Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 12:25:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/10_2023/6ach_9592_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/10_2023/6ach_9592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/10_2023/6ach_9592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/10_2023/6ach_9592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/10_2023/6ach_9592_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/10_2023/6ach_9592_updated.pdb" } resolution = 3.2 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= 0.016 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 136 5.16 5 C 14536 2.51 5 N 4136 2.21 5 O 4416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 365": "NH1" <-> "NH2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "F TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F ARG 365": "NH1" <-> "NH2" Residue "F ARG 367": "NH1" <-> "NH2" Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 363": "NH1" <-> "NH2" Residue "G ARG 365": "NH1" <-> "NH2" Residue "G ARG 367": "NH1" <-> "NH2" Residue "H TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 363": "NH1" <-> "NH2" Residue "H ARG 365": "NH1" <-> "NH2" Residue "H ARG 367": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 23240 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 bond proxies already assigned to first conformer: 2841 Chain: "B" Number of atoms: 2861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 bond proxies already assigned to first conformer: 2841 Chain: "C" Number of atoms: 2861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 bond proxies already assigned to first conformer: 2841 Chain: "D" Number of atoms: 2861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 bond proxies already assigned to first conformer: 2841 Chain: "E" Number of atoms: 2861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 bond proxies already assigned to first conformer: 2841 Chain: "F" Number of atoms: 2861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 bond proxies already assigned to first conformer: 2841 Chain: "G" Number of atoms: 2861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 bond proxies already assigned to first conformer: 2841 Chain: "H" Number of atoms: 2861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 364, 2829 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 bond proxies already assigned to first conformer: 2841 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.54, per 1000 atoms: 0.97 Number of scatterers: 23240 At special positions: 0 Unit cell: (126.896, 126.896, 119.504, 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 136 16.00 P 16 15.00 O 4416 8.00 N 4136 7.00 C 14536 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: 8.66 Conformation dependent library (CDL) restraints added in 6.3 seconds 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 24 sheets defined 42.6% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.864A pdb=" N TYR A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 71 Processing helix chain 'A' and resid 93 through 106 removed outlier: 3.928A pdb=" N LEU A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.834A pdb=" N GLU A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 327 removed outlier: 4.172A pdb=" N GLN A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 349 removed outlier: 3.970A pdb=" N ASP A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.864A pdb=" N TYR B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 71 Processing helix chain 'B' and resid 93 through 106 removed outlier: 3.928A pdb=" N LEU B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 Processing helix chain 'B' and resid 185 through 195 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 283 through 286 No H-bonds generated for 'chain 'B' and resid 283 through 286' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.834A pdb=" N GLU B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 327 removed outlier: 4.172A pdb=" N GLN B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 349 removed outlier: 3.970A pdb=" N ASP B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 removed outlier: 3.864A pdb=" N TYR C 10 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 71 Processing helix chain 'C' and resid 93 through 106 removed outlier: 3.928A pdb=" N LEU C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 165 Processing helix chain 'C' and resid 185 through 195 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 283 through 286 No H-bonds generated for 'chain 'C' and resid 283 through 286' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.834A pdb=" N GLU C 297 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 327 removed outlier: 4.172A pdb=" N GLN C 312 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 349 removed outlier: 3.970A pdb=" N ASP C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 10 removed outlier: 3.864A pdb=" N TYR D 10 " --> pdb=" O TYR D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 71 Processing helix chain 'D' and resid 93 through 106 removed outlier: 3.928A pdb=" N LEU