Starting phenix.real_space_refine on Sun Aug 24 18:11:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgy_37235/08_2025/8kgy_37235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgy_37235/08_2025/8kgy_37235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kgy_37235/08_2025/8kgy_37235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgy_37235/08_2025/8kgy_37235.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgy_37235/08_2025/8kgy_37235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgy_37235/08_2025/8kgy_37235.cif" } resolution = 2.59 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= 0.005 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 107 5.16 5 C 13880 2.51 5 N 3861 2.21 5 O 3998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21846 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3552 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 21, 'TRANS': 466} Chain breaks: 2 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 308 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 20, 'ARG:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 160 Chain: "B" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3670 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 21, 'TRANS': 467} Chain breaks: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 6, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 83 Chain: "C" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3658 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 21, 'TRANS': 467} Chain breaks: 2 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3641 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 3 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "E" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3648 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 3 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 3, 'ASP:plan': 7, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "F" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3677 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 3 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 64 Time building chain proxies: 5.98, per 1000 atoms: 0.27 Number of scatterers: 21846 At special positions: 0 Unit cell: (119.85, 112.2, 158.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 107 16.00 O 3998 8.00 N 3861 7.00 C 13880 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: 2.20 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5292 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 9 sheets defined 57.8% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 65 through 88 removed outlier: 4.453A pdb=" N ASP A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 103 through 110 removed outlier: 3.973A pdb=" N ARG A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.757A pdb=" N TYR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.666A pdb=" N LYS A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.590A pdb=" N MET A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.759A pdb=" N CYS A 254 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.504A pdb=" N PHE A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.502A pdb=" N HIS A 355 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.523A pdb=" N GLU A 373 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 420 removed outlier: 3.551A pdb=" N ARG A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.971A pdb=" N ASN A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 455 through 476 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 501 through 528 removed outlier: 4.066A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 Processing helix chain 'B' and resid 65 through 88 removed outlier: 4.517A pdb=" N ASP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 removed outlier: 4.078A pdb=" N ASN B 100 " --> pdb=" O GLN B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.927A pdb=" N ARG B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 175 removed outlier: 3.560A pdb=" N TYR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 removed outlier: 3.654A pdb=" N ASN B 192 " --> pdb=" O ASN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.684A pdb=" N LYS B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 244 Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.817A pdb=" N CYS B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.570A pdb=" N PHE B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.550A pdb=" N PHE B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.535A pdb=" N HIS B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.642A pdb=" N GLU B 373 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 396 removed outlier: 3.630A pdb=" N VAL B 396 " --> pdb=" O ALA B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 420 Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.793A pdb=" N ASN B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 448 Processing helix chain 'B' and resid 455 through 476 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 501 through 528 removed outlier: 4.092A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 553 removed outlier: 3.501A pdb=" N ALA B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 87 removed outlier: 4.380A pdb=" N ASP C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 removed outlier: 3.611A pdb=" N ARG C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.766A pdb=" N TYR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.655A pdb=" N TYR C 193 " --> pdb=" O PRO C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 212 removed outlier: 3.680A pdb=" N LYS C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 244 removed outlier: 3.719A pdb=" N MET C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.816A pdb=" N CYS C 254 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.568A pdb=" N PHE C 283 " --> pdb=" O GLY C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.508A pdb=" N HIS C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 410 through 420 removed outlier: 3.513A pdb=" N ASP C 414 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.733A pdb=" N ASN C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 448 Processing helix chain 'C' and resid 455 through 479 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 501 through 528 removed outlier: 4.061A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 554 removed outlier: 3.510A pdb=" N VAL C 549 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 554 " --> pdb=" O TYR C 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 89 removed outlier: 4.565A pdb=" N ASP D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYS D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 103 through 110 removed outlier: 3.684A pdb=" N ARG D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 175 removed outlier: 3.793A pdb=" N TYR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 removed outlier: 3.531A pdb=" N TYR D 193 " --> pdb=" O PRO D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 212 removed outlier: 3.689A pdb=" N LYS D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 244 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.783A pdb=" N CYS D 254 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.515A pdb=" N PHE D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 344 through 355 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.612A pdb=" N GLU D 373 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 396 removed outlier: 3.545A pdb=" N VAL D 396 " --> pdb=" O ALA D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 420 Processing helix chain 'D' and resid 426 through 431 removed outlier: 3.829A pdb=" N ASN D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 448 Processing helix chain 'D' and resid 455 through 476 Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 502 through 528 removed outlier: 3.513A pdb=" N VAL D 506 " --> pdb=" O GLU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 554 removed outlier: 3.795A pdb=" N GLY D 554 " --> pdb=" O TYR D 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 89 removed outlier: 4.618A pdb=" N ASP E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU E 89 " --> pdb=" O LEU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'E' and resid 103 through 110 removed outlier: 4.150A pdb=" N ARG E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 175 removed outlier: 3.539A pdb=" N TYR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 193 removed outlier: 3.824A pdb=" N TYR E 193 " --> pdb=" O PRO E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 212 removed outlier: 3.690A pdb=" N LYS E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 250 through 254 removed outlier: 3.809A pdb=" N CYS E 254 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 270 through 285 Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 344 through 355 Processing helix chain 'E' and resid 370 through 374 removed outlier: 3.612A pdb=" N GLU E 373 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 420 Processing helix chain 'E' and resid 426 through 431 removed outlier: 3.773A pdb=" N ASN E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 448 Processing helix chain 'E' and resid 455 through 476 Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 501 through 528 removed outlier: 4.050A pdb=" N ILE E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 554 removed outlier: 3.778A pdb=" N GLY E 554 " --> pdb=" O TYR E 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 88 removed outlier: 4.505A pdb=" N ASP F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 87 " --> pdb=" O ASP F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 102 removed outlier: 3.827A pdb=" N ASN F 100 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 110 removed outlier: 3.660A pdb=" N ARG F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 175 removed outlier: 3.779A pdb=" N TYR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 193 removed outlier: 3.700A pdb=" N TYR F 193 " --> pdb=" O PRO F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 212 removed outlier: 3.698A pdb=" N LYS F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 244 removed outlier: 3.730A pdb=" N MET F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.789A pdb=" N CYS F 254 " --> pdb=" O ALA F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 270 through 285 removed outlier: 3.535A pdb=" N PHE F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 294 Processing helix chain 'F' and resid 310 through 323 Processing helix chain 'F' and resid 344 through 355 removed outlier: 3.519A pdb=" N HIS F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 374 removed outlier: 3.635A pdb=" N GLU F 373 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 410 through 420 Processing helix chain 'F' and resid 426 through 431 removed outlier: 3.761A pdb=" N ASN F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 448 Processing helix chain 'F' and resid 455 through 476 Processing helix chain 'F' and resid 490 through 499 Processing helix chain 'F' and resid 501 through 528 removed outlier: 4.053A pdb=" N ILE F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 553 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 6.648A pdb=" N CYS A 146 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA A 223 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 148 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS A 147 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA A 184 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY A 149 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL A 186 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG A 151 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 115 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 115 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS E 147 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA E 184 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY E 149 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL E 186 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG E 151 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS E 146 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA E 223 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY E 148 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 338 removed outlier: 7.819A pdb=" N VAL A 306 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 330 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 379 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 401 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.646A pdb=" N CYS B 146 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA B 223 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY B 148 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS B 147 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA B 184 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY B 149 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL B 186 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG B 151 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 115 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LYS D 147 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA D 184 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY D 149 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL D 186 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG D 151 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS D 146 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA D 223 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY D 148 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 331 removed outlier: 10.610A pdb=" N LYS B 302 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ALA B 329 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE B 304 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLY B 331 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B 306 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU B 379 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 401 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 220 through 223 removed outlier: 6.669A pdb=" N CYS C 146 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA C 223 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY C 148 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS C 147 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA C 184 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY C 149 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL C 186 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG C 151 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY F 149 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS F 146 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA F 223 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY F 148 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 337 through 338 removed outlier: 8.053A pdb=" N VAL C 306 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL C 330 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR C 303 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE C 380 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 305 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 379 " --> pdb=" O ALA C 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 337 through 338 removed outlier: 8.066A pdb=" N PHE D 304 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 330 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL D 306 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU D 379 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D 401 " --> pdb=" O ILE D 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 337 through 338 removed outlier: 7.089A pdb=" N PHE E 304 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLY E 331 " --> pdb=" O PHE E 304 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL E 306 " --> pdb=" O GLY E 331 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR E 303 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE E 380 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL E 305 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU E 379 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE E 401 " --> pdb=" O ILE E 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 337 through 338 removed outlier: 7.908A pdb=" N VAL F 306 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL F 330 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU F 379 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE F 401 " --> pdb=" O ILE F 425 " (cutoff:3.500A) 1230 hydrogen bonds defined for protein. 3513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7256 1.34 - 1.46: 3546 1.46 - 1.57: 11339 1.57 - 1.69: 0 1.69 - 1.81: 178 Bond restraints: 22319 Sorted by residual: bond pdb=" CA ARG F 103 " pdb=" C ARG F 103 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.38e-02 5.25e+03 2.07e+00 bond pdb=" CA ARG C 103 " pdb=" C ARG C 103 " ideal model delta sigma weight residual 1.522 1.505 0.017 1.43e-02 4.89e+03 1.34e+00 bond pdb=" C ILE F 380 " pdb=" O ILE F 380 " ideal model delta sigma weight residual 1.232 1.241 -0.009 1.01e-02 9.80e+03 8.17e-01 bond pdb=" C ILE A 380 " pdb=" O ILE A 380 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.24e-01 bond pdb=" N PRO A 408 " pdb=" CA PRO A 408 " ideal model delta sigma weight residual 1.473 1.466 0.007 8.50e-03 1.38e+04 7.12e-01 ... (remaining 22314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 29425 1.24 - 2.47: 644 2.47 - 3.71: 147 3.71 - 4.95: 28 4.95 - 6.19: 7 Bond angle restraints: 30251 Sorted by residual: angle pdb=" N VAL B 102 " pdb=" CA VAL B 102 " pdb=" C VAL B 102 " ideal model delta sigma weight residual 113.07 107.66 5.41 1.37e+00 5.33e-01 1.56e+01 angle pdb=" N VAL F 102 " pdb=" CA VAL F 102 " pdb=" C VAL F 102 " ideal model delta sigma weight residual 113.07 108.83 4.24 1.36e+00 5.41e-01 9.72e+00 angle pdb=" CA GLY C 308 " pdb=" C GLY C 308 " pdb=" N PHE C 309 " ideal model delta sigma weight residual 114.58 117.22 -2.64 8.60e-01 1.35e+00 9.43e+00 angle pdb=" C VAL F 555 " pdb=" N THR F 556 " pdb=" CA THR F 556 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.39e+00 angle pdb=" C ARG D 420 " pdb=" N ASN D 421 " pdb=" CA ASN D 421 " ideal model delta sigma weight residual 122.82 126.31 -3.49 1.42e+00 4.96e-01 6.03e+00 ... (remaining 30246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 12110 17.18 - 34.37: 893 34.37 - 51.55: 128 51.55 - 68.74: 31 68.74 - 85.92: 24 Dihedral angle restraints: 13186 sinusoidal: 4886 harmonic: 8300 Sorted by residual: dihedral pdb=" CA ARG E 143 " pdb=" C ARG E 143 " pdb=" N THR E 144 " pdb=" CA THR E 144 " ideal model delta harmonic sigma weight residual -180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP F 344 " pdb=" CB ASP F 344 " pdb=" CG ASP F 344 " pdb=" OD1 ASP F 344 " ideal model delta sinusoidal sigma weight residual -30.00 -89.23 59.23 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 344 " pdb=" CB ASP C 344 " pdb=" CG ASP C 344 " pdb=" OD1 ASP C 344 " ideal model delta sinusoidal sigma weight residual -30.00 -89.09 59.09 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 13183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2345 0.038 - 0.076: 748 0.076 - 0.114: 246 0.114 - 0.152: 33 0.152 - 0.190: 3 Chirality restraints: 3375 Sorted by residual: chirality pdb=" CA THR B 144 " pdb=" N THR B 144 " pdb=" C THR B 144 " pdb=" CB THR B 144 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" CA THR E 144 " pdb=" N THR E 144 " pdb=" C THR E 144 " pdb=" CB THR E 144 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA THR C 144 " pdb=" N THR C 144 " pdb=" C THR C 144 " pdb=" CB THR C 144 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 3372 not shown) Planarity restraints: 3928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 144 " 0.037 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 145 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 