Starting phenix.real_space_refine on Thu Mar 5 15:54:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q85_52886/03_2026/9q85_52886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q85_52886/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9q85_52886/03_2026/9q85_52886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q85_52886/03_2026/9q85_52886.map" model { file = "/net/cci-nas-00/data/ceres_data/9q85_52886/03_2026/9q85_52886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q85_52886/03_2026/9q85_52886.cif" } 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-5986/lib/python3.9/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: 5.88, 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: 2.26 Conformation dependent library (CDL) restraints added in 1.0 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: 4.31 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: 8.07 Time building geometry restraints manager: 2.97 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 1.414 1.379 0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" CA ILE M 124 " pdb=" CB ILE M 124 " ideal model delta sigma weight residual 1.533 1.552 -0.019 1.19e-02 7.06e+03 2.65e+00 bond pdb=" CB GLU L 40 " pdb=" CG GLU L 40 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CA ASP A1355 " pdb=" CB ASP A1355 " ideal model delta sigma weight residual 1.529 1.554 -0.025 1.74e-02 3.30e+03 2.06e+00 bond pdb=" N ASN F 62 " pdb=" CA ASN F 62 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.00e+00 ... (remaining 23873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 32650 1.99 - 3.98: 585 3.98 - 5.97: 70 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=" C GLY F 257 " pdb=" N LYS F 258 " pdb=" CA LYS F 258 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" N ILE O 70 " pdb=" CA ILE O 70 " pdb=" C ILE O 70 " ideal model delta sigma weight residual 113.53 109.66 3.87 9.80e-01 1.04e+00 1.56e+01 angle pdb=" CA GLU F 61 " pdb=" CB GLU F 61 " pdb=" CG GLU F 61 " ideal model delta sigma weight residual 114.10 121.99 -7.89 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CA ARG A1107 " pdb=" CB ARG A1107 " pdb=" CG ARG A1107 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+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: 3896 0.097 - 0.194: 180 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.330 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.004 0.046 23878 Z= 0.184 Angle : 0.690 9.953 33342 Z= 0.375 Chirality : 0.043 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 covalent geometry : bond 0.00409 (23878) covalent geometry : angle 0.69035 (33342) hydrogen bonds : bond 0.12631 ( 1296) hydrogen bonds : angle 5.89415 ( 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 : 0.789 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: 0.1498 time to fit residues: 72.6321 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 : 0.769 ------------------------------------------------------------------------------- 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: 0.9980 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: 4.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 511 HIS A 654 HIS A 720 ASN A1241 GLN A1260 ASN F 264 ASN G 21 HIS G 117 GLN G 211 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.046439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.031748 restraints weight = 182645.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.032648 restraints weight = 88021.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.033249 restraints weight = 54283.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.033566 restraints weight = 39260.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.033846 restraints weight = 32233.132| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 23878 Z= 0.268 Angle : 0.641 9.808 33342 Z= 0.345 Chirality : 0.041 0.351 4080 Planarity : 0.005 0.074 3582 Dihedral : 19.821 93.081 5338 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.15 % Allowed : 24.71 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 2674 helix: 1.28 (0.14), residues: 1398 sheet: -0.73 (0.31), residues: 278 loop : -0.37 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 234 TYR 0.022 0.002 TYR G 120 PHE 0.034 0.002 PHE F 77 TRP 0.011 0.002 TRP F 4 HIS 0.005 0.001 HIS F 21 Details of bonding type rmsd covalent geometry : bond 0.00550 (23878) covalent geometry : angle 0.64083 (33342) hydrogen bonds : bond 0.04735 ( 1296) hydrogen bonds : angle 4.61278 ( 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 255 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 170 time to evaluate : 0.852 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 352 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8670 (mttt) REVERT: A 689 ASN cc_start: 0.9536 (OUTLIER) cc_final: 0.9132 (t0) REVERT: A 829 MET cc_start: 0.9154 (mmm) cc_final: 0.8920 (mmm) REVERT: A 927 GLN cc_start: 0.9504 (OUTLIER) cc_final: 0.9268 (mm-40) REVERT: F 5 ARG cc_start: 0.9541 (mmm-85) cc_final: 0.9159 (mmm-85) REVERT: F 18 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8817 (tttt) REVERT: F 25 ARG cc_start: 0.9523 (mtt180) cc_final: 0.9122 (mmm-85) REVERT: F 191 GLU cc_start: 0.9322 (tp30) cc_final: 0.8921 (tp30) REVERT: F 265 ILE cc_start: 0.9782 (OUTLIER) cc_final: 0.9277 (mt) REVERT: F 268 ASP cc_start: 0.9373 (t0) cc_final: 0.9123 (p0) REVERT: F 269 TYR cc_start: 0.9495 (t80) cc_final: 0.9079 (t80) REVERT: G 53 MET cc_start: 0.9397 (tpt) cc_final: 0.9180 (tpt) REVERT: G 131 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8904 (mm-40) REVERT: G 198 MET cc_start: 0.8890 (mtt) cc_final: 0.8505 (mtp) REVERT: G 260 MET cc_start: 0.8946 (ttm) cc_final: 0.8740 (ttm) REVERT: O 34 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8939 (tp30) REVERT: O 35 PHE cc_start: 0.9631 (m-80) cc_final: 0.8917 (m-80) REVERT: O 109 MET cc_start: 0.6585 (mpp) cc_final: 0.6197 (mpp) REVERT: O 172 TYR cc_start: 0.9497 (m-80) cc_final: 0.8755 (m-80) REVERT: O 203 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8393 (tp) REVERT: O 207 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9185 (mm) REVERT: L 31 LEU cc_start: 0.9742 (tp) cc_final: 0.9321 (tp) REVERT: L 33 LYS cc_start: 0.9608 (tttp) cc_final: 0.9300 (ttpp) REVERT: L 35 PHE cc_start: 0.9271 (m-80) cc_final: 0.8622 (m-80) REVERT: L 54 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8152 (mt) REVERT: L 76 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9254 (mm) REVERT: L 133 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9175 (pp) REVERT: M 76 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7586 (mm) REVERT: M 103 LEU cc_start: 0.9365 (tt) cc_final: 0.9099 (tt) outliers start: 85 outliers final: 34 residues processed: 246 average time/residue: 0.1396 time to fit residues: 56.4347 Evaluate side-chains 196 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LYS 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 507 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1129 ASN 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 F residue 249 PHE Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain G residue 47 ASP 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 270 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 203 ILE 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 133 LEU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 163 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 239 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 GLN G 19 ASN G 211 GLN G 236 ASN L 37 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.047816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.032904 restraints weight = 179635.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.033866 restraints weight = 85461.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.034458 restraints weight = 52250.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.034829 restraints weight = 37730.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.035091 restraints weight = 30771.283| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23878 Z= 0.118 Angle : 0.542 14.177 33342 Z= 0.287 Chirality : 0.038 0.248 4080 Planarity : 0.003 0.055 3582 Dihedral : 19.582 90.720 5332 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.82 % Allowed : 24.65 % Favored : 71.53 % 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: 0.89 (0.16), residues: 2674 helix: 1.51 (0.14), residues: 1404 sheet: -0.63 (0.31), residues: 296 loop : -0.27 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 57 TYR 0.015 0.001 TYR O 36 PHE 0.020 0.001 PHE L 28 TRP 0.031 0.002 TRP F 4 HIS 0.004 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00253 (23878) covalent geometry : angle 0.54197 (33342) hydrogen bonds : bond 0.03232 ( 1296) hydrogen bonds : angle 4.20631 ( 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 239 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 176 time to evaluate : 0.821 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: symmetry clash REVERT: A 321 MET cc_start: 0.8948 (mmp) cc_final: 0.8743 (mmt) REVERT: A 571 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9090 (pt) REVERT: A 829 MET cc_start: 0.9156 (mmm) cc_final: 0.8814 (mmm) REVERT: A 927 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.8899 (mt0) REVERT: A 1235 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: F 18 LYS cc_start: 0.9241 (ttpt) cc_final: 0.8911 (tttt) REVERT: F 25 ARG cc_start: 0.9579 (mtt180) cc_final: 0.9203 (mmm-85) REVERT: F 32 MET cc_start: 0.9047 (pmm) cc_final: 0.8806 (pmm) REVERT: F 53 MET cc_start: 0.9062 (tpt) cc_final: 0.8618 (tpp) REVERT: F 57 ARG cc_start: 0.9502 (tpp80) cc_final: 0.9278 (mmm-85) REVERT: F 190 ARG cc_start: 0.9482 (OUTLIER) cc_final: 0.9212 (ptm160) REVERT: F 191 GLU cc_start: 0.9455 (tp30) cc_final: 0.8964 (tp30) REVERT: F 269 TYR cc_start: 0.9490 (t80) cc_final: 0.9120 (t80) REVERT: G 53 MET cc_start: 0.9351 (tpt) cc_final: 0.9114 (mmm) REVERT: G 131 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8850 (mm-40) REVERT: G 198 MET cc_start: 0.8742 (mtt) cc_final: 0.8530 (mtp) REVERT: G 219 MET cc_start: 0.9267 (ppp) cc_final: 0.8975 (ppp) REVERT: G 232 GLN cc_start: 0.9778 (mm110) cc_final: 0.9445 (mp10) REVERT: O 172 TYR cc_start: 0.9421 (m-80) cc_final: 0.8658 (m-80) REVERT: O 203 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8467 (tp) REVERT: O 207 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9159 (mm) REVERT: L 8 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9113 (mt) REVERT: L 30 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8823 (tm-30) REVERT: L 31 LEU cc_start: 0.9764 (tp) cc_final: 0.9340 (tp) REVERT: L 33 LYS cc_start: 0.9572 (tttp) cc_final: 0.9241 (ttpp) REVERT: L 35 PHE cc_start: 0.9273 (m-80) cc_final: 0.8568 (m-80) REVERT: L 76 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9291 (mm) REVERT: M 76 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7689 (mm) outliers start: 63 outliers final: 29 residues processed: 230 average time/residue: 0.1376 time to fit residues: 52.3067 Evaluate side-chains 198 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1235 GLU 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 203 LEU Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 264 ASN 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 18 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 157 TYR Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 206 PHE Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 42 SER 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 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: 10.0000 chunk 31 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1260 ASN A1272 ASN A1273 HIS ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 ASN L 37 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.044097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.029653 restraints weight = 193298.