 243 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9197 (pttp) REVERT: G 260 MET cc_start: 0.8724 (ttm) cc_final: 0.8449 (ttm) REVERT: O 30 GLN cc_start: 0.9820 (tp40) cc_final: 0.9592 (tm-30) REVERT: O 34 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8874 (mm-30) REVERT: O 35 PHE cc_start: 0.9618 (m-80) cc_final: 0.8936 (m-80) REVERT: O 172 TYR cc_start: 0.9173 (m-80) cc_final: 0.8819 (m-80) REVERT: O 207 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9002 (mm) REVERT: L 35 PHE cc_start: 0.9158 (m-80) cc_final: 0.8735 (m-80) REVERT: L 45 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9174 (p) REVERT: L 76 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9193 (mm) REVERT: L 133 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9141 (pp) REVERT: L 194 PHE cc_start: 0.9391 (m-80) cc_final: 0.8406 (m-80) REVERT: L 209 ASP cc_start: 0.8985 (p0) cc_final: 0.8764 (p0) REVERT: L 213 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9364 (mm) outliers start: 75 outliers final: 30 residues processed: 250 average time/residue: 0.1480 time to fit residues: 61.2885 Evaluate side-chains 202 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 211 GLN Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain G residue 243 LYS Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 213 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain M residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 239 optimal weight: 0.0040 chunk 224 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 215 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 166 optimal weight: 40.0000 overall best weight: 2.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 720 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 ASN F 264 ASN G 19 ASN G 117 GLN G 236 ASN L 37 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.047787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.032856 restraints weight = 180999.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.033802 restraints weight = 86909.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.034404 restraints weight = 53577.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.034796 restraints weight = 38732.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.035006 restraints weight = 31435.984| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23878 Z= 0.191 Angle : 0.597 14.207 33342 Z= 0.323 Chirality : 0.041 0.321 4080 Planarity : 0.004 0.053 3582 Dihedral : 19.791 91.925 5330 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.94 % Allowed : 24.65 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.16), residues: 2674 helix: 1.38 (0.14), residues: 1394 sheet: -0.61 (0.33), residues: 267 loop : -0.43 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 94 TYR 0.020 0.002 TYR A 552 PHE 0.030 0.002 PHE L 5 TRP 0.018 0.002 TRP A 18 HIS 0.004 0.001 HIS A 654 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (23878) covalent geometry : angle 0.59670 / 0.32 (33342) hydrogen bonds : bond 0.04279 / 2.85 ( 1296) hydrogen bonds : angle 4.60827 / 3.28 ( 3588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8776 (t) REVERT: A 352 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8660 (mttt) REVERT: F 4 TRP cc_start: 0.8824 (p-90) cc_final: 0.8562 (p-90) REVERT: F 5 ARG cc_start: 0.9583 (mmm-85) cc_final: 0.9068 (mmm-85) REVERT: F 18 LYS cc_start: 0.9233 (ttpt) cc_final: 0.8947 (tttt) REVERT: F 25 ARG cc_start: 0.9435 (mtt180) cc_final: 0.8806 (mtm-85) REVERT: F 53 MET cc_start: 0.9114 (tpt) cc_final: 0.8656 (tpp) REVERT: F 60 ASP cc_start: 0.8993 (m-30) cc_final: 0.8748 (m-30) REVERT: F 190 ARG cc_start: 0.9505 (OUTLIER) cc_final: 0.9200 (ptm160) REVERT: F 191 GLU cc_start: 0.9285 (tp30) cc_final: 0.8814 (tp30) REVERT: F 269 TYR cc_start: 0.9554 (t80) cc_final: 0.9134 (t80) REVERT: G 53 MET cc_start: 0.9376 (tpt) cc_final: 0.9118 (tpt) REVERT: G 219 MET cc_start: 0.9249 (ppp) cc_final: 0.8987 (ppp) REVERT: G 260 MET cc_start: 0.8690 (ttm) cc_final: 0.8386 (ttm) REVERT: O 