Starting phenix.real_space_refine on Sat Jun 29 23:56:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/06_2024/8dwu_27760.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/06_2024/8dwu_27760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/06_2024/8dwu_27760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/06_2024/8dwu_27760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/06_2024/8dwu_27760.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/06_2024/8dwu_27760.pdb" } resolution = 3.4 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= 0.004 sd= 0.061 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 182 5.16 5 C 12443 2.51 5 N 3305 2.21 5 O 3760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 19690 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 251, 2000 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 241} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2713 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 344, 2713 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2675 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 342, 2675 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 332} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 344, 2705 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 335} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 2713 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 344, 2713 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 335} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2703 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1351 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 169} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1410 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 176} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1412 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.07, per 1000 atoms: 0.51 Number of scatterers: 19690 At special positions: 0 Unit cell: (195.847, 191.956, 112.839, 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 182 16.00 O 3760 8.00 N 3305 7.00 C 12443 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: 7.31 Conformation dependent library (CDL) restraints added in 3.4 seconds 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4820 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 25 sheets defined 44.2% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 185 through 192 removed outlier: 4.061A pdb=" N GLU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.508A pdb=" N HIS A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 4.490A pdb=" N GLU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 260 " --> pdb=" O CYS A 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 185 through 193 removed outlier: 4.147A pdb=" N GLU B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.568A pdb=" N GLU B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 4.368A pdb=" N GLU B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 260 " --> pdb=" O CYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 280 removed outlier: 3.701A pdb=" N LEU B 273 " --> pdb=" O MET B 269 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 328 through 333 removed outlier: 4.108A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 333' Processing helix chain 'B' and resid 335 through 345 removed outlier: 3.564A pdb=" N LYS B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 4.498A pdb=" N VAL B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 removed outlier: 3.621A pdb=" N CYS C 44 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 185 through 191 removed outlier: 3.756A pdb=" N GLU C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 222 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.652A pdb=" N HIS C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 4.409A pdb=" N GLU C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR C 259 " --> pdb=" O MET C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.968A pdb=" N LEU C 266 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 263 through 267' Processing helix chain 'C' and resid 269 through 280 removed outlier: 3.828A pdb=" N LEU C 273 " --> pdb=" O MET C 269 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 295 Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 315 through 328 Processing helix chain 'C' and resid 328 through 333 removed outlier: 3.667A pdb=" N VAL C 332 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 333' Processing helix chain 'C' and resid 335 through 345 removed outlier: 3.504A pdb=" N LYS C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 removed outlier: 4.482A pdb=" N VAL C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 350 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 351 " --> pdb=" O HIS C 347 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 138 through 144 Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'D' and resid 185 through 192 Processing helix chain 'D' and resid 215 through 222 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.599A pdb=" N GLU D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 258 removed outlier: 4.288A pdb=" N GLU D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 removed outlier: 3.935A pdb=" N LEU D 273 " --> pdb=" O MET D 269 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 315 through 328 Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.569A pdb=" N LYS D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.822A pdb=" N VAL D 349 " --> pdb=" O HIS D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 44 Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 145 through 148 Processing helix chain 'E' and resid 186 through 196 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.551A pdb=" N GLU E 230 " --> pdb=" O SER E 226 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 258 removed outlier: 3.746A pdb=" N PHE E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.948A pdb=" N LEU E 273 " --> pdb=" O MET E 269 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 296 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 315 through 328 Processing helix chain 'E' and resid 328 through 333 removed outlier: 4.109A pdb=" N LEU E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 345 removed outlier: 3.781A pdb=" N LYS E 339 " --> pdb=" O THR E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 360 removed outlier: 3.711A pdb=" N ALA E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.601A pdb=" N ARG F 45 " --> pdb=" O PHE F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.605A pdb=" N LYS F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 145 through 148 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 186 through 192 removed outlier: 3.540A pdb=" N GLY F 192 " --> pdb=" O ASP F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 222 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 247 through 258 removed outlier: 4.440A pdb=" N GLU F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.939A pdb=" N LEU F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 295 Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 315 through 328 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.508A pdb=" N VAL F 332 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU F 333 " --> pdb=" O ALA F 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 328 through 333' Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.506A pdb=" N LYS F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 358 removed outlier: 3.826A pdb=" N VAL F 349 " --> pdb=" O HIS F 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 192 Processing helix chain 'J' and resid 215 through 222 Processing helix chain 'J' and resid 222 through 231 removed outlier: 3.739A pdb=" N GLU J 230 " --> pdb=" O SER J 226 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS J 231 " --> pdb=" O ALA J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 258 removed outlier: 4.346A pdb=" N GLU J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 280 removed outlier: 3.995A pdb=" N LEU J 273 " --> pdb=" O MET J 269 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA J 275 " --> pdb=" O ASP J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 296 Processing helix chain 'J' and resid 301 through 312 Processing helix chain 'J' and resid 315 through 328 Processing helix chain 'J' and resid 331 through 334 removed outlier: 3.629A pdb=" N GLU J 334 " --> pdb=" O ASP J 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 331 through 334' Processing helix chain 'J' and resid 335 through 345 removed outlier: 3.707A pdb=" N LYS J 339 " --> pdb=" O THR J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 345 through 357 removed outlier: 3.800A pdb=" N VAL J 349 " --> pdb=" O HIS J 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 192 removed outlier: 4.275A pdb=" N LEU H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 222 Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.773A pdb=" N HIS H 231 " --> pdb=" O ALA H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 258 removed outlier: 4.323A pdb=" N GLU H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 280 removed outlier: 4.052A pdb=" N LEU H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 274 " --> pdb=" O ALA H 270 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA H 275 " --> pdb=" O ASP H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 296 removed outlier: 3.522A pdb=" N ASN H 296 " --> pdb=" O ALA H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 312 Processing helix chain 'H' and resid 315 through 328 Processing helix chain 'H' and resid 335 through 345 removed outlier: 3.576A pdb=" N LYS H 339 " --> pdb=" O THR H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 357 removed outlier: 3.754A pdb=" N VAL H 349 " --> pdb=" O HIS H 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 192 removed outlier: 3.706A pdb=" N