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.030525 restraints weight = 92577.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.031058 restraints weight = 56950.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.031409 restraints weight = 41767.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.031607 restraints weight = 34261.199| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 23878 Z= 0.386 Angle : 0.723 11.561 33342 Z= 0.384 Chirality : 0.043 0.227 4080 Planarity : 0.005 0.057 3582 Dihedral : 20.015 92.152 5330 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 6.00 % Allowed : 24.17 % Favored : 69.84 % 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: 0.74 (0.16), residues: 2674 helix: 1.40 (0.13), residues: 1407 sheet: -0.71 (0.33), residues: 278 loop : -0.37 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 62 TYR 0.027 0.002 TYR A 552 PHE 0.032 0.003 PHE F 77 TRP 0.028 0.002 TRP F 4 HIS 0.007 0.002 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00777 (23878) covalent geometry : angle 0.72252 (33342) hydrogen bonds : bond 0.05596 ( 1296) hydrogen bonds : angle 4.69520 ( 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 246 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 147 time to evaluate : 0.818 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 6 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.8803 (m) REVERT: A 90 MET cc_start: 0.9146 (tpp) cc_final: 0.8861 (tpp) REVERT: A 689 ASN cc_start: 0.9386 (OUTLIER) cc_final: 0.9130 (t0) REVERT: A 927 GLN cc_start: 0.9579 (OUTLIER) cc_final: 0.9297 (mm-40) REVERT: A 1235 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: F 25 ARG cc_start: 0.9521 (mtt180) cc_final: 0.9115 (mtm-85) REVERT: F 32 MET cc_start: 0.9302 (pmm) cc_final: 0.8911 (pmm) REVERT: F 188 PHE cc_start: 0.9726 (m-10) cc_final: 0.9493 (m-10) REVERT: F 190 ARG cc_start: 0.9603 (OUTLIER) cc_final: 0.9029 (ptm160) REVERT: F 191 GLU cc_start: 0.9499 (tp30) cc_final: 0.9143 (tp30) REVERT: F 198 MET cc_start: 0.9244 (ppp) cc_final: 0.8986 (tmm) REVERT: F 268 ASP cc_start: 0.9341 (t70) cc_final: 0.9030 (p0) REVERT: F 269 TYR cc_start: 0.9572 (t80) cc_final: 0.9187 (t80) REVERT: G 103 CYS cc_start: 0.9565 (OUTLIER) cc_final: 0.9059 (t) REVERT: G 198 MET cc_start: 0.8712 (mtt) cc_final: 0.8508 (mtp) REVERT: G 219 MET cc_start: 0.9323 (ppp) cc_final: 0.8954 (ppp) REVERT: G 232 GLN cc_start: 0.9765 (mm110) cc_final: 0.9474 (mp10) REVERT: G 270 THR cc_start: 0.9498 (m) cc_final: 0.9167 (p) REVERT: O 30 GLN cc_start: 0.9827 (tm-30) cc_final: 0.9610 (tm-30) REVERT: O 35 PHE cc_start: 0.9664 (m-80) cc_final: 0.9092 (m-80) REVERT: O 172 TYR cc_start: 0.9436 (m-80) cc_final: 0.8775 (m-80) REVERT: O 207 ILE cc_start: 0.9591 (OUTLIER) cc_final: 0.9307 (mm) REVERT: L 8 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8846 (tp) REVERT: L 33 LYS cc_start: 0.9651 (tttp) cc_final: 0.9328 (ttpp) REVERT: L 47 PHE cc_start: 0.9553 (OUTLIER) cc_final: 0.9088 (p90) outliers start: 99 outliers final: 59 residues processed: 231 average time/residue: 0.1414 time to fit residues: 54.1506 Evaluate side-chains 208 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 140 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 147 LYS 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 560 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 749 VAL 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 964 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 A residue 1260 ASN Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 247 SER 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 47 ASP 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 235 HIS Chi-restraints excluded: chain G residue 263 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 38 TYR Chi-restraints excluded: chain O residue 45 THR 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 149 PHE 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 8 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 65 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 73 SER Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 96 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 134 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 30.0000 chunk 249 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1260 ASN F 264 ASN L 37 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.045560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.030975 restraints weight = 185539.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.031868 restraints weight = 87101.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.032440 restraints weight = 53187.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.032799 restraints weight = 38449.