23 GLU cc_start: 0.8292 (mp0) cc_final: 0.8076 (mp0) REVERT: O 30 GLN cc_start: 0.9815 (tp40) cc_final: 0.9596 (tm-30) REVERT: O 34 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8952 (mm-30) REVERT: O 172 TYR cc_start: 0.9291 (m-80) cc_final: 0.8691 (m-80) REVERT: L 31 LEU cc_start: 0.9764 (tp) cc_final: 0.9284 (tp) REVERT: L 33 LYS cc_start: 0.9498 (tttp) cc_final: 0.9070 (ttpp) REVERT: L 35 PHE cc_start: 0.9177 (m-80) cc_final: 0.8437 (m-80) REVERT: L 37 GLN cc_start: 0.9100 (mm110) cc_final: 0.8792 (mp10) REVERT: L 54 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8032 (mt) REVERT: L 76 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9245 (mm) REVERT: L 133 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9144 (pp) REVERT: L 194 PHE cc_start: 0.9389 (m-80) cc_final: 0.8476 (m-80) REVERT: M 76 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7554 (mm) outliers start: 65 outliers final: 33 residues processed: 230 average time/residue: 0.1490 time to fit residues: 56.3423 Evaluate side-chains 197 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 94 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 185 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 195 optimal weight: 0.5980 chunk 169 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 740 GLN F 264 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.046347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.031579 restraints weight = 184123.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.032479 restraints weight = 88777.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.033057 restraints weight = 55072.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.033370 restraints weight = 40072.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.033632 restraints weight = 33264.781| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23878 Z= 0.254 Angle : 0.643 14.518 33342 Z= 0.343 Chirality : 0.042 0.307 4080 Planarity : 0.004 0.054 3582 Dihedral : 19.879 90.968 5330 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.97 % Allowed : 24.23 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2674 helix: 1.46 (0.14), residues: 1398 sheet: -0.77 (0.32), residues: 284 loop : -0.35 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1107 TYR 0.019 0.002 TYR L 217 PHE 0.040 0.002 PHE F 77 TRP 0.030 0.002 TRP F 106 HIS 0.008 0.002 HIS G 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.25 (23878) covalent geometry : angle 0.64259 / 0.34 (33342) hydrogen bonds : bond 0.04881 / 3.21 ( 1296) hydrogen bonds : angle 4.59787 / 3.29 ( 3588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 161 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8698 (mttt) REVERT: A 689 ASN cc_start: 0.9525 (OUTLIER) cc_final: 0.9164 (t0) REVERT: A 927 GLN cc_start: 0.9513 (OUTLIER) cc_final: 0.9280 (mm-40) REVERT: F 5 ARG cc_start: 0.9478 (mmm-85) cc_final: 0.9273 (mtp85) REVERT: F 18 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8928 (tttt) REVERT: F 25 ARG cc_start: 0.9467 (mtt180) cc_final: 0.8929 (mtm-85) REVERT: F 32 MET cc_start: 0.9228 (pmm) cc_final: 0.8979 (pmm) REVERT: F 53 MET cc_start: 0.9103 (tpt) cc_final: 0.8708 (tpp) REVERT: F 190 ARG cc_start: 0.9532 (OUTLIER) cc_final: 0.8972 (ptm160) REVERT: F 191 GLU cc_start: 0.9375 (tp30) cc_final: 0.8840 (tp30) REVERT: F 268 ASP cc_start: 0.9427 (t70) cc_final: 0.9165 (p0) REVERT: F 269 TYR cc_start: 0.9507 (t80) cc_final: 0.9102 (t80) REVERT: G 53 MET cc_start: 0.9387 (tpt) cc_final: 0.9089 (mmm) REVERT: G 219 MET cc_start: 0.9310 (ppp) cc_final: 0.8991 (ppp) REVERT: G 232 GLN cc_start: 0.9776 (mm110) cc_final: 0.9461 (mp10) REVERT: G 260 MET cc_start: 0.8827 (ttm) cc_final: 0.8604 (ttm) REVERT: O 34 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9030 (mm-30) REVERT: O 35 PHE cc_start: 0.9649 (m-80) cc_final: 0.9046 (m-80) REVERT: O 172 TYR cc_start: 0.9382 (m-80) cc_final: 0.8574 (m-80) REVERT: L 10 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9209 (pm20) REVERT: L 23 