D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 283 through 286 No H-bonds generated for 'chain 'D' and resid 283 through 286' Processing helix chain 'D' and resid 289 through 299 removed outlier: 3.834A pdb=" N GLU D 297 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 327 removed outlier: 4.172A pdb=" N GLN D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR D 314 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP D 315 " --> pdb=" O GLU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 349 removed outlier: 3.970A pdb=" N ASP D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 10 removed outlier: 3.864A pdb=" N TYR E 10 " --> pdb=" O TYR E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 71 Processing helix chain 'E' and resid 93 through 106 removed outlier: 3.928A pdb=" N LEU E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 165 Processing helix chain 'E' and resid 185 through 195 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 248 through 250 No H-bonds generated for 'chain 'E' and resid 248 through 250' Processing helix chain 'E' and resid 267 through 276 Processing helix chain 'E' and resid 283 through 286 No H-bonds generated for 'chain 'E' and resid 283 through 286' Processing helix chain 'E' and resid 289 through 299 removed outlier: 3.834A pdb=" N GLU E 297 " --> pdb=" O ASN E 293 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU E 298 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 327 removed outlier: 4.172A pdb=" N GLN E 312 " --> pdb=" O LYS E 308 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR E 314 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP E 315 " --> pdb=" O GLU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 349 removed outlier: 3.970A pdb=" N ASP E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.864A pdb=" N TYR F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 71 Processing helix chain 'F' and resid 93 through 106 removed outlier: 3.928A pdb=" N LEU F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 165 Processing helix chain 'F' and resid 185 through 195 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 267 through 276 Processing helix chain 'F' and resid 283 through 286 No H-bonds generated for 'chain 'F' and resid 283 through 286' Processing helix chain 'F' and resid 289 through 299 removed outlier: 3.834A pdb=" N GLU F 297 " --> pdb=" O ASN F 293 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU F 298 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR F 299 " --> pdb=" O ALA F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 327 removed outlier: 4.172A pdb=" N GLN F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE F 313 " --> pdb=" O LYS F 309 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR F 314 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP F 315 " --> pdb=" O GLU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 349 removed outlier: 3.970A pdb=" N ASP F 336 " --> pdb=" O TYR F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 10 removed outlier: 3.864A pdb=" N TYR G 10 " --> pdb=" O TYR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 71 Processing helix chain 'G' and resid 93 through 106 removed outlier: 3.928A pdb=" N LEU G 106 " --> pdb=" O PHE G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 165 Processing helix chain 'G' and resid 185 through 195 Processing helix chain 'G' and resid 207 through 216 Processing helix chain 'G' and resid 248 through 250 No H-bonds generated for 'chain 'G' and resid 248 through 250' Processing helix chain 'G' and resid 267 through 276 Processing helix chain 'G' and resid 283 through 286 No H-bonds generated for 'chain 'G' and resid 283 through 286' Processing helix chain 'G' and resid 289 through 299 removed outlier: 3.834A pdb=" N GLU G 297 " --> pdb=" O ASN G 293 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU G 298 " --> pdb=" O VAL G 294 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 327 removed outlier: 4.172A pdb=" N GLN G 312 " --> pdb=" O LYS G 308 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE G 313 " --> pdb=" O LYS G 309 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR G 314 " --> pdb=" O ILE G 310 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP G 315 " --> pdb=" O GLU G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 349 removed outlier: 3.970A pdb=" N ASP G 336 " --> pdb=" O TYR G 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 10 removed outlier: 3.864A pdb=" N TYR H 10 " --> pdb=" O TYR H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 71 Processing helix chain 'H' and resid 93 through 106 removed outlier: 3.928A pdb=" N LEU H 106 " --> pdb=" O PHE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 165 Processing helix chain 'H' and resid 185 through 195 Processing helix chain 'H' and resid 207 through 216 Processing helix chain 'H' and resid 248 through 250 No H-bonds generated for 'chain 'H' and resid 248 through 250' Processing helix chain 'H' and resid 267 through 276 Processing helix chain 'H' and resid 283 through 286 No H-bonds generated for 'chain 'H' and resid 283 through 286' Processing helix chain 'H' and resid 289 