Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 13:23:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/10_2023/7zl1_14774_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/10_2023/7zl1_14774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/10_2023/7zl1_14774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/10_2023/7zl1_14774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/10_2023/7zl1_14774_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/10_2023/7zl1_14774_trim.pdb" } resolution = 2.5 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= 0.003 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 S 80 5.16 5 C 8448 2.51 5 N 2272 2.21 5 O 2883 1.98 5 H 13574 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 27257 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "A" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "D" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "C" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "E" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "H" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "G" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "F" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3251 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 138 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 147 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 147 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 144 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "E" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 138 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "H" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 135 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "G" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 147 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "F" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 141 Classifications: {'water': 47} Link IDs: {None: 46} Time building chain proxies: 10.84, per 1000 atoms: 0.40 Number of scatterers: 27257 At special positions: 0 Unit cell: (101.156, 99.484, 99.484, 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 80 16.00 O 2883 8.00 N 2272 7.00 C 8448 6.00 H 13574 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 357 " distance=2.04 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS G 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS G 317 " distance=2.04 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 357 " distance=2.04 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS H 318 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS H 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 357 " distance=2.04 Simple disulfide: pdb=" SG CYS D 210 " - pdb=" SG CYS D 271 " distance=2.04 Simple disulfide: pdb=" SG CYS D 317 " - pdb=" SG CYS E 318 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS E 317 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 357 " distance=2.04 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 271 " distance=2.05 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS F 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS F 317 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 357 " distance=2.04 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 271 " distance=2.05 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 357 " distance=2.04 Simple disulfide: pdb=" SG CYS H 210 " - pdb=" SG CYS H 271 " distance=2.05 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 357 " distance=2.04 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 271 " distance=2.04 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 357 " distance=2.04 Simple disulfide: pdb=" SG CYS F 210 " - pdb=" SG CYS F 271 " distance=2.04 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 Links applied NAG-ASN " NAG A1000 " - " ASN A 220 " " NAG B1000 " - " ASN B 220 " " NAG C1000 " - " ASN C 220 " " NAG D1000 " - " ASN D 220 " " NAG E1000 " - " ASN E 220 " " NAG F1000 " - " ASN F 220 " " NAG G1000 " - " ASN G 220 " " NAG H1000 " - " ASN H 220 " Time building additional restraints: 25.51 Conformation dependent library (CDL) restraints added in 2.2 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 16 sheets defined 13.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.525A pdb=" N GLY B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 359 removed outlier: 4.199A pdb=" N HIS B 358 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.550A pdb=" N GLY A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 removed outlier: 4.464A pdb=" N HIS A 358 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.588A pdb=" N GLY D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 359 removed outlier: 4.325A pdb=" N HIS D 358 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.588A pdb=" N GLY C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 removed outlier: 4.325A pdb=" N HIS C 358 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 removed outlier: 3.751A pdb=" N SER E 173 " --> pdb=" O TRP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 279 No H-bonds generated for 'chain 'E' and resid 277 through 279' Processing helix chain 'E' and resid 324 through 328 Processing helix chain 'E' and resid 344 through 352 removed outlier: 3.641A pdb=" N GLY E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 removed outlier: 3.890A pdb=" N HIS E 358 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 173 Processing