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: L 31 LEU cc_start: 0.9830 (tp) cc_final: 0.9429 (tp) REVERT: L 33 LYS cc_start: 0.9590 (tttp) cc_final: 0.9337 (ttpp) REVERT: L 35 PHE cc_start: 0.9289 (m-80) cc_final: 0.8718 (m-80) REVERT: L 54 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8119 (mt) REVERT: L 76 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9274 (mm) REVERT: M 76 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7731 (mm) outliers start: 82 outliers final: 43 residues processed: 233 average time/residue: 0.1414 time to fit residues: 55.0977 Evaluate side-chains 206 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 139 THR Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 206 PHE Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 95 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 134 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 235 optimal weight: 0.0770 chunk 237 optimal weight: 20.0000 chunk 231 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 906 ASN A1260 ASN A1297 ASN F 264 ASN L 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.047298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.032394 restraints weight = 180845.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.033356 restraints weight = 86133.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.033877 restraints weight = 52729.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.034290 restraints weight = 38923.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.034493 restraints weight = 31418.935| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23878 Z= 0.131 Angle : 0.565 14.532 33342 Z= 0.300 Chirality : 0.041 0.315 4080 Planarity : 0.003 0.055 3582 Dihedral : 19.820 90.668 5330 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.33 % Allowed : 26.29 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2674 helix: 1.59 (0.14), residues: 1405 sheet: -0.67 (0.32), residues: 291 loop : -0.30 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 57 TYR 0.014 0.001 TYR G 120 PHE 0.023 0.001 PHE L 173 TRP 0.040 0.002 TRP F 4 HIS 0.005 0.001 HIS G 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (23878) covalent geometry : angle 0.56478 / 0.30 (33342) hydrogen bonds : bond 0.03642 / 2.42 ( 1296) hydrogen bonds : angle 4.34146 / 3.11 ( 3588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8781 (t) REVERT: A 90 MET cc_start: 0.9445 (tpp) cc_final: 0.9204 (tpp) REVERT: A 352 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8699 (mttt) REVERT: A 689 ASN cc_start: 0.9537 (OUTLIER) cc_final: 0.9011 (t0) REVERT: A 1235 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: F 4 TRP cc_start: 0.8771 (p-90) cc_final: 0.8132 (p-90) REVERT: F 5 ARG cc_start: 0.9408 (mmm-85) cc_final: 0.9188 (mpp80) REVERT: F 18 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8935 (tttt) REVERT: F 25 ARG cc_start: 0.9492 (mtt180) cc_final: 0.9181 (mtm-85) REVERT: F 32 MET cc_start: 0.9187 (pmm) cc_final: 0.8908 (pmm) REVERT: F 37 GLU cc_start: 0.9556 (mt-10) cc_final: 0.9004 (mm-30) REVERT: F 53 MET cc_start: 0.9038 (tpt) cc_final: 0.8617 (tpp) REVERT: F 77 PHE cc_start: 0.9681 (p90) cc_final: 0.9469 (p90) REVERT: F 190 ARG cc_start: 0.9520 (OUTLIER) cc_final: 0.9205 (ptm160) REVERT: F 191 GLU cc_start: 0.9377 (tp30) cc_final: 0.8861 (tp30) REVERT: F 264 ASN cc_start: 0.9795 (OUTLIER) cc_final: 0.9469 (m110) REVERT: F 268 ASP cc_start: 0.9388 (t70) cc_final: 0.9055 (p0) REVERT: G 53 MET cc_start: 0.9351 (tpt) cc_final: 0.9059 (mmm) REVERT: G 219 MET cc_start: 0.9298 (ppp) cc_final: 0.8938 (ppp) REVERT: G 260 MET cc_start: 0.8864 (ttm) cc_final: 0.8596 (ttm) REVERT: O 35 PHE cc_start: 0.9659 (m-80) cc_final: 0.9098 (m-80) REVERT: O 172 TYR cc_start: 0.9409 (m-80) cc_final: 0.8705 (m-80) REVERT: L 30 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8921 (tm-30) REVERT: L 31 LEU cc_start: 0.9749 (tp) cc_final: 0.9344 (tp) REVERT: L 33 LYS cc_start: 0.9536 (tttp) cc_final: 0.9261 (ttpp) REVERT: L 35 PHE cc_start: 0.9220 (m-80) cc_final: 0.8379 (m-80) REVERT: L 41 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7933 (pp30) REVERT: L 76 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9298 (mm) REVERT: M 76 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7697 (mm) outliers start: 55 outliers final: 30 residues processed: 212 average time/residue: 0.1480 time to fit residues: 51.8480 Evaluate side-chains 196 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1260 ASN Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 198 MET Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 139 THR Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 206 PHE Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 94 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 234 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 251 optimal weight: 50.0000 chunk 200 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 23 optimal weight: 40.0000 chunk 86 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 268 optimal weight: 50.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1241 GLN A1273 HIS A1297 ASN F 264 ASN G 147 ASN O 115 ASN L 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.045220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.030667 restraints weight = 188221.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.031531 restraints weight = 90224.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.032045 restraints weight = 55844.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.032451 restraints weight = 41169.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.032662 restraints weight = 33357.436| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 23878 Z= 0.328 Angle : 0.700 13.517 33342 Z= 0.371 Chirality : 0.042 0.206 4080 Planarity : 0.004 0.051 3582 Dihedral : 19.878 90.514 5330 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.78 % Allowed : 25.68 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.16), residues: 2674 helix: 1.45 (0.14), residues: 1403 sheet: -0.78 (0.33), residues: 278 loop : -0.33 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1107 TYR 0.019 0.002 TYR A 681 PHE 0.021 0.002 PHE L 173 TRP 0.014 0.002 TRP F 4 HIS 0.006 0.002 HIS G 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.33 (23878) covalent geometry : angle 0.69987 / 0.37 (33342) hydrogen bonds : bond 0.05519 / 3.60 ( 1296) hydrogen bonds : angle 4.61702 / 3.31 ( 3588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 150 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9420 (tpp) cc_final: 0.9069 (mmm) REVERT: A 747 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: A 752 MET cc_start: 0.9478 (mmm) cc_final: 0.9178 (mmm) REVERT: A 927 GLN cc_start: 0.9577 (OUTLIER) cc_final: 0.9282 (mm-40) REVERT: A 1235 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: F 32 MET cc_start: 0.9180 (pmm) cc_final: 0.8782 (pmm) REVERT: F 190 ARG cc_start: 0.9581 (OUTLIER) cc_final: 0.9045 (ptm160) REVERT: F 191 GLU cc_start: 0.9454 (tp30) cc_final: 0.9059 (tp30) REVERT: F 269 TYR cc_start: 0.9530 (t80) cc_final: 0.9156 (t80) REVERT: G 53 MET cc_start: 0.9388 (tpt) cc_final: 0.9015 (mmm) REVERT: G 103 CYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9007 (t) REVERT: G 219 MET cc_start: 0.9349 (ppp) cc_final: 0.8961 (ppp) REVERT: G 232 GLN cc_start: 0.9775 (mm110) cc_final: 0.9491 (mp10) REVERT: G 260 MET cc_start: 0.8894 (ttm) cc_final: 0.8660 (ttm) REVERT: O 30 GLN cc_start: 0.9782 (tm-30) cc_final: 0.9565 (tm-30) REVERT: O 35 PHE cc_start: 0.9661 (m-80) cc_final: 0.9163 (m-80) REVERT: O 172 TYR cc_start: 0.9492 (m-80) cc_final: 0.8897 (m-80) REVERT: L 23 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: L 33 LYS cc_start: 0.9599 (tttp) cc_final: 0.8934 (ttpp) REVERT: L 37 GLN cc_start: 0.9364 (mm110) cc_final: 0.8894 (mp10) REVERT: L 54 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8262 (mt) REVERT: L 76 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9334 (mm) REVERT: M 76 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7743 (mm) outliers start: 79 outliers final: 49 residues processed: 216 average time/residue: 0.1422 time to fit residues: 50.4068 Evaluate side-chains 204 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 198 MET Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 139 THR Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 206 PHE Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 97 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 20 optimal weight: 9.9990 chunk 23 optimal weight: 50.0000 chunk 163 optimal weight: 40.0000 chunk 149 optimal weight: 40.0000 chunk 147 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 127 optimal weight: 0.1980 chunk 260 optimal weight: 0.0870 chunk 223 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 ASN F 264 ASN L 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.046100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.031476 restraints weight = 183759.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.032373 restraints weight = 86968.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.032951 restraints weight = 53395.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.033266 restraints weight = 38756.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.033544 restraints weight = 32000.306| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23878 Z= 0.163 Angle : 0.586 14.976 33342 Z= 0.310 Chirality : 0.041 0.352 4080 Planarity : 0.004 0.056 3582 Dihedral : 19.864 90.685 5330 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.21 % Allowed : 27.32 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2674 helix: 1.63 (0.14), residues: 1405 sheet: -0.59 (0.34), residues: 273 loop : -0.31 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 5 TYR 0.020 0.001 TYR L 217 PHE 0.022 0.002 PHE L 173 TRP 0.016 0.002 TRP F 4 HIS 0.003 0.001 HIS G 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (23878) covalent geometry : angle 0.58569 / 0.31 (33342) hydrogen bonds : bond 0.03882 / 2.58 ( 1296) hydrogen bonds : angle 4.36278 / 3.13 ( 3588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 SER cc_start: 0.9201 (OUTLIER) cc_final: 0.8920 (t) REVERT: A 90 MET cc_start: 0.9401 (tpp) cc_final: 0.9053 (mmm) REVERT: A 927 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.8885 (mt0) REVERT: A 1235 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: F 32 MET cc_start: 0.9250 (pmm) cc_final: 0.8838 (pmm) REVERT: F 190 ARG cc_start: 0.9552 (OUTLIER) cc_final: 0.9226 (ptm160) REVERT: F 191 GLU cc_start: 0.9427 (tp30) cc_final: 0.9009 (tp30) REVERT: F 264 ASN cc_start: 0.9778 (m110) cc_final: 0.9486 (m110) REVERT: F 268 ASP cc_start: 0.9311 (t70) cc_final: 0.9001 (p0) REVERT: F 269 TYR cc_start: 0.9496 (t80) cc_final: 0.9075 (t80) REVERT: G 53 MET cc_start: 0.9375 (tpt) cc_final: 0.9054 (mmm) REVERT: G 219 MET cc_start: 0.9344 (ppp) cc_final: 0.8941 (ppp) REVERT: G 260 MET cc_start: 0.8876 (ttm) cc_final: 0.8611 (ttm) REVERT: O 35 PHE cc_start: 0.9662 (m-80) cc_final: 0.9135 (m-80) REVERT: O 172 TYR cc_start: 0.9455 (m-80) cc_final: 0.8774 (m-80) REVERT: L 23 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: L 25 VAL cc_start: 0.9589 (m) cc_final: 0.9351 (p) REVERT: L 33 LYS cc_start: 0.9578 (tttp) cc_final: 0.8838 (ttpp) REVERT: L 37 GLN cc_start: 0.9362 (mm110) cc_final: 0.9010 (mp10) REVERT: L 54 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8206 (mt) REVERT: L 76 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9333 (mm) REVERT: M 76 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7729 (mm) outliers start: 53 outliers final: 37 residues processed: 199 average time/residue: 0.1293 time to fit residues: 42.2962 Evaluate side-chains 191 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 198 MET Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 139 THR Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 206 PHE Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 97 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 214 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1297 ASN ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.045284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.030702 restraints weight = 186937.