145 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 145 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 485 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 486 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 486 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 486 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 361 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 362 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 362 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 362 " 0.025 5.00e-02 4.00e+02 ... (remaining 3925 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4673 2.78 - 3.31: 20838 3.31 - 3.84: 35726 3.84 - 4.37: 40682 4.37 - 4.90: 72123 Nonbonded interactions: 174042 Sorted by model distance: nonbonded pdb=" OG SER F 153 " pdb=" OD1 ASP F 155 " model vdw 2.249 3.040 nonbonded pdb=" O THR F 239 " pdb=" OG1 THR F 243 " model vdw 2.260 3.040 nonbonded pdb=" O THR C 239 " pdb=" OG1 THR C 243 " model vdw 2.262 3.040 nonbonded pdb=" O PRO F 64 " pdb=" NZ LYS F 386 " model vdw 2.264 3.120 nonbonded pdb=" OG SER C 119 " pdb=" O CYS F 112 " model vdw 2.286 3.040 ... (remaining 174037 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 'A' and (resid 64 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 81 or (resid 82 throu \ gh 83 and (name N or name CA or name C or name O or name CB )) or resid 84 throu \ gh 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) or r \ esid 91 through 132 or (resid 133 and (name N or name CA or name C or name O or \ name CB )) or resid 134 through 154 or (resid 155 and (name N or name CA or name \ C or name O or name CB )) or resid 156 through 296 or resid 301 through 556 or \ (resid 557 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 64 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 81 or (resid 82 through 83 and (na \ me N or name CA or name C or name O or name CB )) or resid 84 through 89 or (res \ id 90 and (name N or name CA or name C or name O or name CB )) or resid 91 throu \ gh 143 or (resid 144 and (name N or name CA or name C or name O or name CB )) or \ resid 145 through 154 or (resid 155 and (name N or name CA or name C or name O \ or name CB )) or resid 156 through 158 or (resid 159 through 160 and (name N or \ name CA or name C or name O or name CB )) or resid 161 through 230 or (resid 231 \ and (name N or name CA or name C or name O or name CB )) or resid 232 through 2 \ 80 or (resid 281 and (name N or name CA or name C or name O or name CB )) or res \ id 282 through 285 or (resid 286 through 287 and (name N or name CA or name C or \ name O or name CB )) or resid 288 through 296 or (resid 301 and (name N or name \ CA or name C or name O or name CB )) or resid 302 through 332 or (resid 333 thr \ ough 334 and (name N or name CA or name C or name O or name CB )) or resid 335 o \ r (resid 336 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 37 through 343 or (resid 344 and (name N or name CA or name C or name O or name \ CB )) or resid 345 through 356 or (resid 357 through 359 and (name N or name CA \ or name C or name O or name CB )) or resid 360 through 362 or (resid 363 through \ 365 and (name N or name CA or name C or name O or name CB )) or resid 366 throu \ gh 369 or (resid 370 through 371 and (name N or name CA or name C or name O or n \ ame CB )) or resid 372 through 374 or (resid 375 and (name N or name CA or name \ C or name O or name CB )) or resid 376 or (resid 377 and (name N or name CA or n \ ame C or name O or name CB )) or resid 378 through 385 or (resid 386 through 387 \ and (name N or name CA or name C or name O or name CB )) or resid 388 or (resid \ 389 through 390 and (name N or name CA or name C or name O or name CB )) or res \ id 391 through 394 or (resid 395 and (name N or name CA or name C or name O or n \ ame CB )) or resid 396 through 402 or (resid 403 and (name N or name CA or name \ C or name O or name CB )) or resid 404 through 426 or (resid 427 and (name N or \ name CA or name C or name O or name CB )) or resid 428 through 458 or (resid 459 \ and (name N or name CA or name C or name O or name CB )) or resid 460 through 4 \ 71 or (resid 472 and (name N or name CA or name C or name O or name CB )) or res \ id 473 through 474 or (resid 475 through 476 and (name N or name CA or name C or \ name O or name CB )) or resid 477 through 482 or resid 484 through 502 or (resi \ d 503 and (name N or name CA or name C or name O or name CB )) or resid 504 thro \ ugh 514 or (resid 515 and (name N or name CA or name C or name O or name CB )) o \ r resid 516 through 518 or (resid 519 and (name N or name CA or name C or name O \ or name CB )) or resid 520 through 522 or (resid 523 and (name N or name CA or \ name C or name O or name CB )) or resid 524 through 525 or (resid 526 and (name \ N or name CA or name C or name O or name CB )) or resid 527 through 528 or (resi \ d 529 and (name N or name CA or name C or name O or name CB )) or resid 530 thro \ ugh 543 or (resid 544 and (name N or name CA or name C or name O or name CB )) o \ r resid 545 through 556 or (resid 557 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'C' and (resid 64 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 81 or (resid 82 through 83 and (na \ me N or name CA or name C or name O or name CB )) or resid 84 through 89 or (res \ id 90 and (name N or name CA or name C or name O or name CB )) or resid 91 throu \ gh 132 or (resid 133 and (name N or name CA or name C or name O or name CB )) or \ resid 134 through 143 or (resid 144 and (name N or name CA or name C or name O \ or name CB )) or resid 145 through 154 or (resid 155 and (name N or name CA or n \ ame C or name O or name CB )) or resid 156 through 158 or (resid 159 through 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 2 \ 30 or (resid 231 and (name N or name CA or name C or name O or name CB )) or res \ id 232 through 280 or (resid 281 and (name N or name CA or name C or name O or n \ ame CB )) or resid 282 through 285 or (resid 286 through 287 and (name N or name \ CA or name C or name O or name CB )) or resid 288 through 296 or resid 301 thro \ ugh 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 or (resid 336 and (name N or name CA or name C or name O \ or name CB )) or resid 337 through 343 or (resid 344 and (name N or name CA or \ name C or name O or name CB )) or resid 345 through 356 or (resid 357 through 35 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 370 or (resid 371 and (name N or name CA or name C or name O or name CB )) or re \ sid 372 through 374 or (resid 375 and (name N or name CA or name C or name O or \ name CB )) or resid 376 or (resid 377 