helix chain 'H' and resid 277 through 279 No H-bonds generated for 'chain 'H' and resid 277 through 279' Processing helix chain 'H' and resid 324 through 328 Processing helix chain 'H' and resid 344 through 352 removed outlier: 3.614A pdb=" N GLY H 352 " --> pdb=" O ILE H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 359 removed outlier: 4.430A pdb=" N HIS H 358 " --> pdb=" O GLU H 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 173 removed outlier: 3.522A pdb=" N SER G 173 " --> pdb=" O TRP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 279 No H-bonds generated for 'chain 'G' and resid 277 through 279' Processing helix chain 'G' and resid 324 through 328 Processing helix chain 'G' and resid 344 through 352 Processing helix chain 'G' and resid 355 through 359 removed outlier: 4.406A pdb=" N HIS G 358 " --> pdb=" O GLU G 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 174 removed outlier: 3.537A pdb=" N ARG F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 328 Processing helix chain 'F' and resid 344 through 352 removed outlier: 3.591A pdb=" N GLY F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 removed outlier: 4.347A pdb=" N HIS F 358 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 288 through 293 removed outlier: 5.406A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 285 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP B 212 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY B 335 " --> pdb=" O TRP B 212 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS B 214 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU B 333 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 255 through 258 removed outlier: 6.252A pdb=" N LEU B 240 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE B 223 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU B 308 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B 370 " --> pdb=" O HIS B 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 293 removed outlier: 5.357A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 285 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP A 212 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLY A 335 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS A 214 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU A 333 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 255 through 258 removed outlier: 6.136A pdb=" N LEU A 240 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE A 223 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 308 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU A 370 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 288 through 293 removed outlier: 6.539A pdb=" N LEU D 283 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR D 292 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR D 281 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TRP D 212 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY D 335 " --> pdb=" O TRP D 212 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS D 214 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU D 333 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 255 through 258 removed outlier: 6.225A pdb=" N LEU D 240 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE D 223 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU D 308 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU D 370 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 288 through 293 removed outlier: 5.387A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL C 285 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRP C 212 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY C 335 " --> pdb=" O TRP C 212 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS C 214 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU C 333 " --> pdb=" O LYS C 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 255 through 258 removed outlier: 6.215A pdb=" N LEU C 240 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE C 223 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 308 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU C 370 " --> pdb=" O HIS C 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 288 through 293 removed outlier: 6.682A pdb=" N LEU E 283 " --> pdb=" O ALA E 290 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR E 292 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR E 281 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP E 212 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLY E 335 " --> pdb=" O TRP E 212 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS E 214 " --> pdb=" O LEU E 333 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU E 333 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 255 through 258 removed outlier: 6.268A pdb=" N LEU E 240 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE E 223 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU E 308 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU E 370 " --> pdb=" O HIS E 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 288 through 293 removed outlier: 5.336A pdb=" N LEU H 289 " --> pdb=" O VAL H 285 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL H 285 " --> pdb=" O LEU H 289 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP H 212 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLY H 335 " --> pdb=" O TRP H 212 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS H 214 " --> pdb=" O