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.033052 restraints weight = 31358.388| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23878 Z= 0.150 Angle : 0.551 13.932 33342 Z= 0.293 Chirality : 0.039 0.222 4080 Planarity : 0.003 0.055 3582 Dihedral : 19.732 93.038 5330 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.76 % Allowed : 25.68 % Favored : 70.56 % 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: 1.12 (0.17), residues: 2674 helix: 1.71 (0.14), residues: 1408 sheet: -0.52 (0.34), residues: 269 loop : -0.20 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 72 TYR 0.017 0.001 TYR O 36 PHE 0.018 0.001 PHE L 35 TRP 0.026 0.002 TRP F 106 HIS 0.004 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00318 (23878) covalent geometry : angle 0.55083 (33342) hydrogen bonds : bond 0.03489 ( 1296) hydrogen bonds : angle 4.20604 ( 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 212 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 0.883 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: A 6 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.8819 (m) REVERT: A 546 LYS cc_start: 0.9530 (mtmm) cc_final: 0.9327 (mtmm) REVERT: A 927 GLN cc_start: 0.9522 (OUTLIER) cc_final: 0.8896 (mt0) REVERT: A 1235 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: F 18 LYS cc_start: 0.9281 (ttpt) cc_final: 0.9032 (tttt) REVERT: F 25 ARG cc_start: 0.9469 (mtt180) cc_final: 0.9013 (mtm-85) REVERT: F 32 MET cc_start: 0.9268 (pmm) cc_final: 0.8881 (pmm) REVERT: F 188 PHE cc_start: 0.9726 (m-10) cc_final: 0.9444 (m-10) REVERT: F 190 ARG cc_start: 0.9591 (OUTLIER) cc_final: 0.9257 (ptm160) REVERT: F 191 GLU cc_start: 0.9475 (tp30) cc_final: 0.9102 (tp30) REVERT: F 198 MET cc_start: 0.8919 (ppp) cc_final: 0.8706 (tmm) REVERT: G 103 CYS cc_start: 0.9542 (OUTLIER) cc_final: 0.9018 (t) REVERT: G 219 MET cc_start: 0.9310 (ppp) cc_final: 0.8893 (ppp) REVERT: G 232 GLN cc_start: 0.9763 (mm110) cc_final: 0.9430 (mp10) REVERT: G 270 THR cc_start: 0.9439 (m) cc_final: 0.9060 (p) REVERT: O 31 LEU cc_start: 0.9938 (tt) cc_final: 0.9737 (pp) REVERT: O 35 PHE cc_start: 0.9687 (m-80) cc_final: 0.9383 (m-80) REVERT: O 172 TYR cc_start: 0.9416 (m-80) cc_final: 0.8726 (m-80) REVERT: O 207 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.9255 (mm) REVERT: L 8 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8838 (tp) REVERT: L 33 LYS cc_start: 0.9622 (tttp) cc_final: 0.9038 (pttm) REVERT: L 54 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8186 (mt) REVERT: L 215 MET cc_start: 0.8943 (mmt) cc_final: 0.8664 (mmm) REVERT: M 76 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7932 (mm) outliers start: 62 outliers final: 35 residues processed: 202 average time/residue: 0.1355 time to fit residues: 45.8076 Evaluate side-chains 187 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER 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 474 THR Chi-restraints excluded: chain A residue 571 ILE 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 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 964 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 63 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain G residue 47 ASP 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 263 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 45 THR 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 207 ILE Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 54 ILE 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 213 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 234 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 251 optimal weight: 50.0000 chunk 200 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 86 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 268 optimal weight: 50.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1260 ASN ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 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 = 0.3291 r_free = 0.3291 target = 0.044126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.029771 restraints weight = 193800.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.030626 restraints weight = 92018.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.031179 restraints weight = 56742.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.031495 restraints weight = 41345.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.031744 restraints weight = 34169.169| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23878 Z= 0.302 Angle : 0.638 12.582 33342 Z= 0.342 Chirality : 0.040 0.192 4080 Planarity : 0.004 0.056 3582 Dihedral : 19.842 91.544 5328 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.91 % Allowed : 24.77 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.99 (0.16), residues: 2674 helix: 1.60 (0.14), residues: 1402 sheet: -0.46 (0.34), residues: 258 loop : -0.30 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 57 TYR 0.018 0.002 TYR G 253 PHE 0.016 0.002 PHE L 166 TRP 0.042 0.003 TRP F 4 HIS 0.006 0.002 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00612 (23878) covalent geometry : angle 0.63833 (33342) hydrogen bonds : bond 0.04945 ( 1296) hydrogen bonds : angle 4.44492 ( 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 224 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 143 time to evaluate : 0.905 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: A 689 ASN cc_start: 0.9402 (OUTLIER) cc_final: 0.9159 (t0) REVERT: A 752 MET cc_start: 0.9477 (mmm) cc_final: 0.9195 (mmm) REVERT: A 927 GLN cc_start: 0.9563 (OUTLIER) cc_final: 0.9308 (mm110) REVERT: A 1235 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: A 1260 ASN cc_start: 0.9241 (OUTLIER) cc_final: 0.8934 (t0) REVERT: F 4 TRP cc_start: 0.8678 (p-90) cc_final: 0.8345 (p-90) REVERT: F 25 ARG cc_start: 0.9460 (mtt180) cc_final: 0.9009 (mtm-85) REVERT: F 32 MET cc_start: 