and (name N or name CA or name C or name O \ or name CB )) or resid 378 through 384 or (resid 385 through 387 and (name N or \ name CA or name C or name O or name CB )) or resid 388 or (resid 389 through 39 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 391 through \ 394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or re \ sid 396 through 411 or (resid 412 through 415 and (name N or name CA or name C o \ r name O or name CB )) or resid 416 through 426 or (resid 427 and (name N or nam \ e CA or name C or name O or name CB )) or resid 428 through 471 or (resid 472 an \ d (name N or name CA or name C or name O or name CB )) or resid 473 through 474 \ or (resid 475 through 476 and (name N or name CA or name C or name O or name CB \ )) or resid 477 through 482 or resid 484 through 491 or (resid 492 and (name N o \ r name CA or name C or name O or name CB )) or resid 493 through 502 or (resid 5 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 504 through \ 514 or (resid 515 and (name N or name CA or name C or name O or name CB )) or r \ esid 516 through 522 or (resid 523 and (name N or name CA or name C or name O or \ name CB )) or resid 524 through 525 or (resid 526 and (name N or name CA or nam \ e C or name O or name CB )) or resid 527 through 528 or (resid 529 and (name N o \ r name CA or name C or name O or name CB )) or resid 530 through 543 or (resid 5 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 545 through \ 557)) selection = (chain 'D' and (resid 64 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 through 132 or (resid 133 and \ (name N or name CA or name C or name O or name CB )) or resid 134 through 143 o \ r (resid 144 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 45 through 158 or (resid 159 through 160 and (name N or name CA or name C or nam \ e O or name CB )) or resid 161 through 230 or (resid 231 and (name N or name CA \ or name C or name O or name CB )) or resid 232 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 285 or (r \ esid 286 through 287 and (name N or name CA or name C or name O or name CB )) or \ resid 288 through 296 or (resid 301 and (name N or name CA or name C or name O \ or name CB )) or resid 302 through 332 or (resid 333 through 334 and (name N or \ name CA or name C or name O or name CB )) or resid 335 or (resid 336 and (name N \ or name CA or name C or name O or name CB )) or resid 337 through 343 or (resid \ 344 and (name N or name CA or name C or name O or name CB )) or resid 345 throu \ gh 349 or (resid 350 and (name N or name CA or name C or name O or name CB )) or \ resid 351 through 356 or (resid 357 through 359 and (name N or name CA or name \ C or name O or name CB )) or resid 360 through 364 or (resid 365 and (name N or \ name CA or name C or name O or name CB )) or resid 366 through 369 or (resid 370 \ through 371 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 72 through 374 or (resid 375 and (name N or name CA or name C or name O or name \ CB )) or resid 376 or (resid 377 and (name N or name CA or name C or name O or n \ ame CB )) or resid 378 through 383 or (resid 384 through 387 and (name N or name \ CA or name C or name O or name CB )) or resid 388 or (resid 389 through 390 and \ (name N or name CA or name C or name O or name CB )) or resid 391 through 394 o \ r (resid 395 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 96 through 402 or (resid 403 and (name N or name CA or name C or name O or name \ CB )) or resid 404 through 411 or (resid 412 through 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 through 426 or (resid 427 and (na \ me N or name CA or name C or name O or name CB )) or resid 428 through 471 or (r \ esid 472 and (name N or name CA or name C or name O or name CB )) or resid 473 t \ hrough 474 or (resid 475 through 476 and (name N or name CA or name C or name O \ or name CB )) or resid 477 through 482 or resid 484 through 491 or (resid 492 an \ d (name N or name CA or name C or name O or name CB )) or resid 493 through 494 \ or (resid 495 and (name N or name CA or name C or name O or name CB )) or resid \ 496 through 502 or (resid 503 and (name N or name CA or name C or name O or name \ CB )) or resid 504 through 514 or (resid 515 and (name N or name CA or name C o \ r name O or name CB )) or resid 516 through 525 or (resid 526 and (name N or nam \ e CA or name C or name O or name CB )) or resid 527 through 528 or (resid 529 an \ d (name N or name CA or name C or name O or name CB )) or resid 530 through 543 \ or (resid 544 and (name N or name CA or name C or name O or name CB )) or resid \ 545 through 555 or (resid 556 through 557 and (name N or name CA or name C or na \ me O or name CB )))) selection = (chain 'E' and (resid 64 through 81 or (resid 82 through 83 and (name N or name \ CA or name C or name O or name CB )) or resid 84 through 89 or (resid 90 and (na \ me N or name CA or name C or name O or name CB )) or resid 91 through 132 or (re \ sid 133 and (name N or name CA or name C or name O or name CB )) or resid 134 th \ rough 143 or (resid 144 and (name N or name CA or name C or name O or name CB )) \ or resid 145 through 154 or (resid 155 and (name N or name CA or name C or name \ O or name CB )) or resid 156 through 230 or (resid 231 and (name N or name CA o \ r name C or name O or name CB )) or resid 232 through 280 or (resid 281 and (nam \ e N or name CA or name C or name O or name CB )) or resid 282 through 285 or (re \ sid 286 through 287 and (name N or name CA or name C or name O or name CB )) or \ resid 288 through 296 or (resid 301 and (name N or name CA or name C or name O o \ r name CB )) or resid 302 through 325 or (resid 326 and (name N or name CA or na \ me C or name O or name CB )) or resid 327 through 332 or (resid 333 through 334 \ and (name N or name CA or name C or name O or name CB )) or resid 335 or (resid \ 336 and (name N or name CA or name C or name O or name CB )) or resid 337 throug \ h 356 or (resid 357 through 359 and (name N or name CA or name C or name O or na \ me CB )) or resid 360 through 362 or (resid 363 through 365 and (name N or name \ CA or name C or name O or name CB )) or resid 366 through 369 or (resid 370 thro \ ugh 371 and (name N or name CA or name C or name O or name CB )) or resid 372 th \ rough 374 or (resid 375 and (name N or name CA or name C or name O or name CB )) \ or resid 376 or (resid 377 and (name N or name CA or name C or name O or name C \ B )) or resid 378 through 383 or (resid 384 through 387 and (name N or name CA o \ r name C or name O or name CB )) or resid 388 or (resid 389 through 390 and (nam \ e N or name CA or name C or name O or name CB )) or resid 391 through 