Starting phenix.real_space_refine on Sat Jul 4 21:26:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q85_52886/07_2026/9q85_52886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q85_52886/07_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_52886/07_2026/9q85_52886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q85_52886/07_2026/9q85_52886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q85_52886/07_2026/9q85_52886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q85_52886/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 5.74, per 1000 atoms: 0.25 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: 2.01 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: 6.77 Time building geometry restraints manager: 2.69 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: 32553 1.99 - 3.98: 679 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: 3891 0.097 - 0.194: 185 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: 3.900 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.330 Find NCS groups from input model: 0.260 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.550 ------------------------------------------------------------------------------- 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= 0.288 Angle : 0.715 9.953 33342 Z= 0.475 Chirality : 0.044 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 0.00452 / 0.29 (23878) covalent geometry : angle 0.71539 / 0.48 (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 : 0.859 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: 0.6631 (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: 0.7938 (tt) outliers start: 31 outliers final: 7 residues processed: 304 average time/residue: 0.1566 time to fit residues: 75.8063 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 : 0.809 ------------------------------------------------------------------------------- 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: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.9704 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.048162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.033232 restraints weight = 179871.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.034159 restraints weight = 87518.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.034770 restraints weight = 54588.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035105 restraints weight = 39438.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.035395 restraints weight = 32392.121| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23878 Z= 0.248 Angle : 0.661 9.479 33342 Z= 0.359 Chirality : 0.043 0.347 4080 Planarity : 0.005 0.054 3582 Dihedral : 19.801 93.132 5338 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.54 % Allowed : 25.74 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 2674 helix: 1.11 (0.13), residues: 1390 sheet: -0.64 (0.32), residues: 265 loop : -0.53 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 234 TYR 0.020 0.002 TYR O 36 PHE 0.035 0.002 PHE F 77 TRP 0.011 0.001 TRP A 476 HIS 0.005 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.25 (23878) covalent geometry : angle 0.66139 / 0.36 (33342) hydrogen bonds : bond 0.04934 / 3.31 ( 1296) hydrogen bonds : angle 4.86378 / 3.45 ( 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 263 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 188 time to evaluate : 0.812 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 29 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8813 (t) REVERT: A 1100 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8166 (pp20) REVERT: F 18 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8922 (tttt) REVERT: F 25 ARG cc_start: 0.9416 (mtt180) cc_final: 0.9081 (mmm-85) REVERT: F 32 MET cc_start: 0.9068 (ptp) cc_final: 0.8500 (ppp) REVERT: F 33 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9163 (mp) REVERT: F 37 GLU cc_start: 0.9507 (mt-10) cc_final: 0.9059 (tt0) REVERT: F 191 