Starting phenix.real_space_refine on Tue Mar 19 04:41:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/03_2024/6ach_9592_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/03_2024/6ach_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_9592/03_2024/6ach_9592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/03_2024/6ach_9592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/03_2024/6ach_9592_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ach_9592/03_2024/6ach_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-dev-5265/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: 22.18, per 1000 atoms: 0.95 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: 9.28 Conformation dependent library (CDL) restraints added in 8.0 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: 4.31 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: 5.99 Time building geometry restraints manager: 10.11 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 - 17.20: 13688 17.20 - 34.39: 624 34.39 - 51.59: 168 51.59 - 68.79: 96 68.79 - 85.98: 48 Dihedral angle restraints: 14624 sinusoidal: 6176 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 14621 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.010 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 74.000 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.170 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 82.310 ------------------------------------------------------------------------------- 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 : 13.306 85.981 9280 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP G 46 HIS 0.012 0.003 HIS G 193 PHE 0.031 0.006 PHE C 102 TYR 0.035 0.005 TYR B 186 ARG 0.016 0.002 ARG E 190 *********************** 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 : 2.565 Fit side-chains REVERT: A 346 MET cc_start: 0.7943 (mmm) cc_final: 0.7738 (mmt) REVERT: B 346 MET cc_start: 0.7944 (mmm) cc_final: 0.7740 (mmt) REVERT: C 346 MET cc_start: 0.7941 (mmm) cc_final: 0.7737 (mmt) REVERT: D 346 MET cc_start: 0.7945 (mmm) cc_final: 0.7740 (mmt) REVERT: E 346 MET cc_start: 0.7943 (mmm) cc_final: 0.7737 (mmt) REVERT: F 346 MET cc_start: 0.7943 (mmm) cc_final: 0.7738 (mmt) REVERT: G 346 MET cc_start: 0.7943 (mmm) cc_final: 0.7738 (mmt) REVERT: H 346 MET cc_start: 0.7943 (mmm) cc_final: 0.7736 (mmt) outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 0.3767 time to fit residues: 334.4502 Evaluate side-chains 384 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.492 ------------------------------------------------------------------------------- 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: 0.8980 chunk 87 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 0.0060 chunk 261 optimal weight: 0.8980 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: 0.7718 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 23688 Z= 0.153 Angle : 0.588 6.676 32024 Z= 0.303 Chirality : 0.044 0.138 3448 Planarity : 0.004 0.036 4200 Dihedral : 9.594 53.207 3752 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.08 % Allowed : 10.36 % 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: -2.05 (0.14), residues: 2912 helix: -0.87 (0.13), residues: 1416 sheet: -0.83 (0.21), residues: 504 loop : -2.17 (0.16), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 46 HIS 0.005 0.001 HIS G 193 PHE 0.015 0.002 PHE A 99 TYR 0.008 0.001 TYR D 284 ARG 0.002 0.000 ARG F 347 *********************** 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 440 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 392 time to evaluate : 2.519 Fit side-chains outliers start: 48 outliers final: 40 residues processed: 432 average time/residue: 0.3289 time to fit residues: 221.7183 Evaluate side-chains 396 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 356 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 362 SER 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: 0.9990 chunk 178 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 chunk 283 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 316 ASN A 359 HIS B 32 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN B 359 HIS C 32 HIS ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS D 32 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS E 32 HIS E 107 ASN E 359 HIS F 32 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS G 32 HIS ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 ASN G 359 HIS H 32 HIS ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 ASN H 359 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 23688 Z= 0.447 Angle : 0.677 7.003 32024 Z= 0.348 Chirality : 0.048 0.161 3448 Planarity : 0.005 0.036 4200 Dihedral : 8.318 54.773 3752 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.15 % Allowed : 10.62 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.57 (0.14), residues: 2912 helix: -0.24 (0.13), residues: 1416 sheet: -1.17 (0.21), residues: 512 loop : -1.99 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 46 HIS 0.004 0.001 HIS E 187 PHE 0.013 0.002 PHE D 4 TYR 0.015 0.002 TYR F 284 ARG 0.006 0.001 ARG D 364 *********************** 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 448 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 375 time to evaluate : 2.635 Fit side-chains REVERT: A 46 TRP cc_start: 0.7641 (t-100) cc_final: 0.7268 (t-100) REVERT: B 46 TRP cc_start: 0.7647 (t-100) cc_final: 0.7271 (t-100) REVERT: C 46 TRP cc_start: 0.7640 (t-100) cc_final: 0.7268 (t-100) REVERT: D 46 TRP cc_start: 0.7646 (t-100) cc_final: 0.7272 (t-100) REVERT: E 46 TRP cc_start: 0.7644 (t-100) cc_final: 0.7271 (t-100) REVERT: F 46 TRP cc_start: 0.7641 (t-100) cc_final: 0.7269 (t-100) REVERT: G 46 TRP cc_start: 0.7643 (t-100) cc_final: 0.7269 (t-100) REVERT: H 46 TRP cc_start: 0.7644 (t-100) cc_final: 0.7270 (t-100) outliers start: 73 outliers final: 56 residues processed: 430 average time/residue: 0.3385 time to fit residues: 225.9249 Evaluate side-chains 395 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 339 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 135 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 179 GLN F 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 23688 Z= 0.233 Angle : 0.575 8.633 32024 Z= 0.292 Chirality : 0.044 0.151 3448 Planarity : 0.003 0.032 4200 Dihedral : 7.836 52.283 3752 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.42 % Allowed : 13.53 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 2912 helix: 0.30 (0.14), residues: 1432 sheet: -0.96 (0.21), residues: 488 loop : -1.67 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 46 HIS 0.003 0.001 HIS E 32 PHE 0.012 0.002 PHE C 99 TYR 0.010 0.001 TYR F 284 ARG 0.004 0.001 ARG C 364 *********************** REFINEMENT MACRO_CYCLE 4 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 410 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 354 time to evaluate : 2.403 Fit side-chains REVERT: A 46 TRP cc_start: 0.7665 (t-100) cc_final: 0.7318 (t-100) REVERT: B 46 TRP cc_start: 0.7673 (t-100) cc_final: 0.7322 (t-100) REVERT: C 46 TRP cc_start: 0.7666 (t-100) cc_final: 0.7318 (t-100) REVERT: D 46 TRP cc_start: 0.7672 (t-100) cc_final: 0.7323 (t-100) REVERT: E 46 TRP cc_start: 0.7669 (t-100) cc_final: 0.7320 (t-100) REVERT: F 46 TRP cc_start: 0.7667 (t-100) cc_final: 0.7318 (t-100) REVERT: G 46 TRP cc_start: 0.7668 (t-100) cc_final: 0.7319 (t-100) REVERT: H 46 TRP cc_start: 0.7667 (t-100) cc_final: 0.7318 (t-100) outliers start: 56 outliers final: 42 residues processed: 396 average time/residue: 0.3360 time to fit residues: 208.2347 Evaluate side-chains 396 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 354 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 242 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN B 183 ASN C 183 ASN C 316 ASN D 179 GLN D 183 ASN D 316 ASN E 183 ASN E 316 ASN F 183 ASN F 316 ASN G 183 ASN H 183 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 23688 Z= 0.326 Angle : 0.604 6.962 32024 Z= 0.307 Chirality : 0.045 0.159 3448 Planarity : 0.003 0.032 4200 Dihedral : 7.775 52.726 3752 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.79 % Allowed : 13.31 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 2912 helix: 0.63 (0.14), residues: 1416 sheet: -0.78 (0.22), residues: 488 loop : -1.60 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 46 HIS 0.003 0.001 HIS C 32 PHE 0.010 0.002 PHE D 99 TYR 0.012 0.002 TYR A 284 ARG 0.006 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 5 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 447 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 359 time to evaluate : 3.242 Fit side-chains REVERT: A 16 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 46 TRP cc_start: 0.7689 (t-100) cc_final: 0.7356 (t-100) REVERT: B 16 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8393 (tp) REVERT: B 46 TRP cc_start: 0.7701 (t-100) cc_final: 0.7330 (t-100) REVERT: C 16 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8396 (tp) REVERT: C 46 TRP cc_start: 0.7688 (t-100) cc_final: 0.7357 (t-100) REVERT: D 16 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8393 (tp) REVERT: D 46 TRP cc_start: 0.7699 (t-100) cc_final: 0.7331 (t-100) REVERT: E 16 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8391 (tp) REVERT: E 46 TRP cc_start: 0.7691 (t-100) cc_final: 0.7358 (t-100) REVERT: F 16 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8391 (tp) REVERT: F 46 TRP cc_start: 0.7688 (t-100) cc_final: 0.7357 (t-100) REVERT: G 16 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8394 (tp) REVERT: G 46 TRP cc_start: 0.7688 (t-100) cc_final: 0.7357 (t-100) REVERT: H 16 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8394 (tp) REVERT: H 46 TRP cc_start: 0.7689 (t-100) cc_final: 0.7357 (t-100) outliers start: 88 outliers final: 56 residues processed: 431 average time/residue: 0.3329 time to fit residues: 227.2157 Evaluate side-chains 421 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 357 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 68 optimal weight: 0.2980 chunk 278 optimal weight: 0.7980 chunk 231 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN C 183 ASN D 183 ASN E 183 ASN F 183 ASN G 183 ASN H 183 ASN ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 23688 Z= 0.362 Angle : 0.613 6.155 32024 Z= 0.315 Chirality : 0.046 0.158 3448 Planarity : 0.003 0.033 4200 Dihedral : 7.769 52.421 3752 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.45 % Allowed : 13.66 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 2912 helix: 0.64 (0.13), residues: 1416 sheet: -0.64 (0.22), residues: 488 loop : -1.47 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 46 HIS 0.007 0.001 HIS G 193 PHE 0.011 0.002 PHE H 99 TYR 0.013 0.002 TYR B 227 ARG 0.006 0.001 ARG E 364 *********************** REFINEMENT MACRO_CYCLE 6 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 431 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 351 time to evaluate : 2.808 Fit side-chains REVERT: A 16 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8396 (tp) REVERT: A 46 TRP cc_start: 0.7718 (t-100) cc_final: 0.7371 (t-100) REVERT: B 16 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8394 (tp) REVERT: B 46 TRP cc_start: 0.7721 (t-100) cc_final: 0.7374 (t-100) REVERT: C 16 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8398 (tp) REVERT: C 46 TRP cc_start: 0.7717 (t-100) cc_final: 0.7370 (t-100) REVERT: D 16 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8394 (tp) REVERT: D 46 TRP cc_start: 0.7720 (t-100) cc_final: 0.7375 (t-100) REVERT: E 16 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8393 (tp) REVERT: E 46 TRP cc_start: 0.7718 (t-100) cc_final: 0.7373 (t-100) REVERT: F 16 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8393 (tp) REVERT: F 46 TRP cc_start: 0.7717 (t-100) cc_final: 0.7373 (t-100) REVERT: G 16 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8394 (tp) REVERT: G 46 TRP cc_start: 0.7718 (t-100) cc_final: 0.7373 (t-100) REVERT: H 16 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8394 (tp) REVERT: H 46 TRP cc_start: 0.7717 (t-100) cc_final: 0.7371 (t-100) outliers start: 80 outliers final: 64 residues processed: 407 average time/residue: 0.3336 time to fit residues: 213.6941 Evaluate side-chains 434 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 362 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 203 optimal weight: 20.0000 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 277 optimal weight: 7.9990 chunk 173 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 183 ASN B 179 GLN B 183 ASN C 179 GLN C 183 ASN D 183 ASN E 183 ASN F 183 ASN G 179 GLN G 183 ASN H 179 GLN H 183 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23688 Z= 0.207 Angle : 0.545 6.354 32024 Z= 0.277 Chirality : 0.043 0.150 3448 Planarity : 0.003 0.028 4200 Dihedral : 7.451 50.053 3752 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.67 % Allowed : 13.57 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2912 helix: 0.91 (0.14), residues: 1432 sheet: -0.29 (0.23), residues: 488 loop : -1.21 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 46 HIS 0.004 0.001 HIS D 193 PHE 0.011 0.001 PHE F 99 TYR 0.013 0.001 TYR A 227 ARG 0.003 0.000 ARG F 190 *********************** REFINEMENT MACRO_CYCLE 7 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 436 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 351 time to evaluate : 2.530 Fit side-chains REVERT: A 18 CYS cc_start: 0.8335 (m) cc_final: 0.8042 (m) REVERT: A 46 TRP cc_start: 0.7609 (t-100) cc_final: 0.7291 (t-100) REVERT: B 46 TRP cc_start: 0.7613 (t-100) cc_final: 0.7290 (t-100) REVERT: C 46 TRP cc_start: 0.7609 (t-100) cc_final: 0.7286 (t-100) REVERT: D 46 TRP cc_start: 0.7615 (t-100) cc_final: 0.7292 (t-100) REVERT: E 46 TRP cc_start: 0.7610 (t-100) cc_final: 0.7288 (t-100) REVERT: F 18 CYS cc_start: 0.8335 (m) cc_final: 0.8045 (m) REVERT: F 46 TRP cc_start: 0.7608 (t-100) cc_final: 0.7293 (t-100) REVERT: G 18 CYS cc_start: 0.8335 (m) cc_final: 0.8045 (m) REVERT: G 46 TRP cc_start: 0.7608 (t-100) cc_final: 0.7293 (t-100) REVERT: H 18 CYS cc_start: 0.8336 (m) cc_final: 0.8043 (m) REVERT: H 46 TRP cc_start: 0.7608 (t-100) cc_final: 0.7292 (t-100) outliers start: 85 outliers final: 63 residues processed: 397 average time/residue: 0.3429 time to fit residues: 213.7177 Evaluate side-chains 422 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 359 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN D 183 ASN E 183 ASN F 183 ASN G 183 ASN ** G 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN ** H 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 23688 Z= 0.468 Angle : 0.662 6.258 32024 Z= 0.339 Chirality : 0.048 0.157 3448 Planarity : 0.004 0.034 4200 Dihedral : 7.757 52.163 3752 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.32 % Allowed : 14.60 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.15), residues: 2912 helix: 0.74 (0.14), residues: 1416 sheet: -0.34 (0.23), residues: 488 loop : -1.36 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 46 HIS 0.006 0.002 HIS H 193 PHE 0.010 0.002 PHE H 99 TYR 0.014 0.002 TYR G 284 ARG 0.007 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 8 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 428 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 351 time to evaluate : 2.366 Fit side-chains REVERT: A 16 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8411 (tp) REVERT: A 46 TRP cc_start: 0.7626 (t-100) cc_final: 0.7320 (t-100) REVERT: B 16 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8414 (tp) REVERT: B 46 TRP cc_start: 0.7627 (t-100) cc_final: 0.7321 (t-100) REVERT: C 16 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8415 (tp) REVERT: C 46 TRP cc_start: 0.7623 (t-100) cc_final: 0.7316 (t-100) REVERT: D 16 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8410 (tp) REVERT: D 46 TRP cc_start: 0.7626 (t-100) cc_final: 0.7322 (t-100) REVERT: E 16 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8411 (tp) REVERT: E 46 TRP cc_start: 0.7625 (t-100) cc_final: 0.7319 (t-100) REVERT: F 16 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8411 (tp) REVERT: F 46 TRP cc_start: 0.7623 (t-100) cc_final: 0.7319 (t-100) REVERT: G 16 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8411 (tp) REVERT: G 46 TRP cc_start: 0.7623 (t-100) cc_final: 0.7319 (t-100) REVERT: H 16 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8412 (tp) REVERT: H 46 TRP cc_start: 0.7624 (t-100) cc_final: 0.7318 (t-100) outliers start: 77 outliers final: 59 residues processed: 407 average time/residue: 0.3403 time to fit residues: 217.4858 Evaluate side-chains 427 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 360 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 242 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.8980 chunk 265 optimal weight: 0.0270 chunk 242 optimal weight: 8.9990 chunk 258 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 203 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 chunk 233 optimal weight: 20.0000 chunk 244 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN B 183 ASN C 183 ASN D 183 ASN E 183 ASN F 183 ASN G 183 ASN H 183 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23688 Z= 0.145 Angle : 0.533 7.193 32024 Z= 0.270 Chirality : 0.042 0.148 3448 Planarity : 0.003 0.027 4200 Dihedral : 7.290 48.112 3752 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.04 % Allowed : 15.54 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2912 helix: 1.05 (0.14), residues: 1432 sheet: -0.08 (0.23), residues: 488 loop : -1.14 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 46 HIS 0.004 0.001 HIS D 193 PHE 0.011 0.001 PHE A 99 TYR 0.009 0.001 TYR H 132 ARG 0.002 0.000 ARG H 190 *********************** REFINEMENT MACRO_CYCLE 9 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 426 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 379 time to evaluate : 2.574 Fit side-chains REVERT: A 18 CYS cc_start: 0.8291 (m) cc_final: 0.8006 (m) REVERT: A 46 TRP cc_start: 0.7648 (t-100) cc_final: 0.7340 (t-100) REVERT: B 18 CYS cc_start: 0.8294 (m) cc_final: 0.8003 (m) REVERT: B 46 TRP cc_start: 0.7650 (t-100) cc_final: 0.7344 (t-100) REVERT: C 18 CYS cc_start: 0.8299 (m) cc_final: 0.8010 (m) REVERT: C 46 TRP cc_start: 0.7647 (t-100) cc_final: 0.7341 (t-100) REVERT: D 18 CYS cc_start: 0.8292 (m) cc_final: 0.8001 (m) REVERT: D 46 TRP cc_start: 0.7651 (t-100) cc_final: 0.7345 (t-100) REVERT: E 18 CYS cc_start: 0.8294 (m) cc_final: 0.8005 (m) REVERT: E 46 TRP cc_start: 0.7649 (t-100) cc_final: 0.7343 (t-100) REVERT: F 18 CYS cc_start: 0.8291 (m) cc_final: 0.8003 (m) REVERT: F 46 TRP cc_start: 0.7645 (t-100) cc_final: 0.7341 (t-100) REVERT: G 18 CYS cc_start: 0.8295 (m) cc_final: 0.8002 (m) REVERT: G 46 TRP cc_start: 0.7643 (t-100) cc_final: 0.7339 (t-100) REVERT: H 18 CYS cc_start: 0.8294 (m) cc_final: 0.8001 (m) REVERT: H 46 TRP cc_start: 0.7647 (t-100) cc_final: 0.7339 (t-100) outliers start: 47 outliers final: 31 residues processed: 410 average time/residue: 0.3314 time to fit residues: 213.5289 Evaluate side-chains 415 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 384 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 286 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 176 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN B 183 ASN C 183 ASN D 183 ASN E 183 ASN F 183 ASN G 183 ASN H 183 