LEU H 333 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU H 333 " --> pdb=" O LYS H 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 255 through 258 removed outlier: 6.246A pdb=" N LEU H 240 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE H 223 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU H 308 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU H 370 " --> pdb=" O HIS H 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 288 through 293 removed outlier: 5.339A pdb=" N LEU G 289 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL G 285 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP G 212 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY G 335 " --> pdb=" O TRP G 212 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS G 214 " --> pdb=" O LEU G 333 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU G 333 " --> pdb=" O LYS G 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 255 through 258 removed outlier: 6.195A pdb=" N LEU G 240 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE G 223 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU G 308 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU G 370 " --> pdb=" O HIS G 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 288 through 293 removed outlier: 5.339A pdb=" N LEU F 289 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL F 285 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP F 212 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLY F 335 " --> pdb=" O TRP F 212 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LYS F 214 " --> pdb=" O LEU F 333 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU F 333 " --> pdb=" O LYS F 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 255 through 258 removed outlier: 6.218A pdb=" N LEU F 240 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE F 223 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU F 308 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU F 370 " --> pdb=" O HIS F 197 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1248 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: 11.31 Time building geometry restraints manager: 25.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13574 1.04 - 1.25: 2109 1.25 - 1.46: 4595 1.46 - 1.66: 6808 1.66 - 1.87: 112 Bond restraints: 27198 Sorted by residual: bond pdb=" CA LYS B 214 " pdb=" CB LYS B 214 " ideal model delta sigma weight residual 1.539 1.436 0.103 4.88e-02 4.20e+02 4.47e+00 bond pdb=" CB CYS A 210 " pdb=" SG CYS A 210 " ideal model delta sigma weight residual 1.808 1.868 -0.060 3.30e-02 9.18e+02 3.28e+00 bond pdb=" C1 NAG D1000 " pdb=" C2 NAG D1000 " ideal model delta sigma weight residual 1.532 1.568 -0.036 2.00e-02 2.50e+03 3.28e+00 bond pdb=" CA LYS F 214 " pdb=" CB LYS F 214 " ideal model delta sigma weight residual 1.539 1.451 0.088 4.88e-02 4.20e+02 3.27e+00 bond pdb=" N GLN F 167 " pdb=" CA GLN F 167 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.23e+00 ... (remaining 27193 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.78: 570 106.78 - 113.64: 30969 113.64 - 120.51: 8466 120.51 - 127.37: 7726 127.37 - 134.23: 232 Bond angle restraints: 47963 Sorted by residual: angle pdb=" N LYS D 314 " pdb=" CA LYS D 314 " pdb=" C LYS D 314 " ideal model delta sigma weight residual 111.33 115.88 -4.55 1.21e+00 6.83e-01 1.41e+01 angle pdb=" N MET F 261 " pdb=" CA MET F 261 " pdb=" C MET F 261 " ideal model delta sigma weight residual 110.41 114.81 -4.40 1.18e+00 7.18e-01 1.39e+01 angle pdb=" C LEU C 270 " pdb=" N CYS C 271 " pdb=" CA CYS C 271 " ideal model delta sigma weight residual 121.89 115.52 6.37 1.74e+00 3.30e-01 1.34e+01 angle pdb=" C LEU E 270 " pdb=" N CYS E 271 " pdb=" CA CYS E 271 " ideal model delta sigma weight residual 121.86 116.16 5.70 1.58e+00 4.01e-01 1.30e+01 angle pdb=" C LEU H 270 " pdb=" N CYS H 271 " pdb=" CA CYS H 271 " ideal model delta sigma weight residual 121.86 116.20 5.66 1.58e+00 4.01e-01 1.28e+01 ... (remaining 47958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9205 17.99 - 35.97: 777 35.97 - 53.96: 207 53.96 - 71.95: 207 71.95 - 89.93: 28 Dihedral angle restraints: 10424 sinusoidal: 4672 harmonic: 5752 Sorted by residual: dihedral pdb=" CB CYS D 317 " pdb=" SG CYS D 317 " pdb=" SG CYS E 318 " pdb=" CB CYS E 318 " ideal model delta sinusoidal sigma weight residual 93.00 170.56 -77.56 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS C 318 " pdb=" SG CYS C 318 " pdb=" SG CYS F 317 " pdb=" CB CYS F 317 " ideal model delta sinusoidal sigma weight residual -86.00 -144.44 58.44 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CB CYS H 210 " pdb=" SG CYS H 210 " pdb=" SG CYS H 271 " pdb=" CB CYS H 271 " ideal model delta sinusoidal sigma weight residual -86.00 -33.05 -52.95 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 10421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1195 0.042 - 0.085: 597 0.085 - 0.127: 193 0.127 - 0.169: 44 0.169 - 0.212: 11 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA PRO B 176 " pdb=" N PRO B 176 " pdb=" C PRO B 176 " pdb=" CB PRO B 176 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO F 176 " pdb=" N PRO F 176 " pdb=" C PRO F 176 " pdb=" CB PRO F 176 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C1 NAG F1000 " pdb=" ND2 ASN F 220 " pdb=" C2 NAG F1000 " pdb=" O5 NAG F1000 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 2037 not shown) Planarity restraints: 