LEU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 222 Processing helix chain 'I' and resid 222 through 231 removed outlier: 3.603A pdb=" N HIS I 231 " --> pdb=" O ALA I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 261 removed outlier: 4.449A pdb=" N GLU I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR I 259 " --> pdb=" O MET I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 280 removed outlier: 4.140A pdb=" N LEU I 273 " --> pdb=" O MET I 269 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU I 274 " --> pdb=" O ALA I 270 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA I 275 " --> pdb=" O ASP I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 295 Processing helix chain 'I' and resid 301 through 312 Processing helix chain 'I' and resid 315 through 328 Processing helix chain 'I' and resid 328 through 333 removed outlier: 3.621A pdb=" N VAL I 332 " --> pdb=" O HIS I 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU I 333 " --> pdb=" O ALA I 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 328 through 333' Processing helix chain 'I' and resid 335 through 345 removed outlier: 3.669A pdb=" N LYS I 339 " --> pdb=" O THR I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 358 removed outlier: 3.793A pdb=" N VAL I 349 " --> pdb=" O HIS I 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.405A pdb=" N ARG A 99 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 164 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 104 " --> pdb=" O MET C 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.405A pdb=" N ARG A 99 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 164 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C 99 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 39 removed outlier: 4.789A pdb=" N THR A 156 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 53 removed outlier: 6.837A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 85 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 137 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A 86 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 135 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 88 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE A 133 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 90 " --> pdb=" O TRP A 131 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N TRP A 131 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 206 removed outlier: 3.944A pdb=" N PHE A 211 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.638A pdb=" N TYR B 123 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG B 99 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 101 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL E 163 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG E 99 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE E 104 " --> pdb=" O MET E 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.638A pdb=" N TYR B 123 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG B 99 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 101 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL E 163 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG E 99 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 39 Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 53 removed outlier: 7.166A pdb=" N LYS B 66 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 84 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 135 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 206 removed outlier: 3.830A pdb=" N PHE B 211 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 206 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 209 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.612A pdb=" N VAL C 71 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS C 66 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 85 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 84 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS C 135 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 86 " --> pdb=" O PHE C 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 206 removed outlier: 3.767A pdb=" N CYS C 202 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 213 " --> pdb=" O CYS C 202 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE C 211 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 206 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 209 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 38 removed outlier: 3.918A pdb=" N CYS D 159 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 155 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'D' and resid 202 through 206 removed outlier: 3.547A pdb=" N CYS D 202 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE D 211 " --> pdb=" O LEU D 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 66 through 72 removed outlier: 6.777A pdb=" N LYS E 66 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E 85 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU E 86 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS E 135 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU E 88 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE E 133 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU E 90 " --> pdb=" O TRP E 131 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N TRP E 131 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 202 through 206 removed outlier: 3.895A pdb=" N CYS E 202 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 213 " --> pdb=" O CYS E 202 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE E 211 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 29 through 39 removed outlier: 3.700A pdb=" N PHE F 32 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS F 159 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 155 " --> pdb=" O ILE F 38 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR F 156 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE F 104 " --> pdb=" O MET F 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 29 through 39 removed outlier: 3.700A pdb=" N PHE F 32 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS F 159 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 155 " --> pdb=" O ILE F 38 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG F 99 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 57 through 58 removed outlier: 6.827A pdb=" N LYS F 66 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU F 86 " --> pdb=" O PHE F 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 202 through 206 removed outlier: 3.781A pdb=" N CYS F 202 " --> pdb=" O ALA F 213 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA F 213 " --> pdb=" O CYS F 202 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE F 211 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 202 through 206 removed outlier: 4.004A pdb=" N PHE J 211 " --> pdb=" O LEU J 204 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 202 through 206 removed outlier: 3.870A pdb=" N CYS H 202 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA H 213 " --> pdb=" O CYS H 202 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE H 211 " --> pdb=" O LEU H 204 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 202 through 206 removed outlier: 3.859A pdb=" N PHE I 211 " --> pdb=" O LEU I 204 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2334 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: 5.65 Time building geometry restraints manager: 8.10 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: 6236 1.34 - 1.46: 4173 1.46 - 1.58: 9366 1.58 - 1.71: 2 1.71 - 1.83: 274 Bond restraints: 20051 Sorted by residual: bond pdb=" CA SER B 21 " pdb=" CB SER B 21 " ideal model delta sigma weight residual 1.536 1.484 0.052 1.46e-02 4.69e+03 1.28e+01 bond pdb=" CA SER A 21 " pdb=" CB SER A 21 " ideal model delta sigma weight residual 1.537 1.485 0.051 1.67e-02 3.59e+03 9.48e+00 bond pdb=" CG MET I 228 " pdb=" SD MET I 228 " ideal model delta sigma weight residual 1.803 1.736 0.067 2.50e-02 1.60e+03 7.18e+00 bond pdb=" CB ARG C 198 " pdb=" CG ARG C 198 " ideal model delta sigma weight residual 1.520 1.599 -0.079 3.00e-02 1.11e+03 7.00e+00 bond pdb=" N GLU B 20 " pdb=" CA GLU B 20 " ideal model delta sigma weight residual 1.453 1.484 -0.032 1.31e-02 5.83e+03 5.79e+00 ... (remaining 20046 not shown) Histogram of bond angle deviations from ideal: 92.61 - 101.00: 64 101.00 - 109.40: 1813 109.40 - 117.79: 12766 117.79 - 126.18: 12056 126.18 - 134.58: 335 Bond angle restraints: 27034 Sorted by residual: angle pdb=" CA MET I 228 " pdb=" CB MET I 228 " pdb=" CG MET I 228 " ideal model delta sigma weight residual 114.10 130.44 -16.34 2.00e+00 2.50e-01 6.67e+01 angle pdb=" N MET I 228 " pdb=" CA MET I 228 " pdb=" CB MET I 228 " ideal model delta sigma weight residual 110.20 121.66 -11.46 1.49e+00 4.50e-01 5.92e+01 angle pdb=" CA MET I 288 " pdb=" CB MET I 288 " pdb=" CG MET I 288 " ideal model delta sigma weight residual 114.10 128.86 -14.76 2.00e+00 2.50e-01 5.45e+01 angle pdb=" N MET C 228 " pdb=" CA MET C 228 " pdb=" CB MET C 228 " ideal model delta sigma weight residual 110.20 120.84 -10.64 1.49e+00 4.50e-01 5.10e+01 angle pdb=" CA MET C 228 " pdb=" CB MET C 228 " pdb=" CG MET C 228 " ideal model delta sigma weight residual 114.10 127.99 -13.89 2.00e+00 2.50e-01 4.82e+01 ... (remaining 27029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 11014 17.64 - 35.27: 1002 35.27 - 52.91: 171 52.91 - 70.55: 34 70.55 - 88.19: 20 Dihedral angle restraints: 12241 sinusoidal: 4861 harmonic: 7380 Sorted by residual: dihedral pdb=" CA SER I 197 " pdb=" C SER I 197 " pdb=" N ARG I 198 " pdb=" CA ARG I 198 " ideal model delta harmonic sigma weight residual 180.00 152.72 27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA SER D 197 " pdb=" C SER D 197 " pdb=" N ARG D 198 " pdb=" CA ARG D 198 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER J 197 " pdb=" C SER J 197 " pdb=" N ARG J 198 " pdb=" CA ARG J 198 " ideal model delta harmonic sigma weight residual 180.00 152.75 27.25 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 12238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2556 0.082 - 0.165: 372 0.165 - 0.247: 56 0.247 - 0.330: 10 0.330 - 0.412: 6 Chirality restraints: 3000 Sorted by residual: chirality pdb=" CB ILE F 52 " pdb=" CA ILE F 52 " pdb=" CG1 ILE F 52 " pdb=" CG2 ILE F 52 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB ILE D 52 " pdb=" CA ILE D 52 " pdb=" CG1 ILE D 52 " pdb=" CG2 ILE D 52 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA MET C 288 " pdb=" N MET C 288 " pdb=" C MET C 288 " pdb=" CB MET C 288 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 2997 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 198 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C ARG C 198 " 0.068 2.00e-02 2.50e+03 pdb=" O ARG C 198 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE C 199 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 324 " -0.017 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE E 324 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE E 324 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE E 324 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE E 324 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 324 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 324 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 198 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ARG F 198 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG F 198 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE F 199 " -0.019 2.00e-02 2.50e+03 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2191 2.76 - 3.29: 19697 3.29 - 3.83: 30658 3.83 - 4.36: 36118 4.36 - 4.90: 61570 Nonbonded interactions: 150234 Sorted by model distance: nonbonded pdb=" O LEU E 76 " pdb=" OG SER E 80 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR E 200 " pdb=" OE1 GLN E 212 " model vdw 2.231 2.440 nonbonded pdb=" NZ LYS E 129 " pdb=" OG1 THR F 25 " model vdw 2.238 2.520 nonbonded pdb=" O CYS C 256 " pdb=" OG1 THR C 260 " model vdw 2.243 2.440 nonbonded pdb=" OE2 GLU E 20 " pdb=" OH TYR F 87 " model vdw 2.248 2.440 ... (remaining 150229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 17 through 172 or (resid 173 through 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 or (resid 183 and (name N o \ r name CA or name C or name O or name CB )) or resid 184 through 357)) selection = (chain 'C' and (resid 17 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 357)) selection = (chain 'D' and (resid 17 through 172 or (resid 173 through 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 through 357)) selection = (chain 'E' and (resid 17 through 172 or (resid 173 through 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 through 357)) selection = (chain 'F' and (resid 17 through 172 or (resid 173 through 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 or (resid 183 and (name N o \ r name CA or name C or name O or name CB )) or resid 184 through 357)) } ncs_group { reference = (chain 'H' and resid 185 through 357) selection = (chain 'I' and resid 185 through 357) selection = (chain 'J' and resid 185 through 357) } 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: 0.010 Normalize map: mean=0, sd=1: 2.730 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: 0.000 Extract box with map and model: 5.290 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 48.550 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.080 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 20051 Z= 0.355 Angle : 1.260 17.400 27034 Z= 0.667 Chirality : 0.064 0.412 3000 Planarity : 0.006 0.056 3481 Dihedral : 14.455 88.185 7421 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.20 % Favored : 92.28 % Rotamer: Outliers : 0.14 % Allowed : 0.37 % Favored : 99.49 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -1.91 (0.17), residues: 2487 helix: 0.00 (0.17), residues: 940 sheet: -1.76 (0.30), residues: 319 loop : -2.18 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP I 338 HIS 0.014 0.002 HIS B 347 PHE 0.057 0.003 PHE E 324 TYR 0.027 0.002 TYR F 327 ARG 0.017 0.002 ARG F 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.6678 (mtp) cc_final: 0.6419 (mtm) REVERT: B 228 MET cc_start: 0.2223 (ppp) cc_final: 0.1915 (ppp) REVERT: E 176 MET cc_start: 0.4657 (ptm) cc_final: 0.3907 (ppp) REVERT: J 233 MET cc_start: 0.0213 (ptm) cc_final: -0.1668 (ppp) REVERT: I 176 MET cc_start: 0.3514 (ptp) cc_final: 0.0231 (ppp) outliers start: 3 outliers final: 1 residues processed: 172 average time/residue: 0.3440 time to fit residues: 89.0844 Evaluate side-chains 123 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 chunk 118 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 225 optimal weight: 20.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN D 177 ASN D 316 GLN F 40 ASN ** F 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 GLN J 265 ASN ** J 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20051 Z= 0.359 Angle : 0.757 9.669 27034 Z= 0.400 Chirality : 0.046 0.233 3000 Planarity : 0.004 0.048 3481 Dihedral : 5.677 29.733 2662 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.00 % Favored : 91.60 % Rotamer: Outliers : 0.37 % Allowed : 6.74 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -1.41 (0.17), residues: 2487 helix: 0.55 (0.17), residues: 971 sheet: -1.62 (0.26), residues: 411 loop : -2.03 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 338 HIS 0.005 0.001 HIS E 231 PHE 0.022 0.002 PHE D 41 TYR 0.019 0.002 TYR F 327 ARG 0.005 0.001 ARG I 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.6374 (mtp) cc_final: 0.6164 (mtp) REVERT: A 233 MET cc_start: -0.0835 (tmm) cc_final: -0.1597 (tmm) REVERT: E 176 MET cc_start: 0.3758 (ptm) cc_final: 0.3489 (ppp) REVERT: F 228 MET cc_start: 0.5128 (ppp) cc_final: 0.4830 (ppp) REVERT: J 233 MET cc_start: 0.0508 (ptm) cc_final: 0.0282 (ppp) REVERT: I 176 MET cc_start: 0.3226 (ptp) cc_final: 0.0927 (ppp) outliers start: 8 outliers final: 2 residues processed: 132 average time/residue: 0.3226 time to fit residues: 66.5671 Evaluate side-chains 121 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain J residue 341 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 225 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN E 320 GLN E 347 HIS ** F 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20051 Z= 0.342 Angle : 0.726 9.789 27034 Z= 0.384 Chirality : 0.044 0.168 3000 Planarity : 0.004 0.053 3481 Dihedral : 5.499 29.052 2660 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.84 % Favored : 91.84 % Rotamer: Outliers : 0.84 % Allowed : 9.35 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -1.31 (0.17), residues: 2487 helix: 0.59 (0.17), residues: 980 sheet: -1.54 (0.27), residues: 405 loop : -1.95 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 67 HIS 0.006 0.001 HIS A 214 PHE 0.017 0.002 PHE A 199 TYR 0.019 0.001 TYR B 280 ARG 0.005 0.001 ARG E 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6919 (tpt) cc_final: 0.6674 (tpt) REVERT: A 233 MET cc_start: -0.0621 (tmm) cc_final: -0.0977 (tmm) REVERT: B 48 MET cc_start: 0.8034 (tpt) cc_final: 0.7769 (tpt) REVERT: J 228 MET cc_start: 0.6347 (ppp) cc_final: 0.5948 (ppp) REVERT: J 233 MET cc_start: 0.0032 (ptm) cc_final: -0.0271 (ppp) REVERT: H 176 MET cc_start: -0.1846 (tmm) cc_final: -0.2688 (ptt) REVERT: H 228 MET cc_start: 0.4721 (ppp) cc_final: 0.4419 (ppp) REVERT: I 176 MET cc_start: 0.3666 (ptp) cc_final: 0.1075 (ppp) REVERT: I 233 MET cc_start: -0.0310 (ptm) cc_final: -0.0976 (ptt) outliers start: 18 outliers final: 7 residues processed: 136 average time/residue: 0.3014 time to fit residues: 65.8099 Evaluate side-chains 121 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 341 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 40.0000 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 24 optimal weight: 50.0000 chunk 107 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 226 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20051 Z= 0.261 Angle : 0.686 9.223 27034 Z= 0.359 Chirality : 0.043 0.258 3000 Planarity : 0.003 0.059 3481 Dihedral : 5.292 29.662 2660 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.64 % Favored : 92.04 % Rotamer: Outliers : 0.93 % Allowed : 10.74 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -1.07 (0.17), residues: 2487 helix: 0.85 (0.17), residues: 971 sheet: -1.45 (0.27), residues: 394 loop : -1.84 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 67 HIS 0.008 0.001 HIS C 231 PHE 0.017 0.002 PHE A 199 TYR 0.013 0.001 TYR B 280 ARG 0.005 0.000 ARG E 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6858 (tpt) cc_final: 0.6646 (tpt) REVERT: A 176 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5898 (mtp) REVERT: C 35 MET cc_start: 0.6837 (tpp) cc_final: 0.6358 (tpp) REVERT: C 228 MET cc_start: 0.3852 (pmm) cc_final: 0.3110 (pmm) REVERT: E 176 MET cc_start: 0.2426 (ptm) cc_final: 0.2208 (ptm) REVERT: F 233 MET cc_start: 0.0589 (ppp) cc_final: 0.0050 (ptm) REVERT: J 228 MET cc_start: 0.6003 (ppp) cc_final: 0.5728 (ppp) REVERT: H 176 MET cc_start: -0.1677 (tmm) cc_final: -0.2186 (ptt) REVERT: I 176 MET cc_start: 0.3090 (ptp) cc_final: 0.1913 (ppp) REVERT: I 233 MET cc_start: -0.0783 (ptm) cc_final: -0.1130 (ptt) REVERT: I 254 MET cc_start: 0.6223 (ppp) cc_final: 0.5606 (ppp) outliers start: 20 outliers final: 8 residues processed: 130 average time/residue: 0.2860 time to fit residues: 60.7657 Evaluate side-chains 123 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 204 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20051 Z= 0.223 Angle : 0.662 10.109 27034 Z= 0.345 Chirality : 0.043 0.176 3000 Planarity : 0.003 0.059 3481 Dihedral : 5.147 27.040 2660 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.56 % Favored : 92.12 % Rotamer: Outliers : 1.30 % Allowed : 11.95 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -0.88 (0.17), residues: 2487 helix: 1.00 (0.17), residues: 973 sheet: -1.26 (0.26), residues: 414 loop : -1.77 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 67 HIS 0.003 0.001 HIS B 328 PHE 0.017 0.001 PHE A 199 TYR 0.012 0.001 TYR B 280 ARG 0.004 0.000 ARG C 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6454 (tpt) REVERT: A 176 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5608 (mtp) REVERT: C 35 MET cc_start: 0.6779 (tpp) cc_final: 0.6494 (tpp) REVERT: C 233 MET cc_start: 0.1664 (ptp) cc_final: 0.1041 (ptp) REVERT: F 233 MET cc_start: 0.0541 (ppp) cc_final: -0.0076 (ptm) REVERT: F 341 MET cc_start: 0.4904 (ppp) cc_final: 0.4536 (ppp) REVERT: H 176 MET cc_start: -0.1506 (tmm) cc_final: -0.2240 (ptt) REVERT: I 176 MET cc_start: 0.3147 (ptp) cc_final: 0.1770 (ppp) REVERT: I 228 MET cc_start: 0.6858 (pmm) cc_final: 0.6624 (pmm) REVERT: I 233 MET cc_start: -0.0849 (ptm) cc_final: -0.1318 (ptt) outliers start: 28 outliers final: 9 residues processed: 136 average time/residue: 0.2865 time to fit residues: 62.4359 Evaluate side-chains 125 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 246 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.9980 chunk 215 optimal weight: 0.0020 chunk 47 optimal weight: 0.0060 chunk 140 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 overall best weight: 2.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20051 Z= 0.225 Angle : 0.679 12.931 27034 Z= 0.350 Chirality : 0.043 0.192 3000 Planarity : 0.003 0.062 3481 Dihedral : 5.104 27.678 2660 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.48 % Favored : 92.20 % Rotamer: Outliers : 1.30 % Allowed : 12.65 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -0.79 (0.17), residues: 2487 helix: 1.11 (0.17), residues: 975 sheet: -1.14 (0.27), residues: 408 loop : -1.80 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 338 HIS 0.003 0.001 HIS B 328 PHE 0.016 0.001 PHE A 199 TYR 0.011 0.001 TYR B 280 ARG 0.003 0.000 ARG F 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 MET cc_start: 0.6807 (tpp) cc_final: 0.6577 (tpp) REVERT: F 233 MET cc_start: 0.0388 (ppp) cc_final: -0.0182 (ptm) REVERT: H 176 MET cc_start: -0.1564 (tmm) cc_final: -0.1792 (ptt) REVERT: H 228 MET cc_start: 0.4870 (ppp) cc_final: 0.4185 (ppp) REVERT: I 176 MET cc_start: 0.3336 (ptp) cc_final: 0.1961 (ppp) REVERT: I 233 MET cc_start: -0.1076 (ptm) cc_final: -0.1479 (ptt) outliers start: 28 outliers final: 13 residues processed: 137 average time/residue: 0.2863 time to fit residues: 62.6850 Evaluate side-chains 128 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain H residue 279 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.0411 > 50: distance: 30 - 36: 21.853 distance: 36 - 37: 34.917 distance: 37 - 38: 20.415 distance: 37 - 40: 21.999 distance: 38 - 39: 3.460 distance: 38 - 44: 21.051 distance: 40 - 41: 23.238 distance: 41 - 42: 22.108 distance: 41 - 43: 17.111 distance: 44 - 45: 7.518 distance: 45 - 46: 23.588 distance: 45 - 48: 6.863 distance: 46 - 47: 11.820 distance: 46 - 52: 17.182 distance: 48 - 49: 14.101 distance: 49 - 50: 23.091 distance: 49 - 51: 18.281 distance: 52 - 53: 4.680 distance: 53 - 54: 8.415 distance: 53 - 56: 32.067 distance: 54 - 55: 19.418 distance: 54 - 59: 26.888 distance: 56 - 57: 27.799 distance: 56 - 58: 7.998 distance: 59 - 60: 23.649 distance: 60 - 61: 15.812 distance: 60 - 63: 12.425 distance: 61 - 62: 6.921 distance: 61 - 68: 25.871 distance: 62 - 87: 35.473 distance: 63 - 64: 25.201 distance: 64 - 65: 8.272 distance: 65 - 66: 7.518 distance: 65 - 67: 27.880 distance: 68 - 74: 31.622 distance: 69 - 70: 11.329 distance: 69 - 72: 38.297 distance: 70 - 71: 19.494 distance: 70 - 75: 8.142 distance: 71 - 98: 28.896 distance: 72 - 73: 23.258 distance: 73 - 74: 13.387 distance: 75 - 76: 8.978 distance: 76 - 77: 13.925 distance: 76 - 79: 21.558 distance: 77 - 78: 4.240 distance: 77 - 80: 17.061 distance: 80 - 81: 21.982 distance: 81 - 82: 17.272 distance: 81 - 84: 30.572 distance: 82 - 83: 24.786 distance: 82 - 87: 24.423 distance: 83 - 116: 21.386 distance: 84 - 85: 18.597 distance: 84 - 86: 14.832 distance: 87 - 88: 5.115 distance: 88 - 89: 15.109 distance: 88 - 91: 21.565 distance: 89 - 90: 19.324 distance: 89 - 98: 41.432 distance: 90 - 124: 17.020 distance: 91 - 92: 23.233 distance: 92 - 93: 21.787 distance: 92 - 94: 27.106 distance: 93 - 95: 18.279 distance: 94 - 96: 8.615 distance: 95 - 97: 4.779 distance: 96 - 97: 13.621 distance: 98 - 99: 4.158 distance: 99 - 100: 9.354 distance: 99 - 102: 14.015 distance: 100 - 101: 17.074 distance: 100 - 107: 4.408 distance: 101 - 132: 28.889 distance: 102 - 103: 17.772 distance: 103 - 104: 24.811 distance: 104 - 105: 23.746 distance: 105 - 106: 40.548 distance: 107 - 108: 8.033 distance: 108 - 109: 14.022 distance: 108 - 111: 4.768 distance: 109 - 110: 9.595 distance: 109 - 116: 14.616 distance: 110 - 138: 10.918 distance: 111 - 112: 6.909 distance: 112 - 113: 12.112 distance: 113 - 114: 19.513 distance: 113 - 115: 5.534