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23688 Z= 0.286 Angle : 0.606 9.626 32024 Z= 0.301 Chirality : 0.044 0.152 3448 Planarity : 0.003 0.028 4200 Dihedral : 7.359 48.760 3752 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.65 % Allowed : 15.92 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 2912 helix: 1.11 (0.14), residues: 1416 sheet: 0.00 (0.23), residues: 488 loop : -1.19 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 46 HIS 0.004 0.001 HIS H 193 PHE 0.009 0.002 PHE E 99 TYR 0.010 0.001 TYR A 284 ARG 0.005 0.001 ARG H 364 ********************** REFINEMENT MACRO_CYCLE 10 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 385 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 347 time to evaluate : 2.786 Fit side-chains REVERT: A 46 TRP cc_start: 0.7658 (t-100) cc_final: 0.7368 (t-100) REVERT: B 46 TRP cc_start: 0.7659 (t-100) cc_final: 0.7371 (t-100) REVERT: C 46 TRP cc_start: 0.7658 (t-100) cc_final: 0.7369 (t-100) REVERT: D 46 TRP cc_start: 0.7661 (t-100) cc_final: 0.7372 (t-100) REVERT: E 46 TRP cc_start: 0.7660 (t-100) cc_final: 0.7372 (t-100) REVERT: F 46 TRP cc_start: 0.7657 (t-100) cc_final: 0.7370 (t-100) REVERT: G 46 TRP cc_start: 0.7657 (t-100) cc_final: 0.7369 (t-100) REVERT: H 46 TRP cc_start: 0.7657 (t-100) cc_final: 0.7367 (t-100) outliers start: 38 outliers final: 30 residues processed: 379 average time/residue: 0.3552 time to fit residues: 211.5424 Evaluate side-chains 375 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 345 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-dev-5265/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-dev-5265/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: 58.1209 > 50: distance: 53 - 69: 34.212 distance: 57 - 77: 16.578 distance: 61 - 87: 6.332 distance: 64 - 69: 30.898 distance: 65 - 96: 6.005 distance: 69 - 70: 44.838 distance: 70 - 71: 25.724 distance: 70 - 73: 27.285 distance: 71 - 72: 28.309 distance: 71 - 77: 24.191 distance: 73 - 74: 40.836 distance: 73 - 75: 32.030 distance: 74 - 76: 25.999 distance: 77 - 78: 20.331 distance: 78 - 79: 10.675 distance: 78 - 81: 14.336 distance: 79 - 80: 12.810 distance: 79 - 87: 8.385 distance: 81 - 82: 33.480 distance: 82 - 83: 26.746 distance: 82 - 84: 23.251 distance: 83 - 85: 8.175 distance: 84 - 86: 7.314 distance: 85 - 86: 5.004 distance: 87 - 88: 13.711 distance: 88 - 89: 13.029 distance: 88 - 91: 12.391 distance: 89 - 96: 3.905 distance: 91 - 92: 3.346 distance: 93 - 95: 3.520 distance: 96 - 97: 7.535 distance: 97 - 98: 3.531 distance: 97 - 100: 13.109 distance: 98 - 99: 13.663 distance: 98 - 104: 7.858 distance: 100 - 101: 10.914 distance: 104 - 105: 8.702 distance: 105 - 106: 10.984 distance: 106 - 107: 11.255 distance: 106 - 108: 16.601 distance: 108 - 109: 10.132 distance: 109 - 110: 21.778 distance: 109 - 112: 12.754 distance: 110 - 111: 27.375 distance: 110 - 116: 17.875 distance: 112 - 113: 12.753 distance: 112 - 114: 8.194 distance: 113 - 115: 9.871 distance: 116 - 117: 21.913 distance: 117 - 118: 17.256 distance: 117 - 120: 10.218 distance: 118 - 119: 16.215 distance: 118 - 123: 20.031 distance: 120 - 121: 18.468 distance: 120 - 122: 13.552 distance: 123 - 124: 34.543 distance: 124 - 125: 43.808 distance: 124 - 127: 5.012 distance: 125 - 126: 38.351 distance: 125 - 135: 12.759 distance: 127 - 128: 24.948 distance: 128 - 129: 24.296 distance: 128 - 130: 19.202 distance: 129 - 131: 8.591 distance: 130 - 132: 7.610 distance: 131 - 133: 10.772 distance: 132 - 133: 8.515 distance: 133 - 134: 7.868 distance: 135 - 136: 15.786 distance: 136 - 137: 24.865 distance: 136 - 139: 9.994 distance: 137 - 138: 44.540 distance: 137 - 140: 37.512 distance: 140 - 141: 32.959 distance: 140 - 146: 29.926 distance: 141 - 142: 35.660 distance: 141 - 144: 58.121 distance: 142 - 143: 13.856 distance: 142 - 147: 10.231 distance: 144 - 145: 54.301 distance: 145 - 146: 38.455