4016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 266 " -0.322 9.50e-02 1.11e+02 1.11e-01 2.91e+01 pdb=" NE ARG F 266 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG F 266 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG F 266 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG F 266 " 0.056 2.00e-02 2.50e+03 pdb="HH11 ARG F 266 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG F 266 " -0.003 2.00e-02 2.50e+03 pdb="HH21 ARG F 266 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG F 266 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 267 " 0.023 2.00e-02 2.50e+03 2.58e-02 2.67e+01 pdb=" CG TRP B 267 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 267 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 267 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 267 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP B 267 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 267 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 267 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 267 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 267 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP B 267 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP B 267 " 0.066 2.00e-02 2.50e+03 pdb=" HE3 TRP B 267 " -0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 267 " 0.004 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 267 " 0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP B 267 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 267 " 0.019 2.00e-02 2.50e+03 2.29e-02 2.10e+01 pdb=" CG TRP F 267 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP F 267 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP F 267 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP F 267 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TRP F 267 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP F 267 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 267 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 267 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 267 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP F 267 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP F 267 " 0.058 2.00e-02 2.50e+03 pdb=" HE3 TRP F 267 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 267 " 0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 267 " 0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP F 267 " 0.005 2.00e-02 2.50e+03 ... (remaining 4013 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 896 2.10 - 2.72: 46035 2.72 - 3.35: 80619 3.35 - 3.97: 116145 3.97 - 4.60: 175889 Nonbonded interactions: 419584 Sorted by model distance: nonbonded pdb=" O PRO B 176 " pdb=" H1 HOH B1101 " model vdw 1.469 1.850 nonbonded pdb=" O PRO A 176 " pdb=" H1 HOH A1101 " model vdw 1.483 1.850 nonbonded pdb=" O GLY A 375 " pdb=" H1 HOH A1102 " model vdw 1.484 1.850 nonbonded pdb=" O GLY C 375 " pdb=" H1 HOH C1102 " model vdw 1.485 1.850 nonbonded pdb=" O GLY D 375 " pdb=" H1 HOH D1103 " model vdw 1.501 1.850 ... (remaining 419579 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.450 Extract box with map and model: 10.700 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 89.430 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.007 0.103 13624 Z= 0.457 Angle : 0.880 7.221 18496 Z= 0.496 Chirality : 0.056 0.212 2040 Planarity : 0.010 0.115 2352 Dihedral : 14.643 89.932 4728 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 1.00 % Allowed : 5.69 % Favored : 93.31 % Rotamer: Outliers : 0.65 % Allowed : 3.66 % Favored : 95.69 % 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: -0.02 (0.21), residues: 1704 helix: -2.00 (0.30), residues: 136 sheet: 1.04 (0.22), residues: 512 loop : -0.24 (0.22), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 204 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 205 average time/residue: 3.8038 time to fit residues: 836.1526 Evaluate side-chains 163 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 2.264 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 1.7509 time to fit residues: 18.9210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 ASN B 345 ASN C 345 ASN H 345 ASN F 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13624 Z= 0.196 Angle : 0.608 7.119 18496 Z= 0.336 Chirality : 0.047 0.141 2040 Planarity : 0.004 0.043 2352 Dihedral : 6.749 27.816 1824 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.16 % Favored : 94.66 % Rotamer: Outliers : 2.16 % Allowed : 7.54 % Favored : 90.30 % 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: 0.03 (0.22), residues: 1704 helix: -1.13 (0.37), residues: 136 sheet: 0.82 (0.21), residues: 568 loop : -0.24 (0.23), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 181 average time/residue: 3.5079 time to fit residues: 684.9393 Evaluate side-chains 170 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 2.068 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 3 residues processed: 11 average time/residue: 1.4794 time to fit residues: 21.6108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 165 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 13624 Z= 0.278 Angle : 0.629 15.295 18496 Z= 0.343 Chirality : 0.047 0.216 2040 Planarity : 0.004 0.045 2352 Dihedral : 6.369 26.116 1824 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.52 % Favored : 94.37 % Rotamer: Outliers : 2.87 % Allowed : 8.19 % Favored : 88.94 % 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: -0.16 (0.21), residues: 1704 helix: -0.91 (0.42), residues: 128 sheet: 0.67 (0.21), residues: 568 loop : -0.41 (0.22), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 182 average time/residue: 3.5907 time to fit residues: 703.8816 Evaluate side-chains 177 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 2.086 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 10 residues processed: 12 average time/residue: 1.6455 time to fit residues: 25.4669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 254 ASN E 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 13624 Z= 0.288 Angle : 0.626 16.976 18496 Z= 0.337 Chirality : 0.047 0.211 2040 Planarity : 0.004 0.050 2352 Dihedral : 6.161 24.204 1824 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.46 % Favored : 94.42 % Rotamer: Outliers : 2.87 % Allowed : 8.62 % Favored : 88.51 % 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: -0.22 (0.21), residues: 1704 helix: -0.72 (0.46), residues: 120 sheet: 0.69 (0.21), residues: 568 loop : -0.55 (0.21), residues: 1016 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 27 residues processed: 187 average time/residue: 3.5996 time to fit residues: 725.8632 Evaluate side-chains 181 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 17 residues processed: 10 average time/residue: 1.5688 time to fit residues: 21.0242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9408 > 50: distance: 153 - 270: 35.031 distance: 156 - 267: 17.210 distance: 183 - 234: 16.459 distance: 186 - 231: 26.144 distance: 221 - 231: 24.068 distance: 231 - 232: 14.905 distance: 231 - 239: 21.147 distance: 232 - 233: 25.502 distance: 232 - 235: 26.380 distance: 232 - 240: 32.981 distance: 233 - 234: 10.404 distance: 233 - 250: 13.892 distance: 235 - 236: 17.855 distance: 235 - 237: 11.601 distance: 235 - 241: 16.568 distance: 236 - 238: 15.386 distance: 236 - 243: 23.338 distance: 237 - 244: 12.670 distance: 237 - 245: 24.477 distance: 237 - 246: 21.175 distance: 238 - 247: 6.048 distance: 238 - 248: 5.205 distance: 238 - 249: 7.343 distance: 250 - 251: 16.602 distance: 250 - 259: 30.044 distance: 250 - 441: 15.142 distance: 251 - 252: 58.781 distance: 251 - 254: 30.570 distance: 251 - 260: 16.914 distance: 252 - 253: 30.231 distance: 252 - 267: 53.374 distance: 253 - 438: 19.676 distance: 254 - 255: 13.349 distance: 254 - 261: 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405: 32.601 distance: 290 - 291: 12.676 distance: 290 - 300: 30.097 distance: 290 - 301: 28.058 distance: 291 - 292: 15.341 distance: 291 - 293: 7.562 distance: 292 - 294: 32.442 distance: 292 - 302: 24.387 distance: 293 - 295: 21.677 distance: 293 - 303: 9.876 distance: 294 - 296: 11.397 distance: 294 - 304: 9.367 distance: 295 - 296: 11.931 distance: 295 - 305: 6.804 distance: 296 - 297: 12.962 distance: 297 - 306: 10.258 distance: 307 - 308: 17.227 distance: 307 - 315: 46.157 distance: 308 - 309: 32.335 distance: 308 - 311: 32.977 distance: 308 - 316: 18.515 distance: 309 - 310: 20.295 distance: 309 - 326: 12.121 distance: 311 - 312: 30.318 distance: 311 - 317: 52.332 distance: 311 - 318: 19.689 distance: 312 - 313: 5.310 distance: 312 - 314: 6.534 distance: 312 - 319: 26.902 distance: 313 - 320: 5.074 distance: 313 - 321: 15.120 distance: 313 - 322: 11.681 distance: 314 - 323: 16.086 distance: 314 - 324: 15.724 distance: 314 - 325: 5.380 distance: 326 - 327: 25.635 distance: 326 - 332: 13.179 distance: 326 - 378: 65.226 distance: 327 - 328: 43.348 distance: 327 - 330: 29.505 distance: 327 - 333: 7.844 distance: 328 - 329: 38.120 distance: 328 - 337: 44.214 distance: 329 - 375: 54.800 distance: 330 - 331: 7.704 distance: 330 - 334: 14.967 distance: 330 - 335: 22.779 distance: 331 - 336: 24.609 distance: 337 - 338: 47.043 distance: 337 - 349: 36.434 distance: 338 - 339: 18.874 distance: 338 - 341: 54.421 distance: 338 - 350: 53.321 distance: 339 - 340: 34.820 distance: 339 - 358: 43.139 distance: 341 - 342: 37.314 distance: 341 - 351: 37.067 distance: 341 - 352: 28.721 distance: 342 - 343: 3.866 distance: 342 - 344: 10.214 distance: 343 - 345: 4.522 distance: 343 - 353: 11.847 distance: 344 - 346: 8.791 distance: 344 - 354: 7.499 distance: 345 - 347: 4.485 distance: 345 - 355: 8.082 distance: 346 - 347: 7.784 distance: 346 - 356: 5.399 distance: 347 - 348: 7.819 distance: 348 - 357: 8.252 distance: 358 - 359: 28.620 distance: 358 - 367: 17.771 distance: 359 - 360: 40.021 distance: 359 - 362: 43.209 distance: 359 - 368: 13.461 distance: 360 - 361: 56.802 distance: 360 - 375: 16.353 distance: 362 - 363: 9.239 distance: 362 - 369: 22.711 distance: 362 - 370: 25.965 distance: 363 - 364: 15.645 distance: 363 - 371: 8.705 distance: 363 - 372: 8.618 distance: 364 - 365: 8.146 distance: 364 - 366: 8.309 distance: 366 - 373: 8.741 distance: 366 - 374: 5.755 distance: 375 - 376: 7.301 distance: 375 - 381: 13.439 distance: 376 - 377: 44.832 distance: 376 - 379: 50.506 distance: 376 - 382: 52.903 distance: 377 - 378: 44.184 distance: 377 - 386: 42.525 distance: 379 - 380: 60.818 distance: 379 - 383: 41.412 distance: 379 - 384: 40.205 distance: 380 - 385: 52.916 distance: 386 - 387: 35.902 distance: 386 - 394: 22.247 distance: 386 - 494: 28.465 distance: 387 - 388: 51.915 distance: 387 - 390: 5.201 distance: 387 - 395: 25.295 distance: 388 - 389: 17.489 distance: 388 - 405: 35.291 distance: 389 - 491: 25.081 distance: 390 - 391: 16.257 distance: 390 - 392: 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