through 299 removed outlier: 3.834A pdb=" N GLU H 297 " --> pdb=" O ASN H 293 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU H 298 " --> pdb=" O VAL H 294 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR H 299 " --> pdb=" O ALA H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 327 removed outlier: 4.172A pdb=" N GLN H 312 " --> pdb=" O LYS H 308 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE H 313 " --> pdb=" O LYS H 309 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR H 314 " --> pdb=" O ILE H 310 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP H 315 " --> pdb=" O GLU H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 349 removed outlier: 3.970A pdb=" N ASP H 336 " --> pdb=" O TYR H 332 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.799A pdb=" N GLY A 78 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY A 79 " --> pdb=" O PRO A 38 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU A 40 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR A 81 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY A 42 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 83 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.383A pdb=" N THR A 81 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TRP A 46 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE A 83 " --> pdb=" O TRP A 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 198 through 202 removed outlier: 6.501A pdb=" N ILE A 233 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLN A 179 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA A 235 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 14 through 20 removed outlier: 6.799A pdb=" N GLY B 78 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY B 79 " --> pdb=" O PRO B 38 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU B 40 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR B 81 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY B 42 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE B 83 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 43 through 46 removed outlier: 6.383A pdb=" N THR B 81 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TRP B 46 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE B 83 " --> pdb=" O TRP B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 198 through 202 removed outlier: 6.501A pdb=" N ILE B 233 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLN B 179 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 235 " --> pdb=" O GLN B 179 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 14 through 20 removed outlier: 6.799A pdb=" N GLY C 78 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY C 79 " --> pdb=" O PRO C 38 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU C 40 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR C 81 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY C 42 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE C 83 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 43 through 46 removed outlier: 6.383A pdb=" N THR C 81 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TRP C 46 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE C 83 " --> pdb=" O TRP C 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 198 through 202 removed outlier: 6.501A pdb=" N ILE C 233 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLN C 179 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA C 235 " --> pdb=" O GLN C 179 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 14 through 20 removed outlier: 6.799A pdb=" N GLY D 78 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY D 79 " --> pdb=" O PRO D 38 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU D 40 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR D 81 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY D 42 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE D 83 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 43 through 46 removed outlier: 6.383A pdb=" N THR D 81 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TRP D 46 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE D 83 " --> pdb=" O TRP D 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 198 through 202 removed outlier: 6.501A pdb=" N ILE D 233 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLN D 179 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA D 235 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 14 through 20 removed outlier: 6.799A pdb=" N GLY E 78 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY E 79 " --> pdb=" O PRO E 38 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU E 40 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR E 81 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY E 42 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE E 83 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.383A pdb=" N THR E 81 " --> pdb=" O ARG E 44 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TRP E 46 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE E 83 " --> pdb=" O TRP E 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 198 through 202 removed outlier: 6.501A pdb=" N ILE E 233 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLN E 179 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA E 235 " --> pdb=" O GLN E 179 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 14 through 20 removed outlier: 6.799A pdb=" N GLY F 78 " --> pdb=" O HIS F 32 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY F 79 " --> pdb=" O PRO F 38 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU F 40 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR F 81 " --> pdb=" O LEU F 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY F 42 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE F 83 " --> pdb=" O GLY F 42 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 43 through 46 removed outlier: 6.383A pdb=" N THR F 81 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TRP F 46 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE F 83 " --> pdb=" O TRP F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 198 through 202 removed outlier: 6.501A pdb=" N ILE F 233 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLN F 179 " --> pdb=" O ILE F 233 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA F 235 " --> pdb=" O GLN F 179 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 14 through 20 removed outlier: 6.799A pdb=" N GLY G 78 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY G 79 " --> pdb=" O PRO G 38 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU G 40 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR G 81 " --> pdb=" O LEU G 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY G 42 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE G 83 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 43 through 46 removed outlier: 6.383A pdb=" N THR G 81 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TRP G 46 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE G 83 " --> pdb=" O TRP G 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'G' and resid 198 through 202 removed outlier: 6.501A pdb=" N ILE G 233 " --> pdb=" O ALA G 177 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLN G 179 " --> pdb=" O ILE G 233 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA G 235 " --> pdb=" O GLN G 179 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 14 through 20 removed outlier: 6.799A pdb=" N GLY H 78 " --> pdb=" O HIS H 32 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY H 79 " --> pdb=" O PRO H 38 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU H 40 " --> pdb=" O GLY H 79 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR H 81 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY H 42 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE H 83 " --> pdb=" O GLY H 42 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 43 through 46 removed outlier: 6.383A pdb=" N THR H 81 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TRP H 46 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE H 83 " --> pdb=" O TRP H 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'H' and resid 198 through 202 removed outlier: 6.501A pdb=" N ILE H 233 " --> pdb=" O ALA H 177 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLN H 179 " --> pdb=" O ILE H 233 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA H 235 " --> pdb=" O GLN H 179 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2800 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: 7.30 Time building geometry restraints manager: 9.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4008 1.31 - 1.43: 6056 1.43 - 1.56: 13336 1.56 - 1.69: 48 1.69 - 1.81: 240 Bond restraints: 23688 Sorted by residual: bond pdb=" C3B NAD G 400 " pdb=" C4B NAD G 400 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3B NAD C 400 " pdb=" C4B NAD C 400 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3B NAD H 400 " pdb=" C4B NAD H 400 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3B NAD A 400 " pdb=" C4B NAD A 400 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3B NAD F 400 " pdb=" C4B NAD F 400 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 ... (remaining 23683 not shown) Histogram of bond angle deviations from ideal: 97.88 - 106.14: 644 106.14 - 114.39: 13304 114.39 - 122.65: 15686 122.65 - 130.90: 2270 130.90 - 139.16: 120 Bond angle restraints: 32024 Sorted by residual: angle pdb=" N1A NAD C 400 " pdb=" C6A NAD C 400 " pdb=" N6A NAD C 400 " ideal model delta sigma weight residual 119.35 102.50 16.85 3.00e+00 1.11e-01 3.16e+01 angle pdb=" N1A NAD D 400 " pdb=" C6A NAD D 400 " pdb=" N6A NAD D 400 " ideal model delta sigma weight residual 119.35 102.52 16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" N1A NAD E 400 " pdb=" C6A NAD E 400 " pdb=" N6A NAD E 400 " ideal model delta sigma weight residual 119.35 102.54 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" N1A NAD H 400 " pdb=" C6A NAD H 400 " pdb=" N6A NAD H 400 " ideal model delta sigma weight residual 119.35 102.54 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" N1A NAD F 400 " pdb=" C6A NAD F 400 " pdb=" N6A NAD F 400 " ideal model delta sigma weight residual 119.35 102.54 16.81 3.00e+00 1.11e-01 3.14e+01 ... (remaining 32019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.73: 12792 11.73 - 23.45: 1030 23.45 - 35.18: 250 35.18 - 46.90: 80 46.90 - 58.63: 72 Dihedral angle restraints: 14224 sinusoidal: 5776 harmonic: 8448 Sorted by residual: dihedral pdb=" CA ILE E 136 " pdb=" C ILE E 136 " pdb=" N SER E 137 " pdb=" CA SER E 137 " ideal model delta harmonic sigma weight residual -180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ILE H 136 " pdb=" C ILE H 136 " pdb=" N SER H 137 " pdb=" CA SER H 137 " ideal model delta harmonic sigma weight residual -180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ILE B 136 " pdb=" C ILE B 136 " pdb=" N SER B 137 " pdb=" CA SER B 137 " ideal model delta harmonic sigma weight residual 180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 14221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2280 0.064 - 0.128: 964 0.128 - 0.191: 188 0.191 - 0.255: 0 0.255 - 0.319: 16 Chirality restraints: 3448 Sorted by residual: chirality pdb=" C3B NAD B 400 " pdb=" C2B NAD B 400 " pdb=" C4B NAD B 400 " pdb=" O3B NAD B 400 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C3B NAD D 400 " pdb=" C2B NAD D 400 " pdb=" C4B NAD D 400 " pdb=" O3B NAD D 400 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C3D NAD D 400 " pdb=" C2D NAD D 400 " pdb=" C4D NAD D 400 " pdb=" O3D NAD D 400 " both_signs ideal model delta sigma weight residual False -2.73 -2.41 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 3445 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 37 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO F 38 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 38 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 38 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 37 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO D 38 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 38 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 38 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 37 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B 38 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.031 5.00e-02 4.00e+02 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5733 2.79 - 3.32: 20268 3.32 - 3.84: 37626 3.84 - 4.37: 45269 4.37 - 4.90: 79938 Nonbonded interactions: 188834 Sorted by model distance: nonbonded pdb=" OG1 THR H 43 " pdb=" OG1 THR H 112 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR A 43 " pdb=" OG1 THR A 112 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR C 43 " pdb=" OG1 THR C 112 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR B 43 " pdb=" OG1 THR B 112 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR F 43 " pdb=" OG1 THR F 112 " model vdw 2.261 2.440 ... (remaining 188829 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 'A' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 364 or resid 366 through 367 or resid 400)) selection = (chain 'B' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 364 or resid 366 through 367 or resid 400)) selection = (chain 'C' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 364 or resid 366 through 367 or resid 400)) selection = (chain 'D' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 364 or resid 366 through 367 or resid 400)) selection = (chain 'E' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 364 or resid 366 through 367 or resid 400)) selection = (chain 'F' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 364 or resid 366 through 367 or resid 400)) selection = (chain 'G' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 364 or resid 366 through 367 or resid 400)) selection = (chain 'H' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 364 or resid 366 through 367 or resid 400)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 3.200 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 73.420 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.016 0.230 23688 Z= 1.037 Angle : 1.356 16.851 32024 Z= 0.662 Chirality : 0.071 0.319 3448 Planarity : 0.007 0.056 4200 Dihedral : 10.690 58.630 8880 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.03 % Allowed : 4.11 % Favored : 94.86 % 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: -3.92 (0.12), residues: 2912 helix: -2.54 (0.10), residues: 1368 sheet: -1.72 (0.19), residues: 504 loop : -2.85 (0.15), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 584 time to evaluate : 2.416 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 0.3636 time to fit residues: 321.4111 Evaluate side-chains 384 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 225 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 0.0060 chunk 261 optimal weight: 0.9980 overall best weight: 0.5714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 179 GLN A 193 HIS A 293 ASN A 302 ASN A 316 ASN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 179 GLN B 193 HIS B 293 ASN B 302 ASN B 316 ASN ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN C 179 GLN C 193 HIS C 293 ASN C 302 ASN C 316 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 ASN D 179 GLN D 193 HIS D 293 ASN D 302 ASN D 316 ASN ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN E 179 GLN E 193 HIS E 293 ASN E 302 ASN E 316 ASN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 ASN F 179 GLN F 193 HIS F 293 ASN F 302 ASN F 316 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN G 179 GLN G 193 HIS G 293 ASN G 302 ASN G 316 ASN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN H 179 GLN H 193 HIS H 293 ASN H 302 ASN H 316 ASN ** H 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 23688 Z= 0.153 Angle : 0.577 6.640 32024 Z= 0.299 Chirality : 0.043 0.140 3448 Planarity : 0.004 0.035 4200 Dihedral : 5.715 36.314 3352 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.42 % Allowed : 10.02 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.00 (0.14), residues: 2912 helix: -0.84 (0.13), residues: 1416 sheet: -0.78 (0.21), residues: 504 loop : -2.14 (0.16), residues: 992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 400 time to evaluate : 2.642 Fit side-chains outliers start: 56 outliers final: 48 residues processed: 440 average time/residue: 0.3693 time to fit residues: 254.5724 Evaluate side-chains 402 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 354 time to evaluate : 2.515 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2247 time to fit residues: 23.3285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 chunk 283 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 259 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 359 HIS B 32 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 HIS B 359 HIS C 32 HIS ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS C 359 HIS D 32 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 193 HIS D 359 HIS E 32 HIS ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS E 359 HIS F 32 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 HIS F 359 HIS G 32 HIS ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS G 359 HIS H 32 HIS ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 HIS H 359 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 23688 Z= 0.374 Angle : 0.646 6.931 32024 Z= 0.331 Chirality : 0.047 0.159 3448 Planarity : 0.004 0.033 4200 Dihedral : 5.494 38.255 3352 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.91 % Allowed : 10.45 % Favored : 86.64 % 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: -1.50 (0.14), residues: 2912 helix: -0.13 (0.13), residues: 1408 sheet: -1.12 (0.21), residues: 496 loop : -2.04 (0.17), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 376 time to evaluate : 2.717 Fit side-chains outliers start: 44 outliers final: 21 residues processed: 404 average time/residue: 0.3602 time to fit residues: 226.4282 Evaluate side-chains 365 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 344 time to evaluate : 2.497 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2015 time to fit residues: 11.6325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.4403 > 50: distance: 53 - 69: 27.041 distance: 57 - 77: 24.636 distance: 61 - 87: 15.935 distance: 64 - 69: 29.434 distance: 65 - 96: 22.207 distance: 69 - 70: 23.214 distance: 70 - 71: 33.352 distance: 70 - 73: 28.147 distance: 71 - 72: 19.297 distance: 71 - 77: 54.427 distance: 73 - 74: 32.755 distance: 73 - 75: 36.653 distance: 74 - 76: 36.805 distance: 77 - 78: 26.365 distance: 78 - 79: 31.154 distance: 78 - 81: 7.897 distance: 79 - 80: 11.799 distance: 79 - 87: 35.017 distance: 81 - 82: 25.245 distance: 82 - 83: 24.209 distance: 82 - 84: 14.763 distance: 83 - 85: 18.193 distance: 84 - 86: 20.772 distance: 85 - 86: 20.801 distance: 87 - 88: 7.665 distance: 88 - 89: 9.938 distance: 88 - 91: 18.943 distance: 89 - 90: 24.008 distance: 89 - 96: 18.007 distance: 91 - 92: 9.445 distance: 92 - 93: 12.832 distance: 93 - 94: 5.655 distance: 93 - 95: 7.867 distance: 96 - 97: 9.173 distance: 97 - 98: 6.727 distance: 97 - 100: 23.245 distance: 98 - 99: 45.841 distance: 98 - 104: 18.915 distance: 100 - 101: 20.738 distance: 101 - 102: 12.403 distance: 102 - 103: 5.811 distance: 104 - 105: 17.229 distance: 105 - 106: 43.465 distance: 106 - 107: 22.881 distance: 106 - 108: 18.480 distance: 108 - 109: 18.406 distance: 109 - 110: 34.615 distance: 109 - 112: 30.822 distance: 110 - 111: 14.816 distance: 110 - 116: 11.048 distance: 112 - 113: 24.208 distance: 112 - 114: 23.573 distance: 113 - 115: 27.373 distance: 116 - 117: 18.702 distance: 117 - 118: 47.658 distance: 117 - 120: 49.525 distance: 118 - 119: 21.747 distance: 118 - 123: 24.475 distance: 120 - 121: 20.598 distance: 120 - 122: 24.279 distance: 123 - 124: 31.773 distance: 124 - 125: 21.590 distance: 124 - 127: 31.286 distance: 125 - 126: 27.136 distance: 125 - 135: 17.732 distance: 127 - 128: 12.858 distance: 128 - 129: 9.038 distance: 128 - 130: 13.465 distance: 129 - 131: 17.582 distance: 130 - 132: 13.276 distance: 131 - 133: 17.438 distance: 132 - 133: 13.603 distance: 133 - 134: 9.892 distance: 135 - 136: 40.077 distance: 136 - 137: 5.615 distance: 136 - 139: 53.720 distance: 137 - 138: 16.979 distance: 137 - 140: 39.889 distance: 140 - 141: 30.445 distance: 140 - 146: 30.553 distance: 141 - 142: 21.782 distance: 141 - 144: 15.824 distance: 142 - 143: 21.452 distance: 142 - 147: 8.866 distance: 144 - 145: 31.157 distance: 145 - 146: 36.814