0.9345 (pmm) cc_final: 0.8973 (pmm) REVERT: F 49 VAL cc_start: 0.9689 (OUTLIER) cc_final: 0.9440 (m) REVERT: F 106 TRP cc_start: 0.9504 (t60) cc_final: 0.9277 (t60) REVERT: F 188 PHE cc_start: 0.9718 (m-10) cc_final: 0.9464 (m-10) REVERT: F 190 ARG cc_start: 0.9601 (OUTLIER) cc_final: 0.9112 (ptm160) REVERT: F 191 GLU cc_start: 0.9504 (tp30) cc_final: 0.9134 (tp30) REVERT: F 269 TYR cc_start: 0.9541 (t80) cc_final: 0.9232 (t80) REVERT: G 103 CYS cc_start: 0.9561 (OUTLIER) cc_final: 0.9061 (t) REVERT: G 219 MET cc_start: 0.9346 (ppp) cc_final: 0.8914 (ppp) REVERT: G 232 GLN cc_start: 0.9774 (mm110) cc_final: 0.9462 (mp10) REVERT: G 270 THR cc_start: 0.9501 (m) cc_final: 0.9165 (p) REVERT: O 30 GLN cc_start: 0.9687 (tm-30) cc_final: 0.9349 (pp30) REVERT: O 35 PHE cc_start: 0.9672 (m-80) cc_final: 0.9414 (m-80) REVERT: O 172 TYR cc_start: 0.9417 (m-80) cc_final: 0.8822 (m-80) REVERT: O 207 ILE cc_start: 0.9572 (OUTLIER) cc_final: 0.9282 (mm) REVERT: L 8 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8995 (tp) REVERT: L 33 LYS cc_start: 0.9450 (tttp) cc_final: 0.9173 (ttpp) REVERT: L 41 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7997 (pp30) REVERT: L 47 PHE cc_start: 0.9563 (OUTLIER) cc_final: 0.9150 (p90) REVERT: L 54 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8299 (mt) REVERT: L 215 MET cc_start: 0.9007 (mmt) cc_final: 0.8772 (mmm) REVERT: M 76 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8020 (mm) outliers start: 81 outliers final: 52 residues processed: 211 average time/residue: 0.1351 time to fit residues: 47.6507 Evaluate side-chains 201 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 136 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 123 VAL 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 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1260 ASN Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 61 GLU 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 247 SER Chi-restraints excluded: chain F residue 249 PHE 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 103 CYS 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 38 TYR 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 167 VAL Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain O residue 217 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 63 THR 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 L residue 213 ILE Chi-restraints excluded: chain M residue 73 SER 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 96 GLU 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: 50.0000 chunk 149 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 277 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 260 optimal weight: 50.0000 chunk 223 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1260 ASN ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3294 r_free = 0.3294 target = 0.044159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.029803 restraints weight = 191700.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.030673 restraints weight = 89929.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.031229 restraints weight = 55052.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.031594 restraints weight = 40055.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.031780 restraints weight = 32591.706| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23878 Z= 0.263 Angle : 0.620 13.924 33342 Z= 0.329 Chirality : 0.040 0.178 4080 Planarity : 0.004 0.056 3582 Dihedral : 19.865 95.751 5328 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.12 % Allowed : 25.92 % Favored : 69.96 % 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: 1.04 (0.16), residues: 2674 helix: 1.67 (0.14), residues: 1401 sheet: -0.48 (0.34), residues: 257 loop : -0.32 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 57 TYR 0.015 0.002 TYR G 120 PHE 0.014 0.002 PHE A1332 TRP 0.029 0.002 TRP F 4 HIS 0.006 0.001 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00532 (23878) covalent geometry : angle 0.61992 (33342) hydrogen bonds : bond 0.04330 ( 1296) hydrogen bonds : angle 4.41100 ( 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 211 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 143 time to evaluate : 0.790 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 90 MET cc_start: 0.8931 (tpp) cc_final: 0.8146 (tmm) REVERT: A 321 MET cc_start: 0.9275 (mmt) cc_final: 0.8957 (mmt) REVERT: A 689 ASN cc_start: 0.9418 (OUTLIER) cc_final: 0.9215 (t0) REVERT: A 762 VAL cc_start: 0.9776 (t) cc_final: 0.9516 (m) REVERT: A 927 GLN cc_start: 0.9532 (OUTLIER) cc_final: 0.8884 (mt0) REVERT: A 1235 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: F 4 TRP cc_start: 0.8613 (p-90) cc_final: 0.8308 (p-90) REVERT: F 25 ARG cc_start: 0.9435 (mtt180) cc_final: 0.8977 (mtm-85) REVERT: F 32 MET cc_start: 0.9348 (pmm) cc_final: 0.8965 (pmm) REVERT: F 190 ARG cc_start: 0.9609 (OUTLIER) cc_final: 0.9343 (ptm160) REVERT: F 191 GLU cc_start: 0.9499 (tp30) cc_final: 0.9121 (mt-10) REVERT: F 260 MET cc_start: 0.8933 (pmm) cc_final: 0.8661 (pmm) REVERT: F 268 ASP cc_start: 0.9409 (t0) cc_final: 0.8996 (p0) REVERT: F 269 TYR cc_start: 0.9533 (t80) cc_final: 0.9126 (t80) REVERT: G 103 CYS cc_start: 0.9558 (OUTLIER) cc_final: 0.9066 (t) REVERT: G 219 MET cc_start: 0.9323 (ppp) cc_final: 0.8866 (ppp) REVERT: G 232 GLN cc_start: 0.9769 (mm110) cc_final: 0.9443 (mp10) REVERT: O 35 PHE cc_start: 0.9687 (m-80) cc_final: 0.9327 (m-80) REVERT: O 109 MET cc_start: 0.7780 (mpp) cc_final: 0.6410 (mmm) REVERT: O 172 TYR cc_start: 0.9435 (m-80) cc_final: 0.8831 (m-80) REVERT: O 207 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9294 (mp) REVERT: L 8 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9055 (tp) REVERT: L 33 LYS cc_start: 0.9416 (tttp) cc_final: 0.9117 (ttpp) REVERT: L 54 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8321 (mt) REVERT: M 76 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8037 (mm) outliers start: 68 outliers final: 43 residues processed: 200 average time/residue: 0.1370 time to fit residues: 45.6187 Evaluate side-chains 190 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR 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 460 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1114 PHE 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 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 264 ASN Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 103 CYS 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 72 THR Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 139 THR Chi-restraints excluded: chain O residue 149 PHE Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 54 ILE 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 213 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 94 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 214 optimal weight: 0.0070 chunk 238 optimal weight: 5.9990 chunk 92 optimal weight: 0.0020 chunk 28 optimal weight: 30.0000 chunk 178 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.9810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 34 HIS ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.045132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.030669 restraints weight = 186186.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.031569 restraints weight = 87748.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.032116 restraints weight = 53691.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.032456 restraints weight = 39120.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.032713 restraints weight = 32199.012| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23878 Z= 0.152 Angle : 0.569 15.064 33342 Z= 0.298 Chirality : 0.039 0.238 4080 Planarity : 0.003 0.057 3582 Dihedral : 19.658 96.662 5326 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.09 % Allowed : 26.83 % Favored : 70.08 % 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: 1.27 (0.17), residues: 2674 helix: 1.85 (0.14), residues: 1401 sheet: -0.38 (0.34), residues: 258 loop : -0.18 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 57 TYR 0.013 0.001 TYR G 120 PHE 0.029 0.001 PHE L 149 TRP 0.055 0.002 TRP F 106 HIS 0.004 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00317 (23878) covalent geometry : angle 0.56914 (33342) hydrogen bonds : bond 0.03427 ( 1296) hydrogen bonds : angle 4.18888 ( 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 199 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 0.656 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 90 MET cc_start: 0.9012 (tpp) cc_final: 0.8264 (tmm) REVERT: A 534 MET cc_start: 0.7863 (ptm) cc_final: 0.7544 (ptm) REVERT: A 546 LYS cc_start: 0.9561 (mtmm) cc_final: 0.9352 (mtmm) REVERT: A 752 MET cc_start: 0.9406 (mmm) cc_final: 0.8885 (mmm) REVERT: A 927 GLN cc_start: 0.9527 (OUTLIER) cc_final: 0.8942 (mt0) REVERT: A 1235 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: F 4 TRP cc_start: 0.8545 (p-90) cc_final: 0.8153 (p-90) REVERT: F 25 ARG cc_start: 0.9408 (mtt180) cc_final: 0.8956 (mtm-85) REVERT: F 32 MET cc_start: 0.9327 (pmm) cc_final: 0.8914 (pmm) REVERT: F 37 GLU cc_start: 0.9440 (mt-10) cc_final: 0.8875 (tt0) REVERT: F 43 LEU cc_start: 0.9789 (mp) cc_final: 0.9206 (tt) REVERT: F 190 ARG cc_start: 0.9595 (OUTLIER) cc_final: 0.9345 (ptm160) REVERT: F 191 GLU cc_start: 0.9490 (tp30) cc_final: 0.9092 (tp30) REVERT: F 260 MET cc_start: 0.8928 (pmm) cc_final: 0.8627 (pmm) REVERT: F 268 ASP cc_start: 0.9414 (t0) cc_final: 0.9027 (p0) REVERT: F 269 TYR cc_start: 0.9491 (t80) cc_final: 0.9109 (t80) REVERT: G 191 GLU cc_start: 0.8968 (tp30) cc_final: 0.8563 (tp30) REVERT: G 219 MET cc_start: 0.9343 (ppp) cc_final: 0.8955 (ppp) REVERT: G 232 GLN cc_start: 0.9768 (mm110) cc_final: 0.9437 (mp10) REVERT: O 35 PHE cc_start: 0.9680 (m-80) cc_final: 0.9358 (m-80) REVERT: O 109 MET cc_start: 0.7922 (mpp) cc_final: 0.6700 (mmm) REVERT: O 172 TYR cc_start: 0.9429 (m-80) cc_final: 0.8811 (m-80) REVERT: O 207 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9253 (mp) REVERT: L 8 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8720 (tp) REVERT: L 47 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.9211 (p90) REVERT: L 54 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8240 (mt) REVERT: L 76 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9384 (mm) REVERT: L 157 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8693 (t80) REVERT: M 76 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8001 (mm) outliers start: 51 outliers final: 35 residues processed: 192 average time/residue: 0.1354 time to fit residues: 43.3190 Evaluate side-chains 189 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 571 ILE 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 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1114 PHE 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 79 THR Chi-restraints excluded: chain F residue 190 ARG 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 235 HIS Chi-restraints excluded: chain G residue 261 TYR Chi-restraints excluded: chain O residue 18 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 149 PHE Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 42 SER 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 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 157 TYR Chi-restraints excluded: chain L residue 213 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 94 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 58 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 167 optimal weight: 0.0270 chunk 227 optimal weight: 10.0000 chunk 213 optimal weight: 30.0000 chunk 259 optimal weight: 9.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 264 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.044196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.029845 restraints weight = 191900.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.030719 restraints weight = 89918.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.031267 restraints weight = 55032.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.031630 restraints weight = 40060.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.031821 restraints weight = 32617.554| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4731 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= 0.236 Angle : 0.615 15.183 33342 Z= 0.322 Chirality : 0.040 0.252 4080 Planarity : 0.004 0.057 3582 Dihedral : 19.702 96.048 5326 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.76 % Allowed : 26.41 % Favored : 69.84 % 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: 1.20 (0.17), residues: 2674 helix: 1.78 (0.14), residues: 1400 sheet: -0.41 (0.34), residues: 259 loop : -0.20 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 57 TYR 0.014 0.001 TYR G 120 PHE 0.024 0.002 PHE L 149 TRP 0.039 0.002 TRP F 106 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00483 (23878) covalent geometry : angle 0.61469 (33342) hydrogen bonds : bond 0.04183 ( 1296) hydrogen bonds : angle 4.30502 ( 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 210 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 148 time to evaluate : 0.655 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 6 SER cc_start: 0.9276 (OUTLIER) cc_final: 0.8837 (m) REVERT: A 90 MET cc_start: 0.8933 (tpp) cc_final: 0.8511 (mmm) REVERT: A 534 MET cc_start: 0.7922 (ptm) cc_final: 0.7673 (ptm) REVERT: A 752 MET cc_start: 0.9439 (mmm) cc_final: 0.9149 (mmm) REVERT: A 762 VAL cc_start: 0.9791 (t) cc_final: 0.9534 (m) REVERT: A 927 GLN cc_start: 0.9548 (OUTLIER) cc_final: 0.8965 (mt0) REVERT: A 1235 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: F 4 TRP cc_start: 0.8583 (p-90) cc_final: 0.8205 (p-90) REVERT: F 25 ARG cc_start: 0.9431 (mtt180) cc_final: 0.8958 (mtm-85) REVERT: F 32 MET cc_start: 0.9344 (pmm) cc_final: 0.8954 (pmm) REVERT: F 43 LEU cc_start: 0.9793 (mp) cc_final: 0.9219 (tt) REVERT: F 57 ARG cc_start: 0.9516 (tpp80) cc_final: 0.8760 (mmm-85) REVERT: F 190 ARG cc_start: 0.9605 (OUTLIER) cc_final: 0.9305 (ptm160) REVERT: F 191 GLU cc_start: 0.9541 (tp30) cc_final: 0.9124 (mt-10) REVERT: F 211 GLN cc_start: 0.9236 (tp-100) cc_final: 0.8841 (mt0) REVERT: F 268 ASP cc_start: 0.9424 (t0) cc_final: 0.8976 (p0) REVERT: F 269 TYR cc_start: 0.9520 (t80) cc_final: 0.9085 (t80) REVERT: G 103 CYS cc_start: 0.9553 (OUTLIER) cc_final: 0.9064 (t) REVERT: G 191 GLU cc_start: 0.9033 (tp30) cc_final: 0.8615 (tp30) REVERT: G 219 MET cc_start: 0.9338 (ppp) cc_final: 0.8942 (ppp) REVERT: G 232 GLN cc_start: 0.9767 (mm110) cc_final: 0.9450 (mp10) REVERT: O 35 PHE cc_start: 0.9669 (m-80) cc_final: 0.9342 (m-80) REVERT: O 109 MET cc_start: 0.8033 (mpp) cc_final: 0.6648 (mmm) REVERT: O 172 TYR cc_start: 0.9463 (m-80) cc_final: 0.8890 (m-80) REVERT: O 207 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9275 (mp) REVERT: L 33 LYS cc_start: 0.9403 (tttp) cc_final: 0.9081 (ttpp) REVERT: L 47 PHE cc_start: 0.9513 (OUTLIER) cc_final: 0.9214 (p90) REVERT: L 54 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8322 (mt) REVERT: L 157 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8692 (t80) REVERT: M 76 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8193 (mm) outliers start: 62 outliers final: 45 residues processed: 201 average time/residue: 0.1333 time to fit residues: 45.0114 Evaluate side-chains 200 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 145 SER 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 460 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 571 ILE 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 896 SER Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1288 ASN 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 246 PHE Chi-restraints excluded: chain F residue 247 SER 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 103 CYS 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 18 THR Chi-restraints excluded: chain O residue 38 TYR Chi-restraints excluded: chain O residue 59 LEU 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 149 PHE Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain L residue 42 SER 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 122 ASP Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 157 TYR Chi-restraints excluded: chain L residue 213 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 94 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 102 optimal weight: 0.4980 chunk 118 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 183 optimal weight: 0.4980 chunk 171 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.045243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.030827 restraints weight = 186812.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.031732 restraints weight = 87992.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.032283 restraints weight = 53643.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.032634 restraints weight = 39009.