394 or (re \ sid 395 and (name N or name CA or name C or name O or name CB )) or resid 396 th \ rough 398 or (resid 399 and (name N or name CA or name C or name O or name CB )) \ or resid 400 through 402 or (resid 403 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 411 or (resid 412 through 415 and (name N \ or name CA or name C or name O or name CB )) or resid 416 through 426 or (resid \ 427 and (name N or name CA or name C or name O or name CB )) or resid 428 throug \ h 471 or (resid 472 and (name N or name CA or name C or name O or name CB )) or \ resid 473 through 474 or (resid 475 through 476 and (name N or name CA or name C \ or name O or name CB )) or resid 477 through 482 or resid 484 through 491 or (r \ esid 492 and (name N or name CA or name C or name O or name CB )) or resid 493 t \ hrough 494 or (resid 495 and (name N or name CA or name C or name O or name CB ) \ ) or resid 496 through 502 or (resid 503 and (name N or name CA or name C or nam \ e O or name CB )) or resid 504 through 514 or (resid 515 and (name N or name CA \ or name C or name O or name CB )) or resid 516 through 522 or (resid 523 and (na \ me N or name CA or name C or name O or name CB )) or resid 524 through 525 or (r \ esid 526 and (name N or name CA or name C or name O or name CB )) or resid 527 t \ hrough 528 or (resid 529 and (name N or name CA or name C or name O or name CB ) \ ) or resid 530 through 543 or (resid 544 and (name N or name CA or name C or nam \ e O or name CB )) or resid 545 through 557)) selection = (chain 'F' and (resid 64 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 81 or (resid 82 through 83 and (na \ me N or name CA or name C or name O or name CB )) or resid 84 through 89 or (res \ id 90 and (name N or name CA or name C or name O or name CB )) or resid 91 throu \ gh 97 or (resid 98 and (name N or name CA or name C or name O or name CB )) or r \ esid 99 through 132 or (resid 133 and (name N or name CA or name C or name O or \ name CB )) or resid 134 through 143 or (resid 144 and (name N or name CA or name \ C or name O or name CB )) or resid 145 through 154 or (resid 155 and (name N or \ name CA or name C or name O or name CB )) or resid 156 through 158 or (resid 15 \ 9 through 160 and (name N or name CA or name C or name O or name CB )) or resid \ 161 through 230 or (resid 231 and (name N or name CA or name C or name O or name \ CB )) or resid 232 through 280 or (resid 281 and (name N or name CA or name C o \ r name O or name CB )) or resid 282 through 285 or (resid 286 through 287 and (n \ ame N or name CA or name C or name O or name CB )) or resid 288 through 296 or ( \ resid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 \ through 325 or (resid 326 and (name N or name CA or name C or name O or name CB \ )) or resid 327 through 332 or (resid 333 through 334 and (name N or name CA or \ name C or name O or name CB )) or resid 335 or (resid 336 and (name N or name CA \ or name C or name O or name CB )) or resid 337 through 343 or (resid 344 and (n \ ame N or name CA or name C or name O or name CB )) or resid 345 through 349 or ( \ resid 350 and (name N or name CA or name C or name O or name CB )) or resid 351 \ through 356 or (resid 357 through 359 and (name N or name CA or name C or name O \ or name CB )) or resid 360 through 362 or (resid 363 through 365 and (name N or \ name CA or name C or name O or name CB )) or resid 366 through 369 or (resid 37 \ 0 through 371 and (name N or name CA or name C or name O or name CB )) or resid \ 372 through 374 or (resid 375 and (name N or name CA or name C or name O or name \ CB )) or resid 376 or (resid 377 and (name N or name CA or name C or name O or \ name CB )) or resid 378 through 384 or (resid 385 through 387 and (name N or nam \ e CA or name C or name O or name CB )) or resid 388 or (resid 389 through 390 an \ d (name N or name CA or name C or name O or name CB )) or resid 391 through 394 \ or (resid 395 and (name N or name CA or name C or name O or name CB )) or resid \ 396 through 398 or (resid 399 and (name N or name CA or name C or name O or name \ CB )) or resid 400 through 402 or (resid 403 and (name N or name CA or name C o \ r name O or name CB )) or resid 404 through 411 or (resid 412 through 415 and (n \ ame N or name CA or name C or name O or name CB )) or resid 416 through 418 or ( \ resid 419 and (name N or name CA or name C or name O or name CB )) or resid 420 \ through 426 or (resid 427 and (name N or name CA or name C or name O or name CB \ )) or resid 428 through 471 or (resid 472 and (name N or name CA or name C or na \ me O or name CB )) or resid 473 through 474 or (resid 475 through 476 and (name \ N or name CA or name C or name O or name CB )) or resid 477 through 482 or resid \ 484 through 491 or (resid 492 and (name N or name CA or name C or name O or nam \ e CB )) or resid 493 through 494 or (resid 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 through 502 or (resid 503 and (name N or na \ me CA or name C or name O or name CB )) or resid 504 through 514 or (resid 515 a \ nd (name N or name CA or name C or name O or name CB )) or resid 516 through 518 \ or (resid 519 and (name N or name CA or name C or name O or name CB )) or resid \ 520 through 522 or (resid 523 and (name N or name CA or name C or name O or nam \ e CB )) or resid 524 through 525 or (resid 526 and (name N or name CA or name C \ or name O or name CB )) or resid 527 through 528 or (resid 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 543 or (resid 544 a \ nd (name N or name CA or name C or name O or name CB )) or resid 545 through 555 \ or (resid 556 through 557 and (name N or name CA or name C or name O or name CB \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.170 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22319 Z= 0.122 Angle : 0.483 6.186 30251 Z= 0.276 Chirality : 0.042 0.190 3375 Planarity : 0.005 0.055 3928 Dihedral : 12.794 85.920 7894 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.20 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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 aren not related in a simple way. whole: 1.59 (0.16), residues: 2879 helix: 2.62 (0.14), residues: 1482 sheet: -0.19 (0.26), residues: 375 loop : -0.85 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.014 0.001 TYR B 550 PHE 0.015 0.001 PHE E 66 TRP 0.007 0.001 TRP C 338 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00256 (22319) covalent geometry : angle 0.48282 (30251) hydrogen bonds : bond 0.16105 ( 1230) hydrogen bonds : angle 4.29216 ( 3513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: C 317 MET cc_start: 0.8335 (ptt) cc_final: 0.8062 (ptp) REVERT: E 387 GLN cc_start: 0.8598 (mm110) cc_final: 0.8199 (mm110) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.7717 time to fit residues: 87.2240 Evaluate side-chains 85 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.0030 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 HIS E 355 HIS ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.057090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046537 restraints weight = 85159.622| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.66 r_work: 0.2922 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22319 Z= 0.154 Angle : 0.520 6.647 30251 Z= 0.277 Chirality : 0.043 0.184 3375 Planarity : 0.005 0.052 3928 Dihedral : 3.884 17.947 3159 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.72 % Favored : 96.08 % Rotamer: Outliers : 0.18 % Allowed : 3.22 % Favored : 96.60 % 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 aren not related in a simple way. whole: 1.62 (0.16), residues: 2879 helix: 2.57 (0.13), residues: 1528 sheet: -0.31 (0.27), residues: 367 loop : -0.81 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 90 TYR 0.013 0.001 TYR B 319 PHE 0.015 0.001 PHE C 304 TRP 0.007 0.001 TRP E 442 HIS 0.003 0.001 HIS F 355 Details of bonding type rmsd covalent geometry : bond 0.00355 (22319) covalent geometry : angle 0.52001 (30251) hydrogen bonds : bond 0.05105 ( 1230) hydrogen bonds : angle 3.71238 ( 3513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 1.165 Fit side-chains REVERT: C 69 MET cc_start: 0.8534 (mtm) cc_final: 0.8327 (mtt) REVERT: E 387 GLN cc_start: 0.8839 (mm110) cc_final: 0.8382 (mm110) outliers start: 4 outliers final: 0 residues processed: 92 average time/residue: 0.7859 time to fit residues: 81.7713 Evaluate side-chains 81 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 229 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 204 optimal weight: 0.0050 chunk 1 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS B 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.056078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.045597 restraints weight = 85414.533| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.68 r_work: 0.2892 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22319 Z= 0.167 Angle : 0.528 8.399 30251 Z= 0.278 Chirality : 0.043 0.187 3375 Planarity : 0.005 0.058 3928 Dihedral : 3.992 20.026 3159 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 0.60 % Allowed : 5.79 % Favored : 93.61 % 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 aren not related in a simple way. whole: 1.61 (0.16), residues: 2879 helix: 2.55 (0.13), residues: 1533 sheet: -0.38 (0.28), residues: 362 loop : -0.79 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 90 TYR 0.014 0.001 TYR B 319 PHE 0.016 0.001 PHE F 66 TRP 0.007 0.001 TRP E 442 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00394 (22319) covalent geometry : angle 0.52811 (30251) hydrogen bonds : bond 0.05216 ( 1230) hydrogen bonds : angle 3.65576 ( 3513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.929 Fit side-chains REVERT: C 66 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: C 69 MET cc_start: 0.8597 (mtm) cc_final: 0.8361 (mtt) outliers start: 13 outliers final: 5 residues processed: 95 average time/residue: 0.6935 time to fit residues: 75.6217 Evaluate side-chains 88 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 214 optimal weight: 0.0470 chunk 77 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 355 HIS ** F 139 HIS ** 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 = 0.3342 r_free = 0.3342 target = 0.056429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.045934 restraints weight = 85209.391| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.66 r_work: 0.2901 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22319 Z= 0.142 Angle : 0.514 8.696 30251 Z= 0.268 Chirality : 0.042 0.180 3375 Planarity : 0.004 0.043 3928 Dihedral : 3.950 18.303 3159 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 0.55 % Allowed : 7.22 % Favored : 92.23 % 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 aren not related in a simple way. whole: 1.64 (0.16), residues: 2879 helix: 2.60 (0.13), residues: 1533 sheet: -0.41 (0.28), residues: 362 loop : -0.78 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 90 TYR 0.011 0.001 TYR B 319 PHE 0.013 0.001 PHE C 304 TRP 0.007 0.001 TRP D 442 HIS 0.002 0.001 HIS B 448 Details of bonding type rmsd covalent geometry : bond 0.00333 (22319) covalent geometry : angle 0.51422 (30251) hydrogen bonds : bond 0.04737 ( 1230) hydrogen bonds : angle 3.56522 ( 3513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8149 (t80) cc_final: 0.7948 (t80) REVERT: C 69 MET cc_start: 0.8599 (mtm) cc_final: 0.8345 (mtt) outliers start: 12 outliers final: 6 residues processed: 96 average time/residue: 0.6895 time to fit residues: 75.8569 Evaluate side-chains 92 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 177 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 0.0000 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.0010 chunk 63 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 HIS D 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.055768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.045395 restraints weight = 85062.086| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.67 r_work: 0.2885 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22319 Z= 0.165 Angle : 0.531 8.712 30251 Z= 0.276 Chirality : 0.043 0.186 3375 Planarity : 0.004 0.042 3928 Dihedral : 4.002 18.755 3159 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 1.06 % Allowed : 8.23 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.16), residues: 2879 helix: 2.59 (0.13), residues: 1531 sheet: -0.52 (0.28), residues: 362 loop : -0.80 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 90 TYR 0.012 0.001 TYR B 319 PHE 0.015 0.001 PHE F 66 TRP 0.008 0.001 TRP E 442 HIS 0.003 0.001 HIS B 448 Details of bonding type rmsd covalent geometry : bond 0.00391 (22319) covalent geometry : angle 0.53112 (30251) hydrogen bonds : bond 0.05029 ( 1230) hydrogen bonds : angle 3.60094 ( 3513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8198 (t80) cc_final: 0.7980 (t80) REVERT: B 550 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8668 (t80) REVERT: C 66 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: C 69 MET cc_start: 0.8627 (mtm) cc_final: 0.8391 (mtt) outliers start: 23 outliers final: 8 residues processed: 106 average time/residue: 0.6113 time to fit residues: 74.8986 Evaluate side-chains 95 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 25 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 138 optimal weight: 0.0470 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.057975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.047484 restraints weight = 84155.657| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.67 r_work: 0.2954 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22319 Z= 0.094 Angle : 0.484 10.002 30251 Z= 0.248 Chirality : 0.041 0.168 3375 Planarity : 0.004 0.041 3928 Dihedral : 3.773 15.998 3159 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 0.87 % Allowed : 9.05 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.17), residues: 2879 helix: 2.66 (0.13), residues: 1549 sheet: -0.33 (0.28), residues: 352 loop : -0.78 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 90 TYR 0.006 0.001 TYR C 528 PHE 0.011 0.001 PHE C 304 TRP 0.007 0.001 TRP C 338 HIS 0.002 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00208 (22319) covalent geometry : angle 0.48376 (30251) hydrogen bonds : bond 0.03483 ( 1230) hydrogen bonds : angle 3.33438 ( 3513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8119 (t80) cc_final: 0.7904 (t80) REVERT: C 66 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: C 69 MET cc_start: 0.8625 (mtm) cc_final: 0.8379 (mtt) outliers start: 19 outliers final: 6 residues processed: 106 average time/residue: 0.6919 time to fit residues: 84.5339 Evaluate side-chains 95 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 485 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 285 ASN F 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.055855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.045459 restraints weight = 85552.920| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.68 r_work: 0.2894 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22319 Z= 0.164 Angle : 0.538 11.007 30251 Z= 0.275 Chirality : 0.043 0.186 3375 Planarity : 0.004 0.042 3928 Dihedral : 3.908 18.043 3159 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 0.92 % Allowed : 9.65 % Favored : 89.43 % 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 aren not related in a simple way. whole: 1.71 (0.17), residues: 2879 helix: 2.70 (0.13), residues: 1534 sheet: -0.49 (0.28), residues: 356 loop : -0.80 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 103 TYR 0.011 0.001 TYR B 319 PHE 0.013 0.001 PHE C 304 TRP 0.007 0.001 TRP E 442 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00388 (22319) covalent geometry : angle 0.53828 (30251) hydrogen bonds : bond 0.04924 ( 1230) hydrogen bonds : angle 3.51274 ( 3513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.937 Fit side-chains REVERT: A 67 PHE cc_start: 0.8163 (t80) cc_final: 0.7915 (t80) REVERT: B 550 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8796 (t80) REVERT: C 66 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.6638 (m-80) REVERT: C 69 MET cc_start: 0.8648 (mtm) cc_final: 0.8397 (mtt) REVERT: C 194 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8458 (p) outliers start: 20 outliers final: 11 residues processed: 105 average time/residue: 0.6300 time to fit residues: 76.8774 Evaluate side-chains 98 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 75 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.056626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.046165 restraints weight = 84870.656| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.67 r_work: 0.2910 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22319 Z= 0.126 Angle : 0.514 11.474 30251 Z= 0.262 Chirality : 0.042 0.176 3375 Planarity : 0.004 0.041 3928 Dihedral : 3.881 17.151 3159 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 0.97 % Allowed : 9.88 % Favored : 89.15 % 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 aren not related in a simple way. whole: 1.75 (0.16), residues: 2879 helix: 2.71 (0.13), residues: 1536 sheet: -0.37 (0.28), residues: 349 loop : -0.81 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 103 TYR 0.009 0.001 TYR B 319 PHE 0.012 0.001 PHE C 304 TRP 0.007 0.001 TRP D 442 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00297 (22319) covalent geometry : angle 0.51415 (30251) hydrogen bonds : bond 0.04276 ( 1230) hydrogen bonds : angle 3.44263 ( 3513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.921 Fit side-chains REVERT: A 67 PHE cc_start: 0.8183 (t80) cc_final: 0.7967 (t80) REVERT: B 550 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8723 (t80) REVERT: C 66 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: C 194 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8424 (p) outliers start: 21 outliers final: 10 residues processed: 106 average time/residue: 0.6181 time to fit residues: 76.2306 Evaluate side-chains 100 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain E residue 188 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2675 > 50: distance: 54 - 80: 6.425 distance: 58 - 87: 8.432 distance: 62 - 95: 4.357 distance: 71 - 80: 3.992 distance: 72 - 104: 6.548 distance: 81 - 82: 3.891 distance: 81 - 84: 3.098 distance: 82 - 87: 6.830 distance: 83 - 112: 12.249 distance: 84 - 85: 6.115 distance: 84 - 86: 4.300 distance: 87 - 88: 4.415 distance: 88 - 89: 5.855 distance: 88 - 91: 3.199 distance: 89 - 90: 8.239 distance: 89 - 95: 4.336 distance: 90 - 117: 11.997 distance: 91 - 92: 5.092 distance: 92 - 93: 6.627 distance: 93 - 94: 11.386 distance: 95 - 96: 5.265 distance: 96 - 97: 5.678 distance: 96 - 99: 6.149 distance: 97 - 98: 8.481 distance: 97 - 104: 4.367 distance: 99 - 100: 4.556 distance: 100 - 101: 6.130 distance: 101 - 102: 5.192 distance: 105 - 106: 3.517 distance: 105 - 108: 4.638 distance: 106 - 107: 7.084 distance: 106 - 112: 7.267 distance: 108 - 109: 15.151 distance: 109 - 110: 7.220 distance: 109 - 111: 7.587 distance: 112 - 113: 7.347 distance: 113 - 114: 8.820 distance: 113 - 116: 4.288 distance: 114 - 115: 16.601 distance: 114 - 117: 6.208 distance: 118 - 121: 3.914 distance: 119 - 120: 3.301 distance: 122 - 123: 4.237 distance: 123 - 124: 8.537 distance: 124 - 125: 7.544 distance: 126 - 127: 3.813 distance: 127 - 128: 9.797 distance: 128 - 129: 4.201 distance: 128 - 135: 6.485 distance: 130 - 131: 6.580 distance: 131 - 132: 4.854 distance: 132 - 133: 4.640 distance: 133 - 134: 3.941 distance: 135 - 136: 5.212 distance: 136 - 137: 12.219 distance: 137 - 138: 6.829 distance: 139 - 140: 4.929 distance: 140 - 141: 5.941 distance: 140 - 143: 7.449 distance: 141 - 142: 25.536 distance: 141 - 150: 26.864 distance: 143 - 144: 5.773 distance: 145 - 147: 6.829 distance: 146 - 148: 5.708 distance: 148 - 149: 4.561 distance: 150 - 151: 12.583 distance: 151 - 152: 11.335 distance: 151 - 154: 5.540 distance: 152 - 153: 4.656 distance: 154 - 155: 9.389 distance: 155 - 157: 10.524