Starting phenix.real_space_refine (version: dev) on Sun Feb 26 07:07:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/02_2023/7zl1_14774_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/02_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_14774/02_2023/7zl1_14774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/02_2023/7zl1_14774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/02_2023/7zl1_14774_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/02_2023/7zl1_14774_trim.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 12.91, per 1000 atoms: 0.47 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: 25.05 Conformation dependent library (CDL) restraints added in 2.3 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: 1.00 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: 11.36 Time building geometry restraints manager: 25.51 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=" C1 NAG D1000 " pdb=" C2 NAG D1000 " ideal model delta sigma weight residual 1.526 1.568 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" C1 NAG B1000 " pdb=" C2 NAG B1000 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 NAG C1000 " pdb=" C2 NAG C1000 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C1 NAG F1000 " pdb=" C2 NAG F1000 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 3.97e+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=" C1 NAG B1000 " pdb=" C2 NAG B1000 " pdb=" C3 NAG B1000 " ideal model delta sigma weight residual 110.19 115.35 -5.16 9.25e-01 1.17e+00 3.12e+01 angle pdb=" C1 NAG C1000 " pdb=" C2 NAG C1000 " pdb=" C3 NAG C1000 " ideal model delta sigma weight residual 110.19 115.31 -5.12 9.25e-01 1.17e+00 3.06e+01 angle pdb=" C1 NAG D1000 " pdb=" C2 NAG D1000 " pdb=" C3 NAG D1000 " ideal model delta sigma weight residual 110.19 115.24 -5.05 9.25e-01 1.17e+00 2.98e+01 angle pdb=" C1 NAG F1000 " pdb=" C2 NAG F1000 " pdb=" C3 NAG F1000 " ideal model delta sigma weight residual 110.19 115.19 -5.00 9.25e-01 1.17e+00 2.93e+01 angle pdb=" C1 NAG G1000 " pdb=" C2 NAG G1000 " pdb=" C3 NAG G1000 " ideal model delta sigma weight residual 110.19 115.19 -5.00 9.25e-01 1.17e+00 2.92e+01 ... (remaining 47958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9253 17.99 - 35.97: 777 35.97 - 53.96: 207 53.96 - 71.95: 207 71.95 - 89.93: 28 Dihedral angle restraints: 10472 sinusoidal: 4720 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 10469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1192 0.042 - 0.085: 590 0.085 - 0.127: 204 0.127 - 0.169: 43 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 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. 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: 1.970 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: 0.440 Extract box with map and model: 11.940 Check model and map are aligned: 0.350 Process input model: 91.340 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.280 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 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= 0.451 Angle : 0.869 7.091 18496 Z= 0.516 Chirality : 0.056 0.212 2040 Planarity : 0.010 0.115 2352 Dihedral : 14.599 89.932 4776 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 1.00 % Allowed : 5.69 % Favored : 93.31 % Rotamer Outliers : 0.65 % 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 : 2.364 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: 3.8443 time to fit residues: 844.7177 Evaluate side-chains 163 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 2.143 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 1.7134 time to fit residues: 18.3211 ------------------------------------------------------------------------------- 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: 1.9990 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 345 ASN C 345 ASN H 345 ASN F 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 13624 Z= 0.191 Angle : 0.589 6.775 18496 Z= 0.326 Chirality : 0.047 0.139 2040 Planarity : 0.004 0.042 2352 Dihedral : 6.600 29.006 1872 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.99 % Favored : 94.84 % Rotamer Outliers : 2.23 % 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: 0.02 (0.22), residues: 1704 helix: -1.03 (0.38), residues: 136 sheet: 0.83 (0.21), residues: 568 loop : -0.28 (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 201 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 2.240 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: 31 outliers final: 15 residues processed: 185 average time/residue: 3.6698 time to fit residues: 731.7968 Evaluate side-chains 168 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 5 residues processed: 10 average time/residue: 1.7225 time to fit residues: 22.7289 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 13624 Z= 0.287 Angle : 0.632 16.051 18496 Z= 0.346 Chirality : 0.047 0.229 2040 Planarity : 0.004 0.049 2352 Dihedral : 6.422 26.091 1872 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.22 % Favored : 94.66 % Rotamer Outliers : 2.73 % 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: -0.10 (0.21), residues: 1704 helix: -0.67 (0.45), residues: 120 sheet: 0.70 (0.21), residues: 568 loop : -0.40 (0.22), residues: 1016 *********************** 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 197 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 2.522 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: 38 outliers final: 20 residues processed: 176 average time/residue: 3.6443 time to fit residues: 691.2304 Evaluate side-chains 170 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 2.485 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 9 residues processed: 11 average time/residue: 1.5919 time to fit residues: 23.0572 ------------------------------------------------------------------------------- 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: 0.5980 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8570 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 13624 Z= 0.324 Angle : 0.650 16.867 18496 Z= 0.352 Chirality : 0.048 0.222 2040 Planarity : 0.004 0.042 2352 Dihedral : 6.294 24.558 1872 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.46 % Favored : 94.42 % Rotamer Outliers : 2.95 % 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: -0.25 (0.21), residues: 1704 helix: -0.86 (0.47), residues: 120 sheet: 0.50 (0.21), residues: 576 loop : -0.43 (0.21), residues: 1008 *********************** 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 195 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 2.392 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 outliers start: 41 outliers final: 24 residues processed: 179 average time/residue: 3.7057 time to fit residues: 715.7809 Evaluate side-chains 170 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 2.450 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 14 residues processed: 10 average