Starting phenix.real_space_refine on Fri Aug 9 09:37:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/08_2024/7ztc_14957.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/08_2024/7ztc_14957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/08_2024/7ztc_14957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/08_2024/7ztc_14957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/08_2024/7ztc_14957.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/08_2024/7ztc_14957.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 168 5.16 5 C 16100 2.51 5 N 4396 2.21 5 O 4972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25652 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "E" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "F" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "G" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "H" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "W" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "X" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "Y" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "Z" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.14, per 1000 atoms: 0.59 Number of scatterers: 25652 At special positions: 0 Unit cell: (97, 101.85, 285.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 16 15.00 O 4972 8.00 N 4396 7.00 C 16100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.00 Conformation dependent library (CDL) restraints added in 5.4 seconds 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 48 sheets defined 66.2% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.558A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 59' Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.585A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.156A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.965A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.790A pdb=" N TYR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.527A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.680A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.024A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.585A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.612A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.603A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.162A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.515A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.846A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.604A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.310A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.668A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.021A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.645A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.575A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 59' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.603A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.145A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.865A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.839A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.526A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.299A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.721A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.020A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.638A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.627A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 55 through 59' Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.597A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.197A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.504A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.866A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.852A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.549A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.669A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 4.066A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.619A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.614A pdb=" N GLN E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 55 through 59' Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.569A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.179A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.857A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.847A pdb=" N TYR E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 216 removed outlier: 3.516A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.341A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.684A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 4.095A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 removed outlier: 3.575A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'F' and resid 55 through 59 removed outlier: 3.645A pdb=" N GLN F 59 " --> pdb=" O GLY F 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 55 through 59' Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.589A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.196A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.836A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 182 through 194 removed outlier: 3.779A pdb=" N TYR F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 216 removed outlier: 4.161A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 289 through 294 Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.674A pdb=" N LYS F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 4.066A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 removed outlier: 3.612A pdb=" N GLU F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 