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.032878 restraints weight = 31996.208| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23878 Z= 0.135 Angle : 0.592 16.243 33342 Z= 0.303 Chirality : 0.039 0.236 4080 Planarity : 0.003 0.058 3582 Dihedral : 19.538 97.825 5326 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.91 % Allowed : 27.44 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.33 (0.17), residues: 2674 helix: 1.89 (0.14), residues: 1399 sheet: -0.34 (0.34), residues: 257 loop : -0.13 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 57 TYR 0.033 0.001 TYR F 255 PHE 0.024 0.001 PHE L 149 TRP 0.033 0.002 TRP F 106 HIS 0.005 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00287 (23878) covalent geometry : angle 0.59173 (33342) hydrogen bonds : bond 0.03269 ( 1296) hydrogen bonds : angle 4.12415 ( 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 194 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.793 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 90 MET cc_start: 0.8965 (tpp) cc_final: 0.8553 (mmm) REVERT: A 689 ASN cc_start: 0.9455 (OUTLIER) cc_final: 0.9241 (t0) REVERT: A 752 MET cc_start: 0.9425 (mmm) cc_final: 0.8788 (mmm) REVERT: A 762 VAL cc_start: 0.9777 (t) cc_final: 0.9503 (m) REVERT: A 927 GLN cc_start: 0.9500 (OUTLIER) cc_final: 0.8963 (mt0) REVERT: A 1235 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: F 4 TRP cc_start: 0.8596 (p-90) cc_final: 0.8321 (p-90) REVERT: F 18 LYS cc_start: 0.9313 (ttpt) cc_final: 0.9108 (tttt) REVERT: F 25 ARG cc_start: 0.9417 (mtt180) cc_final: 0.8915 (mtm-85) REVERT: F 32 MET cc_start: 0.9327 (pmm) cc_final: 0.8893 (pmm) REVERT: F 43 LEU cc_start: 0.9774 (mp) cc_final: 0.9229 (tt) REVERT: F 57 ARG cc_start: 0.9458 (tpp80) cc_final: 0.8739 (mmm-85) REVERT: F 190 ARG cc_start: 0.9612 (OUTLIER) cc_final: 0.9357 (ptm160) REVERT: F 191 GLU cc_start: 0.9466 (tp30) cc_final: 0.9073 (tp30) REVERT: F 211 GLN cc_start: 0.9213 (tp-100) cc_final: 0.8813 (mt0) REVERT: F 269 TYR cc_start: 0.9541 (t80) cc_final: 0.9136 (t80) REVERT: G 53 MET cc_start: 0.9213 (mmm) cc_final: 0.8848 (mmm) REVERT: G 103 CYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9032 (t) REVERT: G 191 GLU cc_start: 0.8925 (tp30) cc_final: 0.8478 (tp30) REVERT: G 219 MET cc_start: 0.9316 (ppp) cc_final: 0.8916 (ppp) REVERT: G 232 GLN cc_start: 0.9764 (mm110) cc_final: 0.9432 (mp10) REVERT: O 35 PHE cc_start: 0.9647 (m-80) cc_final: 0.9337 (m-80) REVERT: O 109 MET cc_start: 0.7981 (mpp) cc_final: 0.6720 (mmm) REVERT: O 172 TYR cc_start: 0.9441 (m-80) cc_final: 0.8815 (m-80) REVERT: O 207 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9222 (mp) REVERT: L 33 LYS cc_start: 0.9371 (tttp) cc_final: 0.9037 (ttpp) REVERT: L 41 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7761 (pp30) REVERT: L 43 ASN cc_start: 0.9339 (m-40) cc_final: 0.9091 (m110) REVERT: L 47 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.9233 (p90) REVERT: L 157 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8654 (t80) REVERT: L 218 ASN cc_start: 0.9549 (m-40) cc_final: 0.8993 (p0) REVERT: M 76 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8161 (mm) outliers start: 48 outliers final: 32 residues processed: 188 average time/residue: 0.1308 time to fit residues: 41.0301 Evaluate side-chains 186 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 689 ASN 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 935 THR Chi-restraints excluded: chain A residue 1114 PHE 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 79 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 247 SER 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 103 CYS Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain G residue 261 TYR Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 149 PHE Chi-restraints excluded: chain O residue 157 TYR Chi-restraints excluded: chain O residue 207 ILE Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 157 TYR Chi-restraints excluded: chain L residue 213 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 94 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 93 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 19 ASN ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.045167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.030771 restraints weight = 187900.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.031661 restraints weight = 88540.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.032226 restraints weight = 54135.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.032549 restraints weight = 39213.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.032810 restraints weight = 32360.134| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 23878 Z= 0.189 Angle : 0.735 59.200 33342 Z= 0.400 Chirality : 0.040 0.403 4080 Planarity : 0.003 0.058 3582 Dihedral : 19.534 97.736 5326 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.79 % Allowed : 27.62 % Favored : 69.59 % 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: 1.33 (0.17), residues: 2674 helix: 1.88 (0.14), residues: 1399 sheet: -0.34 (0.34), residues: 257 loop : -0.13 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 57 TYR 0.031 0.001 TYR F 255 PHE 0.021 0.001 PHE L 149 TRP 0.030 0.002 TRP F 106 HIS 0.007 0.001 HIS F 21 Details of bonding type rmsd covalent geometry : bond 0.00392 (23878) covalent geometry : angle 0.73541 (33342) hydrogen bonds : bond 0.03264 ( 1296) hydrogen bonds : angle 4.12334 ( 3588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4464.99 seconds wall clock time: 77 minutes 35.08 seconds (4655.08 seconds total)