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.031598 restraints weight = 88851.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.032104 restraints weight = 54526.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.032505 restraints weight = 40276.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.032702 restraints weight = 32721.557| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23878 Z= 0.256 Angle : 0.637 14.731 33342 Z= 0.337 Chirality : 0.042 0.402 4080 Planarity : 0.004 0.054 3582 Dihedral : 19.835 90.612 5328 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.94 % Allowed : 27.07 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2674 helix: 1.59 (0.14), residues: 1407 sheet: -0.59 (0.34), residues: 273 loop : -0.34 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1107 TYR 0.019 0.002 TYR L 217 PHE 0.020 0.002 PHE L 173 TRP 0.045 0.002 TRP F 4 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.26 (23878) covalent geometry : angle 0.63738 / 0.34 (33342) hydrogen bonds : bond 0.04597 / 3.03 ( 1296) hydrogen bonds : angle 4.45703 / 3.20 ( 3588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 148 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.9003 (t) REVERT: A 90 MET cc_start: 0.9363 (tpp) cc_final: 0.9003 (mmm) REVERT: A 752 MET cc_start: 0.9479 (mmm) cc_final: 0.8900 (mmm) REVERT: A 927 GLN cc_start: 0.9531 (OUTLIER) cc_final: 0.9308 (mm110) REVERT: A 1235 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: F 32 MET cc_start: 0.9288 (pmm) cc_final: 0.8827 (pmm) REVERT: F 190 ARG cc_start: 0.9593 (OUTLIER) cc_final: 0.9050 (ptm160) REVERT: F 191 GLU cc_start: 0.9460 (tp30) cc_final: 0.9062 (tp30) REVERT: F 269 TYR cc_start: 0.9515 (t80) cc_final: 0.9158 (t80) REVERT: G 53 MET cc_start: 0.9383 (tpt) cc_final: 0.9137 (mmm) REVERT: G 103 CYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9021 (t) REVERT: G 219 MET cc_start: 0.9362 (ppp) cc_final: 0.8958 (ppp) REVERT: G 232 GLN cc_start: 0.9777 (mm110) cc_final: 0.9467 (mp10) REVERT: G 260 MET cc_start: 0.8901 (ttm) cc_final: 0.8641 (ttm) REVERT: G 270 THR cc_start: 0.9478 (m) cc_final: 0.9138 (p) REVERT: O 35 PHE cc_start: 0.9684 (m-80) cc_final: 0.9168 (m-80) REVERT: O 172 TYR cc_start: 0.9465 (m-80) cc_final: 0.8858 (m-80) REVERT: L 25 VAL cc_start: 0.9621 (m) cc_final: 0.9397 (p) REVERT: L 33 LYS cc_start: 0.9580 (tttp) cc_final: 0.9241 (ttpp) REVERT: L 54 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8260 (mt) REVERT: L 76 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9336 (mm) REVERT: M 76 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7741 (mm) outliers start: 65 outliers final: 50 residues processed: 201 average time/residue: 0.1264 time to fit residues: 42.6908 Evaluate side-chains 203 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 198 MET Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 261 TYR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 38 TYR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 139 THR Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 206 PHE Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 97 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 58 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 167 optimal weight: 30.0000 chunk 227 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 259 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.045288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.030703 restraints weight = 187481.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.031610 restraints weight = 88364.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.032156 restraints weight = 54022.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.032525 restraints weight = 39364.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.032717 restraints weight = 32073.000| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23878 Z= 0.215 Angle : 0.619 14.446 33342 Z= 0.327 Chirality : 0.041 0.332 4080 Planarity : 0.004 0.056 3582 Dihedral : 19.840 90.522 5328 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.45 % Allowed : 27.56 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2674 helix: 1.62 (0.14), residues: 1408 sheet: -0.61 (0.34), residues: 272 loop : -0.35 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 57 TYR 0.022 0.002 TYR L 217 PHE 0.021 0.002 PHE L 173 TRP 0.043 0.002 TRP F 4 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.22 (23878) covalent geometry : angle 0.61903 / 0.33 (33342) hydrogen bonds : bond 0.04115 / 2.73 ( 1296) hydrogen bonds : angle 4.40096 / 3.15 ( 3588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 145 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8734 (t) REVERT: A 29 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.9012 (t) REVERT: A 90 MET cc_start: 0.9310 (tpp) cc_final: 0.8962 (mmm) REVERT: A 752 MET cc_start: 0.9489 (mmm) cc_final: 0.9150 (mmm) REVERT: A 829 MET cc_start: 0.9227 (mmm) cc_final: 0.8978 (mpp) REVERT: A 927 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.8903 (mt0) REVERT: A 1235 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: F 4 TRP cc_start: 0.8812 (p-90) cc_final: 0.8601 (p-90) REVERT: F 5 ARG cc_start: 0.9493 (mmm-85) cc_final: 0.8896 (ttm110) REVERT: F 32 MET cc_start: 0.9311 (pmm) cc_final: 0.8868 (pmm) REVERT: F 190 ARG cc_start: 0.9589 (OUTLIER) cc_final: 0.9262 (ptm160) REVERT: F 191 GLU cc_start: 0.9450 (tp30) cc_final: 0.9097 (tp30) REVERT: F 268 ASP cc_start: 0.9422 (t0) cc_final: 0.9089 (p0) REVERT: F 269 TYR cc_start: 0.9527 (t80) cc_final: 0.9085 (t80) REVERT: G 103 CYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9014 (t) REVERT: G 121 LEU cc_start: 0.9587 (tp) cc_final: 0.9240 (tp) REVERT: G 198 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8432 (mtp) REVERT: G 219 MET cc_start: 0.9375 (ppp) cc_final: 0.8945 (ppp) REVERT: G 232 GLN cc_start: 0.9783 (mm110) cc_final: 0.9470 (mp10) REVERT: G 260 MET cc_start: 0.8971 (ttm) cc_final: 0.8757 (ttm) REVERT: G 270 THR cc_start: 0.9465 (m) cc_final: 0.9122 (p) REVERT: O 35 PHE cc_start: 0.9687 (m-80) cc_final: 0.9175 (m-80) REVERT: O 172 TYR cc_start: 0.9463 (m-80) cc_final: 0.8866 (m-80) REVERT: L 33 LYS cc_start: 0.9570 (tttp) cc_final: 0.9233 (ttpp) REVERT: L 218 ASN cc_start: 0.9217 (m-40) cc_final: 0.8987 (m-40) REVERT: M 76 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7774 (mm) outliers start: 57 outliers final: 44 residues processed: 191 average time/residue: 0.1400 time to fit residues: 44.6718 Evaluate side-chains 196 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 198 MET Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 261 TYR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 38 TYR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 139 THR Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 206 PHE Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 97 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 171 optimal weight: 40.0000 chunk 72 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN L 30 GLN ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.045493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.030931 restraints weight = 186963.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.031833 restraints weight = 87719.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.032391 restraints weight = 53797.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.032742 restraints weight = 38969.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.033000 restraints weight = 31872.747| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23878 Z= 0.178 Angle : 0.608 14.910 33342 Z= 0.317 Chirality : 0.041 0.306 4080 Planarity : 0.003 0.055 3582 Dihedral : 19.761 90.309 5328 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.63 % Allowed : 27.56 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2674 helix: 1.68 (0.14), residues: 1409 sheet: -0.60 (0.34), residues: 269 loop : -0.32 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 57 TYR 0.019 0.001 TYR L 217 PHE 0.023 0.002 PHE O 194 TRP 0.041 0.002 TRP F 4 HIS 0.004 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (23878) covalent geometry : angle 0.60753 / 0.32 (33342) hydrogen bonds : bond 0.03904 / 2.59 ( 1296) hydrogen bonds : angle 4.34018 / 3.10 ( 3588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8719 (t) REVERT: A 29 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.9013 (t) REVERT: A 90 MET cc_start: 0.9301 (tpp) cc_final: 0.8949 (mmm) REVERT: A 752 MET cc_start: 0.9473 (mmm) cc_final: 0.8899 (mmm) REVERT: A 927 GLN cc_start: 0.9515 (OUTLIER) cc_final: 0.8909 (mt0) REVERT: A 1043 MET cc_start: 0.9331 (mmm) cc_final: 0.8590 (mmm) REVERT: A 1235 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: F 5 ARG cc_start: 0.9503 (mmm-85) cc_final: 0.9052 (ttm110) REVERT: F 32 MET cc_start: 0.9311 (pmm) cc_final: 0.8870 (pmm) REVERT: F 190 ARG cc_start: 0.9591 (OUTLIER) cc_final: 0.9052 (ptm160) REVERT: F 191 GLU cc_start: 0.9453 (tp30) cc_final: 0.9082 (tp30) REVERT: G 26 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7146 (m110) REVERT: G 121 LEU cc_start: 0.9587 (tp) cc_final: 0.9240 (tp) REVERT: G 187 MET cc_start: 0.9221 (mtp) cc_final: 0.8985 (mtp) REVERT: G 219 MET cc_start: 0.9356 (ppp) cc_final: 0.8985 (ppp) REVERT: G 232 GLN cc_start: 0.9778 (mm110) cc_final: 0.9453 (mp10) REVERT: G 260 MET cc_start: 0.8994 (ttm) cc_final: 0.8777 (ttm) REVERT: G 270 THR cc_start: 0.9468 (m) cc_final: 0.9124 (p) REVERT: O 35 PHE cc_start: 0.9684 (m-80) cc_final: 0.9172 (m-80) REVERT: O 109 MET cc_start: 0.7268 (mpp) cc_final: 0.5809 (mmm) REVERT: O 172 TYR cc_start: 0.9453 (m-80) cc_final: 0.8825 (m-80) REVERT: L 33 LYS cc_start: 0.9547 (tttp) cc_final: 0.9201 (ttpp) REVERT: L 47 PHE cc_start: 0.9488 (OUTLIER) cc_final: 0.9174 (p90) REVERT: L 54 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8252 (mt) REVERT: M 76 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7846 (mm) outliers start: 60 outliers final: 45 residues processed: 196 average time/residue: 0.1250 time to fit residues: 41.0905 Evaluate side-chains 198 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain G residue 261 TYR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 139 THR Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 206 PHE Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 121 TYR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 97 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 93 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.045517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.030917 restraints weight = 187295.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.031823 restraints weight = 87976.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.032385 restraints weight = 53750.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.032731 restraints weight = 39031.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.032979 restraints weight = 31895.307| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.280 23878 Z= 0.268 Angle : 0.770 59.200 33342 Z= 0.432 Chirality : 0.044 0.865 4080 Planarity : 0.004 0.056 3582 Dihedral : 19.762 90.301 5328 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.69 % Allowed : 27.50 % Favored : 68.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2674 helix: 1.68 (0.14), residues: 1409 sheet: -0.56 (0.34), residues: 269 loop : -0.32 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 5 TYR 0.016 0.001 TYR G 120 PHE 0.020 0.001 PHE L 173 TRP 0.035 0.003 TRP F 4 HIS 0.012 0.001 HIS F 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.27 (23878) covalent geometry : angle 0.76977 / 0.43 (33342) hydrogen bonds : bond 0.03904 / 2.59 ( 1296) hydrogen bonds : angle 4.34172 / 3.11 ( 3588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4350.34 seconds wall clock time: 75 minutes 53.28 seconds (4553.28 seconds total)