371 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.654A pdb=" N GLN G 59 " --> pdb=" O GLY G 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 59' Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.558A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.203A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 removed outlier: 3.871A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 182 through 194 removed outlier: 3.854A pdb=" N TYR G 188 " --> pdb=" O ASP G 184 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 216 removed outlier: 3.536A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 257 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 283 Processing helix chain 'G' and resid 289 through 294 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 removed outlier: 3.639A pdb=" N LYS G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 350 through 355 removed outlier: 4.034A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 removed outlier: 3.590A pdb=" N GLU G 364 " --> pdb=" O GLN G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 371 Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.670A pdb=" N GLN H 59 " --> pdb=" O GLY H 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 55 through 59' Processing helix chain 'H' and resid 78 through 92 removed outlier: 3.611A pdb=" N MET H 82 " --> pdb=" O ASN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 4.182A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 172 through 175 removed outlier: 3.843A pdb=" N ILE H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 172 through 175' Processing helix chain 'H' and resid 182 through 194 removed outlier: 3.796A pdb=" N TYR H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 216 removed outlier: 3.561A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 257 through 262 Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 283 Processing helix chain 'H' and resid 289 through 294 Processing helix chain 'H' and resid 301 through 306 removed outlier: 4.326A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.671A pdb=" N LYS H 315 " --> pdb=" O ASP H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 350 through 355 removed outlier: 4.042A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 removed outlier: 3.566A pdb=" N GLU H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 371 Processing helix chain 'W' and resid 2 through 135 Processing helix chain 'X' and resid 2 through 134 Processing helix chain 'Y' and resid 2 through 133 Processing helix chain 'Z' and resid 2 through 134 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.970A pdb=" N THR A 106 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.589A pdb=" N LEU A 176 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.611A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.606A pdb=" N LYS B 18 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.599A pdb=" N LEU B 176 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.592A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.963A pdb=" N THR C 106 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.573A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.532A pdb=" N LYS D 18 " --> pdb=" O ASP D 11 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 107 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.574A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.959A pdb=" N THR E 106 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.576A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.061A pdb=" N THR F 106 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.670A pdb=" N THR F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.527A pdb=" N LYS G 18 " --> pdb=" O ASP G 11 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR G 106 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.648A pdb=" N THR G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.522A pdb=" N LYS H 18 " --> pdb=" O ASP H 11 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR H 106 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AF2, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.739A pdb=" N THR H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 238 through 241 removed outlier: 3.623A pdb=" N LYS H 238 " --> pdb=" O ILE H 250 " (cutoff:3.500A) 1595 hydrogen bonds defined for protein. 4170 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: 10.78 Time building geometry restraints manager: 10.82 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: 8434 1.34 - 1.46: 3156 1.46 - 1.57: 14250 1.57 - 1.69: 24 1.69 - 1.81: 296 Bond restraints: 26160 Sorted by residual: bond pdb=" CD1 TYR C 169 " pdb=" CE1 TYR C 169 " ideal model delta sigma weight residual 1.382 1.338 0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CD1 TYR H 169 " pdb=" CE1 TYR H 169 " ideal model delta sigma weight residual 1.382 1.341 0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CD1 TYR F 169 " pdb=" CE1 TYR F 169 " ideal model delta sigma weight residual 1.382 1.341 0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CB TYR C 169 " pdb=" CG TYR C 169 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.20e-02 2.07e+03 1.80e+00 bond pdb=" CB THR C 160 " pdb=" CG2 THR C 160 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 ... (remaining 26155 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.90: 769 105.90 - 113.40: 14271 113.40 - 120.91: 11964 120.91 - 128.42: 8429 128.42 - 135.93: 175 Bond angle restraints: 35608 Sorted by residual: angle pdb=" CA TYR F 169 " pdb=" CB TYR F 169 " pdb=" CG TYR F 169 " ideal model delta sigma weight residual 