time/residue: 1.5033 time to fit residues: 20.5817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 ASN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 13624 Z= 0.355 Angle : 0.666 16.675 18496 Z= 0.360 Chirality : 0.049 0.214 2040 Planarity : 0.004 0.054 2352 Dihedral : 6.378 24.377 1872 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.75 % Favored : 94.13 % Rotamer Outliers : 3.45 % 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: -0.41 (0.21), residues: 1704 helix: -1.02 (0.47), residues: 120 sheet: 0.36 (0.19), residues: 648 loop : -0.57 (0.22), residues: 936 *********************** REFINEMENT MACRO_CYCLE 5 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 193 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 2.431 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: 48 outliers final: 26 residues processed: 173 average time/residue: 3.7300 time to fit residues: 695.0651 Evaluate side-chains 167 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 15 residues processed: 11 average time/residue: 1.3052 time to fit residues: 20.1267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 13624 Z= 0.226 Angle : 0.572 15.131 18496 Z= 0.307 Chirality : 0.046 0.184 2040 Planarity : 0.003 0.068 2352 Dihedral : 5.885 23.197 1872 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.75 % Favored : 94.13 % Rotamer Outliers : 3.16 % 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: -0.25 (0.21), residues: 1704 helix: -0.54 (0.49), residues: 120 sheet: 0.65 (0.20), residues: 608 loop : -0.63 (0.22), residues: 976 *********************** REFINEMENT MACRO_CYCLE 6 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 200 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 2.394 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 revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 24 residues processed: 180 average time/residue: 3.3871 time to fit residues: 660.8512 Evaluate side-chains 172 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 2.454 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 13 residues processed: 11 average time/residue: 1.3493 time to fit residues: 20.6303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 13624 Z= 0.258 Angle : 0.598 16.047 18496 Z= 0.319 Chirality : 0.047 0.194 2040 Planarity : 0.003 0.080 2352 Dihedral : 5.878 23.105 1872 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer Outliers : 3.23 % 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: -0.25 (0.21), residues: 1704 helix: -0.51 (0.49), residues: 120 sheet: 0.66 (0.20), residues: 608 loop : -0.64 (0.22), residues: 976 *********************** REFINEMENT MACRO_CYCLE 7 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 186 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 2.318 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 outliers start: 45 outliers final: 27 residues processed: 169 average time/residue: 3.5863 time to fit residues: 662.3043 Evaluate side-chains 168 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 16 residues processed: 11 average time/residue: 1.4272 time to fit residues: 21.8196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 13624 Z= 0.255 Angle : 0.596 16.639 18496 Z= 0.318 Chirality : 0.047 0.198 2040 Planarity : 0.003 0.064 2352 Dihedral : 5.818 23.132 1872 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer Outliers : 2.66 % 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: -0.25 (0.21), residues: 1704 helix: -0.69 (0.47), residues: 128 sheet: 0.67 (0.20), residues: 608 loop : -0.63 (0.22), residues: 968 *********************** REFINEMENT MACRO_CYCLE 8 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 179 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 142 time to evaluate : 2.382 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: 37 outliers final: 23 residues processed: 163 average time/residue: 3.4658 time to fit residues: 611.7374 Evaluate side-chains 159 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 2.292 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 1.5796 time to fit residues: 17.5279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 13624 Z= 0.269 Angle : 0.605 16.062 18496 Z= 0.323 Chirality : 0.047 0.194 2040 Planarity : 0.004 0.092 2352 Dihedral : 5.879 23.809 1872 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.81 % Favored : 94.07 % Rotamer Outliers : 2.80 % 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: -0.25 (0.21), residues: 1704 helix: -0.52 (0.49), residues: 120 sheet: 0.66 (0.20), residues: 608 loop : -0.64 (0.22), residues: 976 *********************** REFINEMENT MACRO_CYCLE 9 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 177 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 2.494 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 revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 161 average time/residue: 3.4408 time to fit residues: 600.9057 Evaluate side-chains 166 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 2.234 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 14 residues processed: 10 average time/residue: 1.5162 time to fit residues: 20.5412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 13624 Z= 0.238 Angle : 0.580 15.476 18496 Z= 0.309 Chirality : 0.046 0.186 2040 Planarity : 0.003 0.087 2352 Dihedral : 5.704 23.556 1872 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer Outliers : 1.80 % 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: -0.23 (0.21), residues: 1704 helix: -0.57 (0.48), residues: 128 sheet: 0.67 (0.20), residues: 608 loop : -0.61 (0.22), residues: 968 ********************** REFINEMENT MACRO_CYCLE 10 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 171 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 2.479 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 revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 162 average time/residue: 3.3960 time to fit residues: 595.7418 Evaluate side-chains 154 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.3122 time to fit residues: 3.2586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 254 ASN G 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105016 restraints weight = 39584.723| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.77 r_work: 0.3062 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 13624 Z= 0.334 Angle : 0.654 16.188 18496 Z= 0.351 Chirality : 0.048 0.206 2040 Planarity : 0.004 0.093 2352 Dihedral : 6.073 23.477 1872 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.28 % Favored : 93.60 % Rotamer Outliers : 2.37 % 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: -0.32 (0.21), residues: 1704 helix: -0.75 (0.48), residues: 120 sheet: 0.63 (0.20), residues: 608 loop : -0.68 (0.22), residues: 976 =============================================================================== Job complete usr+sys time: 11181.17 seconds wall clock time: 197 minutes 30.27 seconds (11850.27 seconds total)