GLU cc_start: 0.9173 (tp30) cc_final: 0.8928 (tp30) REVERT: F 269 TYR cc_start: 0.9602 (t80) cc_final: 0.9106 (t80) REVERT: G 53 MET cc_start: 0.9394 (tpt) cc_final: 0.9006 (mmm) REVERT: G 70 ASP cc_start: 0.9036 (p0) cc_final: 0.8819 (p0) REVERT: G 121 LEU cc_start: 0.9443 (tp) cc_final: 0.9061 (tp) REVERT: G 131 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8881 (mm-40) REVERT: G 232 GLN cc_start: 0.9768 (mm110) cc_final: 0.9467 (mp10) REVERT: G 260 MET cc_start: 0.8775 (ttm) cc_final: 0.8530 (ttm) REVERT: O 30 GLN cc_start: 0.9820 (tp40) cc_final: 0.9591 (tm-30) REVERT: O 34 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8873 (mm-30) REVERT: O 35 PHE cc_start: 0.9617 (m-80) cc_final: 0.8941 (m-80) REVERT: O 172 TYR cc_start: 0.9199 (m-80) cc_final: 0.8856 (m-80) REVERT: O 207 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9001 (mm) REVERT: L 31 LEU cc_start: 0.9731 (tp) cc_final: 0.9107 (pp) REVERT: L 35 PHE cc_start: 0.9176 (m-80) cc_final: 0.8838 (m-80) REVERT: L 76 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9190 (mm) REVERT: L 133 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9118 (pp) REVERT: L 194 PHE cc_start: 0.9389 (m-80) cc_final: 0.8405 (m-80) REVERT: L 209 ASP cc_start: 0.8989 (p0) cc_final: 0.8764 (p0) REVERT: L 213 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9362 (mm) outliers start: 75 outliers final: 30 residues processed: 254 average time/residue: 0.1448 time to fit residues: 60.7227 Evaluate side-chains 200 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 33 ILE 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 G residue 47 ASP 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 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 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: 0.1980 chunk 224 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 178 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 166 optimal weight: 40.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.048089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.033123 restraints weight = 178618.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.034078 restraints weight = 86249.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.034689 restraints weight = 53237.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.035064 restraints weight = 38381.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035258 restraints weight = 31203.347| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1942 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= 0.170 Angle : 0.584 14.592 33342 Z= 0.318 Chirality : 0.041 0.309 4080 Planarity : 0.004 0.054 3582 Dihedral : 19.840 92.914 5332 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.57 % Allowed : 24.95 % Favored : 71.47 % 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: 0.65 (0.16), residues: 2674 helix: 1.34 (0.14), residues: 1398 sheet: -0.63 (0.33), residues: 272 loop : -0.47 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 5 TYR 0.019 0.002 TYR A 552 PHE 0.027 0.002 PHE L 5 TRP 0.045 0.002 TRP F 4 HIS 0.004 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (23878) covalent geometry : angle 0.58356 / 0.32 (33342) hydrogen bonds : bond 0.04045 / 2.69 ( 1296) hydrogen bonds : angle 4.57400 / 3.26 ( 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 234 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.898 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: 0.9045 (OUTLIER) cc_final: 0.8733 (t) REVERT: A 352 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8663 (mttt) REVERT: F 4 TRP cc_start: 0.8781 (p-90) cc_final: 0.8135 (p-90) REVERT: F 5 ARG cc_start: 0.9387 (mmm-85) cc_final: 0.9083 (tpp80) REVERT: F 18 LYS cc_start: 0.9236 (ttpt) cc_final: 0.8940 (tttt) REVERT: F 25 ARG cc_start: 0.9429 (mtt180) cc_final: 0.9035 (mtm-85) REVERT: F 37 GLU cc_start: 0.9540 (mt-10) cc_final: 0.9162 (tt0) REVERT: F 53 MET cc_start: 0.9118 (tpt) cc_final: 0.8666 (tpp) REVERT: F 60 ASP cc_start: 0.8977 (m-30) cc_final: 0.8738 (m-30) REVERT: F 77 PHE cc_start: 0.9399 (p90) cc_final: 0.9169 (p90) REVERT: F 190 ARG cc_start: 0.9501 (OUTLIER) cc_final: 0.9197 (ptm160) REVERT: F 191 GLU cc_start: 0.9256 (tp30) cc_final: 0.8833 (tp30) REVERT: F 269 TYR cc_start: 0.9531 (t80) cc_final: 0.9129 (t80) REVERT: G 53 MET cc_start: 0.9370 (tpt) cc_final: 0.9109 (tpt) REVERT: G 219 MET cc_start: 0.9259 (ppp) cc_final: 0.8996 (ppp) REVERT: G 260 MET cc_start: 0.8694 (ttm) cc_final: 0.8405 (ttm) REVERT: O 23 GLU cc_start: 0.8303 (mp0) cc_final: 0.8093 (mp0) REVERT: O 34 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8901 (mm-30) REVERT: O 172 TYR cc_start: 0.9285 (m-80) cc_final: 0.8679 (m-80) REVERT: L 31 LEU cc_start: 0.9727 (tp) cc_final: 0.9310 (tp) REVERT: L 33 LYS cc_start: 0.9520 (tttp) cc_final: 0.9294 (ttpp) REVERT: L 35 PHE cc_start: 0.9172 (m-80) cc_final: 0.8471 (m-80) REVERT: L 76 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9242 (mm) REVERT: L 133 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9124 (pp) REVERT: L 194 PHE cc_start: 0.9374 (m-80) cc_final: 0.8473 (m-80) REVERT: M 76 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7536 (mm) outliers start: 59 outliers final: 29 residues processed: 228 average time/residue: 0.1467 time to fit residues: 54.9535 Evaluate side-chains 194 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 474 THR Chi-restraints excluded: chain A residue 641 ILE 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 190 ARG Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ASP 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 10 GLU Chi-restraints excluded: chain L residue 23 GLU 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 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 Chi-restraints excluded: chain M residue 95 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 185 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 195 optimal weight: 0.4980 chunk 169 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 740 GLN ** A 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 GLN ** 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 = 0.3338 r_free = 0.3338 target = 0.046240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.031488 restraints weight = 185456.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.032387 restraints weight = 89638.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.032974 restraints weight = 55568.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.033345 restraints weight = 40365.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.033569 restraints weight = 32809.168| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 23878 Z= 0.288 Angle : 0.661 14.411 33342 Z= 0.357 Chirality : 0.042 0.311 4080 Planarity : 0.004 0.054 3582 Dihedral : 19.941 92.246 5332 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.91 % Allowed : 24.11 % Favored : 70.99 % 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: 0.70 (0.16), residues: 2674 helix: 1.39 (0.14), residues: 1397 sheet: -0.80 (0.32), residues: 284 loop : -0.36 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1107 TYR 0.017 0.002 TYR L 217 PHE 0.025 0.002 PHE L 173 TRP 0.031 0.002 TRP F 106 HIS 0.005 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.29 (23878) covalent geometry : angle 0.66095 / 0.36 (33342) hydrogen bonds : bond 0.05231 / 3.43 ( 1296) hydrogen bonds : angle 4.66233 / 3.34 ( 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 244 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 163 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9545 (mmm) cc_final: 0.9163 (tpp) REVERT: A 352 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8693 (mttt) REVERT: A 689 ASN cc_start: 0.9537 (OUTLIER) cc_final: 0.9186 (t0) REVERT: A 927 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.9280 (mm-40) REVERT: F 18 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8908 (tttt) REVERT: F 25 ARG cc_start: 0.9562 (mtt180) cc_final: 0.9202 (mtm-85) REVERT: F 32 MET cc_start: 0.9219 (pmm) cc_final: 0.8928 (pmm) REVERT: F 53 MET cc_start: 0.9117 (tpt) cc_final: 0.8728 (tpp) REVERT: F 191 GLU cc_start: 0.9391 (tp30) cc_final: 0.8939 (tp30) REVERT: F 268 ASP cc_start: 0.9465 (t0) cc_final: 0.9113 (p0) REVERT: F 269 TYR cc_start: 0.9610 (t80) cc_final: 0.9124 (t80) REVERT: G 53 MET cc_start: 0.9386 (tpt) cc_final: 0.9090 (mmm) REVERT: G 219 MET cc_start: 0.9292 (ppp) cc_final: 0.8980 (ppp) REVERT: G 232 GLN cc_start: 0.9786 (mm110) cc_final: 0.9481 (mp10) REVERT: G 260 MET cc_start: 0.8811 (ttm) cc_final: 0.8540 (ttm) REVERT: O 34 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8886 (tt0) REVERT: O 35 PHE cc_start: 0.9671 (m-80) cc_final: 0.9050 (m-80) REVERT: O 172 TYR cc_start: 0.9382 (m-80) cc_final: 0.8549 (m-80) REVERT: L 23 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: L 25 VAL cc_start: 0.9583 (m) cc_final: 0.9365 (p) REVERT: L 30 GLN cc_start: 0.9479 (pm20) cc_final: 0.9244 (pm20) REVERT: L 31 LEU cc_start: 0.9765 (tp) cc_final: 0.9185 (tp) REVERT: L 33 LYS cc_start: 0.9589 (tttp) cc_final: 0.9341 (ttpp) REVERT: L 35 PHE cc_start: 0.9268 (m-80) cc_final: 0.8541 (m-80) REVERT: L 54 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8154 (mt) REVERT: L 76 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9278 (mm) REVERT: M 76 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7724 (mm) outliers start: 81 outliers final: 42 residues processed: 232 average time/residue: 0.1395 time to fit residues: 53.5655 Evaluate side-chains 206 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 1228 SER Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ASP 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 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.3035 > 50: distance: 55 - 61: 6.072 distance: 61 - 62: 31.873 distance: 62 - 63: 10.451 distance: 62 - 65: 32.293 distance: 63 - 64: 20.902 distance: 63 - 69: 13.021 distance: 65 - 66: 8.876 distance: 66 - 67: 8.309 distance: 66 - 68: 7.414 distance: 69 - 70: 13.852 distance: 70 - 71: 28.132 distance: 70 - 73: 16.131 distance: 71 - 72: 10.385 distance: 71 - 77: 31.844 distance: 73 - 74: 6.898 distance: 74 - 75: 7.000 distance: 74 - 76: 11.168 distance: 77 - 78: 3.065 distance: 78 - 79: 22.955 distance: 78 - 81: 29.183 distance: 79 - 80: 26.509 distance: 79 - 85: 22.467 distance: 81 - 82: 17.881 distance: 81 - 83: 9.573 distance: 82 - 84: 20.700 distance: 86 - 87: 5.770 distance: 86 - 89: 18.697 distance: 87 - 88: 16.033 distance: 87 - 92: 5.209 distance: 89 - 90: 19.962 distance: 89 - 91: 8.444 distance: 92 - 93: 3.695 distance: 93 - 94: 5.354 distance: 93 - 96: 5.260 distance: 94 - 95: 6.336 distance: 94 - 100: 22.201 distance: 96 - 97: 7.621 distance: 97 - 99: 5.644 distance: 100 - 101: 33.825 distance: 101 - 102: 21.619 distance: 101 - 104: 19.167 distance: 102 - 103: 12.076 distance: 102 - 108: 54.970 distance: 104 - 105: 13.893 distance: 104 - 106: 17.725 distance: 105 - 107: 9.000 distance: 108 - 109: 37.472 distance: 109 - 110: 39.301 distance: 109 - 112: 29.535 distance: 110 - 111: 25.685 distance: 110 - 116: 41.400 distance: 112 - 113: 21.826 distance: 113 - 114: 8.943 distance: 113 - 115: 16.301 distance: 116 - 117: 54.746 distance: 117 - 118: 36.882 distance: 118 - 119: 21.445 distance: 118 - 120: 28.406 distance: 120 - 121: 19.715 distance: 121 - 122: 17.206 distance: 121 - 124: 5.157 distance: 122 - 123: 19.946 distance: 122 - 132: 22.924 distance: 124 - 125: 3.212 distance: 125 - 126: 13.023 distance: 125 - 127: 8.304 distance: 126 - 128: 14.982 distance: 127 - 129: 15.201 distance: 128 - 130: 7.730 distance: 129 - 130: 13.451 distance: 130 - 131: 14.506 distance: 132 - 133: 19.562 distance: 133 - 134: 12.595 distance: 133 - 136: 25.409 distance: 134 - 135: 14.519 distance: 134 - 140: 21.900 distance: 136 - 137: 18.377 distance: 137 - 138: 28.366 distance: 137 - 139: 25.559