113.90 104.27 9.63 1.80e+00 3.09e-01 2.86e+01 angle pdb=" N GLY D 42 " pdb=" CA GLY D 42 " pdb=" C GLY D 42 " ideal model delta sigma weight residual 113.18 125.53 -12.35 2.37e+00 1.78e-01 2.72e+01 angle pdb=" N GLY E 42 " pdb=" CA GLY E 42 " pdb=" C GLY E 42 " ideal model delta sigma weight residual 113.18 125.00 -11.82 2.37e+00 1.78e-01 2.49e+01 angle pdb=" N GLY F 42 " pdb=" CA GLY F 42 " pdb=" C GLY F 42 " ideal model delta sigma weight residual 113.18 124.90 -11.72 2.37e+00 1.78e-01 2.45e+01 angle pdb=" CA TYR E 169 " pdb=" CB TYR E 169 " pdb=" CG TYR E 169 " ideal model delta sigma weight residual 113.90 105.66 8.24 1.80e+00 3.09e-01 2.09e+01 ... (remaining 35603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.80: 15414 32.80 - 65.60: 268 65.60 - 98.40: 32 98.40 - 131.19: 8 131.19 - 163.99: 6 Dihedral angle restraints: 15728 sinusoidal: 5688 harmonic: 10040 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.99 -163.99 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.41 -163.41 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O2A ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PA ADP H 401 " pdb=" PB ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.19 -163.19 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 15725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2844 0.046 - 0.093: 894 0.093 - 0.139: 313 0.139 - 0.185: 22 0.185 - 0.231: 11 Chirality restraints: 4084 Sorted by residual: chirality pdb=" CA GLN B 49 " pdb=" N GLN B 49 " pdb=" C GLN B 49 " pdb=" CB GLN B 49 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PHE C 124 " pdb=" N PHE C 124 " pdb=" C PHE C 124 " pdb=" CB PHE C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE E 124 " pdb=" N PHE E 124 " pdb=" C PHE E 124 " pdb=" CB PHE E 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4081 not shown) Planarity restraints: 4600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 169 " 0.044 2.00e-02 2.50e+03 2.80e-02 1.56e+01 pdb=" CG TYR F 169 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR F 169 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR F 169 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 169 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR F 169 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR F 169 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 169 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 169 " 0.038 2.00e-02 2.50e+03 2.70e-02 1.46e+01 pdb=" CG TYR E 169 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR E 169 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR E 169 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 169 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 169 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR E 169 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 169 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 166 " 0.008 2.00e-02 2.50e+03 2.69e-02 1.45e+01 pdb=" CG TYR A 166 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 166 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 166 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 166 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 166 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 166 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR A 166 " -0.037 2.00e-02 2.50e+03 ... (remaining 4597 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 337 2.68 - 3.23: 25786 3.23 - 3.79: 38478 3.79 - 4.34: 50792 4.34 - 4.90: 84354 Nonbonded interactions: 199747 Sorted by model distance: nonbonded pdb=" OG1 THR C 160 " pdb=" O LEU C 178 " model vdw 2.123 3.040 nonbonded pdb=" OG1 THR G 160 " pdb=" O LEU G 178 " model vdw 2.133 3.040 nonbonded pdb=" OG1 THR D 160 " pdb=" O LEU D 178 " model vdw 2.133 3.040 nonbonded pdb=" OG1 THR B 160 " pdb=" O LEU B 178 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR F 160 " pdb=" O LEU F 178 " model vdw 2.148 3.040 ... (remaining 199742 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 73.020 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26160 Z= 0.225 Angle : 0.845 12.349 35608 Z= 0.441 Chirality : 0.050 0.231 4084 Planarity : 0.010 0.124 4600 Dihedral : 13.851 163.992 9256 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 2904 helix: -2.50 (0.12), residues: 1096 sheet: -0.67 (0.23), residues: 496 loop : -0.59 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 356 HIS 0.009 0.002 HIS G 87 PHE 0.017 0.001 PHE E 124 TYR 0.064 0.006 TYR E 169 ARG 0.027 0.004 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8866 (mmp) cc_final: 0.8613 (mmp) REVERT: C 44 MET cc_start: 0.7984 (tpt) cc_final: 0.7213 (ttp) REVERT: C 75 ILE cc_start: 0.8704 (mt) cc_final: 0.8255 (tt) REVERT: C 208 ILE cc_start: 0.9168 (mm) cc_final: 0.8946 (mt) REVERT: D 44 MET cc_start: 0.8187 (tpt) cc_final: 0.7245 (ttt) REVERT: D 305 MET cc_start: 0.8378 (mmm) cc_final: 0.7957 (mmt) REVERT: E 9 VAL cc_start: 0.8998 (t) cc_final: 0.8723 (m) REVERT: E 44 MET cc_start: 0.8287 (tpt) cc_final: 0.7862 (tpt) REVERT: E 205 GLU cc_start: 0.7820 (tt0) cc_final: 0.7479 (tt0) REVERT: E 360 GLN cc_start: 0.8240 (mm110) cc_final: 0.7822 (tp40) REVERT: F 24 ASP cc_start: 0.7170 (t0) cc_final: 0.6906 (m-30) REVERT: F 25 ASP cc_start: 0.8104 (t70) cc_final: 0.7527 (t0) REVERT: F 44 MET cc_start: 0.8163 (tpt) cc_final: 0.7808 (tpt) REVERT: F 205 GLU cc_start: 0.7953 (tt0) cc_final: 0.7659 (mt-10) REVERT: F 313 MET cc_start: 0.8887 (tpp) cc_final: 0.8637 (ttp) REVERT: G 43 VAL cc_start: 0.9032 (m) cc_final: 0.8777 (p) REVERT: G 65 LEU cc_start: 0.8918 (mp) cc_final: 0.8630 (mp) REVERT: G 92 ASN cc_start: 0.8140 (t0) cc_final: 0.7865 (m-40) REVERT: H 129 THR cc_start: 0.8152 (p) cc_final: 0.7666 (p) REVERT: H 201 THR cc_start: 0.8361 (m) cc_final: 0.8115 (t) REVERT: H 272 CYS cc_start: 0.7644 (m) cc_final: 0.7240 (m) outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.3616 time to fit residues: 344.2845 Evaluate side-chains 288 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 10.0000 chunk 257 optimal weight: 0.4980 chunk 142 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 266 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 308 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 87 HIS A 88 HIS B 87 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN C 49 GLN C 88 HIS C 101 HIS C 296 ASN C 354 GLN D 87 HIS D 88 HIS D 246 GLN E 87 HIS E 101 HIS E 252 ASN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 HIS ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS F 246 GLN G 87 HIS G 88 HIS H 87 HIS H 88 HIS H 173 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26160 Z= 0.213 Angle : 0.680 8.349 35608 Z= 0.331 Chirality : 0.045 0.221 4084 Planarity : 0.004 0.044 4600 Dihedral : 9.542 149.257 3792 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.02 % Allowed : 8.13 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 2904 helix: -0.39 (0.15), residues: 1096 sheet: 0.02 (0.23), residues: 496 loop : -0.23 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 356 HIS 0.006 0.001 HIS B 87 PHE 0.034 0.002 PHE C 124 TYR 0.057 0.002 TYR F 169 ARG 0.005 0.001 ARG E 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 324 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8502 (mmm) cc_final: 0.8170 (mmm) REVERT: A 123 MET cc_start: 0.8568 (tpp) cc_final: 0.8170 (tpp) REVERT: A 283 MET cc_start: 0.8774 (mmp) cc_final: 0.8359 (mmm) REVERT: B 123 MET cc_start: 0.8658 (tpp) cc_final: 0.8185 (tpp) REVERT: B 169 TYR cc_start: 0.8209 (m-80) cc_final: 0.7996 (m-80) REVERT: B 283 MET cc_start: 0.9186 (mmt) cc_final: 0.8820 (mmt) REVERT: B 288 ASP cc_start: 0.7556 (p0) cc_final: 0.7228 (t0) REVERT: C 44 MET cc_start: 0.8080 (tpt) cc_final: 0.7857 (tpp) REVERT: C 82 MET cc_start: 0.8151 (mmm) cc_final: 0.7857 (tpp) REVERT: C 143 TYR cc_start: 0.8542 (m-80) cc_final: 0.8284 (m-80) REVERT: D 44 MET cc_start: 0.8254 (tpt) cc_final: 0.7568 (ttt) REVERT: D 205 GLU cc_start: 0.7279 (tt0) cc_final: 0.6897 (pt0) REVERT: D 305 MET cc_start: 0.8249 (mmm) cc_final: 0.7904 (mmt) REVERT: E 44 MET cc_start: 0.8403 (tpt) cc_final: 0.8123 (tpt) REVERT: E 355 MET cc_start: 0.8124 (mtp) cc_final: 0.7865 (mtt) REVERT: F 25 ASP cc_start: 0.8142 (t70) cc_final: 0.7532 (t0) REVERT: F 72 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6794 (pp20) REVERT: F 82 MET cc_start: 0.8735 (tpp) cc_final: 0.8332 (mmm) REVERT: F 205 GLU cc_start: 0.7960 (tt0) cc_final: 0.7665 (mt-10) REVERT: F 313 MET cc_start: 0.8779 (tpp) cc_final: 0.8503 (ttt) REVERT: G 82 MET cc_start: 0.8703 (mmm) cc_final: 0.8135 (mmm) REVERT: G 92 ASN cc_start: 0.8417 (t0) cc_final: 0.7784 (m-40) REVERT: G 115 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8537 (t0) REVERT: G 300 SER cc_start: 0.8207 (t) cc_final: 0.7835 (m) REVERT: H 123 MET cc_start: 0.8661 (tpp) cc_final: 0.8322 (tpp) REVERT: H 270 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7153 (mt-10) outliers start: 50 outliers final: 22 residues processed: 359 average time/residue: 0.3215 time to fit residues: 192.0274 Evaluate side-chains 262 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 210 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 309 optimal weight: 30.0000 chunk 334 optimal weight: 30.0000 chunk 275 optimal weight: 3.9990 chunk 306 optimal weight: 30.0000 chunk 105 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS B 115 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN E 252 ASN F 49 GLN F 101 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 26160 Z= 0.415 Angle : 0.771 9.678 35608 Z= 0.381 Chirality : 0.049 0.259 4084 Planarity : 0.005 0.054 4600 Dihedral : 9.181 140.291 3792 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.95 % Allowed : 10.44 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 2904 helix: -0.14 (0.16), residues: 1064 sheet: -0.02 (0.22), residues: 496 loop : -0.54 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 79 HIS 0.007 0.002 HIS C 275 PHE 0.029 0.002 PHE F 124 TYR 0.040 0.002 TYR H 169 ARG 0.004 0.001 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 238 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8612 (mmm) cc_final: 0.8241 (mmm) REVERT: A 283 MET cc_start: 0.8791 (mmp) cc_final: 0.8496 (mmp) REVERT: B 288 ASP cc_start: 0.7551 (p0) cc_final: 0.7294 (t0) REVERT: D 44 MET cc_start: 0.8280 (tpt) cc_final: 0.7483 (ttt) REVERT: D 305 MET cc_start: 0.8426 (mmm) cc_final: 0.8043 (mmt) REVERT: E 355 MET cc_start: 0.8249 (mtp) cc_final: 0.8014 (mtt) REVERT: F 25 ASP cc_start: 0.7686 (t70) cc_final: 0.7419 (t0) REVERT: F 72 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6916 (pp20) REVERT: F 313 MET cc_start: 0.9054 (tpp) cc_final: 0.8549 (ttt) REVERT: G 300 SER cc_start: 0.8468 (t) cc_final: 0.8093 (m) REVERT: H 123 MET cc_start: 0.8770 (tpp) cc_final: 0.8506 (tpp) outliers start: 73 outliers final: 48 residues processed: 296 average time/residue: 0.2879 time to fit residues: 143.4192 Evaluate side-chains 258 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 209 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 40.0000 chunk 232 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 310 optimal weight: 40.0000 chunk 328 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 chunk 294 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: