Starting phenix.real_space_refine on Wed Mar 20 12:02:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/03_2024/7zl1_14774_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/03_2024/7zl1_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_14774/03_2024/7zl1_14774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/03_2024/7zl1_14774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/03_2024/7zl1_14774_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl1_14774/03_2024/7zl1_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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: 12.19, per 1000 atoms: 0.45 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: 25.41 Conformation dependent library (CDL) restraints added in 2.7 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: 2.53 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: 10.87 Time building geometry restraints manager: 26.04 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: 10919 17.99 - 35.97: 996 35.97 - 53.96: 372 53.96 - 71.95: 253 71.95 - 89.93: 28 Dihedral angle restraints: 12568 sinusoidal: 6816 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 12565 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: 2.200 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: 0.480 Extract box with map and model: 10.910 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 91.770 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.160 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:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.600 ------------------------------------------------------------------------------- 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 : 14.805 89.932 4896 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP B 267 HIS 0.013 0.003 HIS A 358 PHE 0.033 0.004 PHE E 247 TYR 0.035 0.006 TYR G 239 ARG 0.031 0.004 ARG D 172 *********************** 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 : 2.183 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: B 254 ASN cc_start: 0.8180 (m110) cc_final: 0.7898 (m110) REVERT: A 255 LYS cc_start: 0.8268 (mttm) cc_final: 0.7997 (mtmm) REVERT: A 288 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7088 (mt-10) REVERT: D 288 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7103 (mt-10) REVERT: C 203 ARG cc_start: 0.7793 (ttt-90) cc_final: 0.7546 (ttt-90) REVERT: E 203 ARG cc_start: 0.7835 (ttt-90) cc_final: 0.7614 (ttt-90) REVERT: E 254 ASN cc_start: 0.8059 (m110) cc_final: 0.7666 (m110) REVERT: H 203 ARG cc_start: 0.7827 (ttt-90) cc_final: 0.7584 (ttt-90) REVERT: G 203 ARG cc_start: 0.7810 (ttt-90) cc_final: 0.7572 (ttt-90) REVERT: G 254 ASN cc_start: 0.8053 (m110) cc_final: 0.7853 (m110) REVERT: G 255 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7950 (mtpt) REVERT: F 172 ARG cc_start: 0.6859 (ptt-90) cc_final: 0.6618 (ptm-80) REVERT: F 173 SER cc_start: 0.7910 (t) cc_final: 0.7678 (p) REVERT: F 203 ARG cc_start: 0.7812 (ttt-90) cc_final: 0.7566 (ttt-90) REVERT: F 231 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7445 (mtt180) outliers start: 9 outliers final: 8 residues processed: 205 average time/residue: 3.7742 time to fit residues: 830.2859 Evaluate side-chains 167 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain F residue 187 MET 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: 0.5980 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8452 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13624 Z= 0.209 Angle : 0.602 6.725 18496 Z= 0.331 Chirality : 0.047 0.136 2040 Planarity : 0.004 0.042 2352 Dihedral : 8.053 58.593 2016 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.99 % Favored : 94.84 % Rotamer: Outliers : 2.23 % Allowed : 7.11 % Favored : 90.66 % 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: 0.05 (0.22), residues: 1704 helix: -1.12 (0.38), residues: 136 sheet: 0.85 (0.21), residues: 568 loop : -0.23 (0.23), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 284 HIS 0.004 0.001 HIS B 358 PHE 0.012 0.002 PHE C 323 TYR 0.016 0.002 TYR A 239 ARG 0.008 0.001 ARG D 266 *********************** 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 206 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 2.227 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: B 203 ARG cc_start: 0.7805 (ttt-90) cc_final: 0.7345 (ttt90) REVERT: B 254 ASN cc_start: 0.8218 (m110) cc_final: 0.7874 (m110) REVERT: A 255 LYS cc_start: 0.8209 (mttm) cc_final: 0.7902 (mttt) REVERT: D 254 ASN cc_start: 0.8208 (m110) cc_final: 0.7922 (m110) REVERT: C 254 ASN cc_start: 0.8130 (m110) cc_final: 0.7853 (m110) REVERT: E 254 ASN cc_start: 0.8075 (m110) cc_final: 0.7774 (m110) REVERT: G 203 ARG cc_start: 0.7736 (ttt-90) cc_final: 0.7523 (ttt-90) REVERT: G 255 LYS cc_start: 0.8317 (ttmm) cc_final: 0.8095 (ttmt) REVERT: F 172 ARG cc_start: 0.6838 (ptt-90) cc_final: 0.6447 (ptm-80) REVERT: F 173 SER cc_start: 0.7914 (t) cc_final: 0.7537 (p) REVERT: F 243 GLN cc_start: 0.5989 (OUTLIER) cc_final: 0.5735 (pp30) outliers start: 31 outliers final: 16 residues processed: 190 average time/residue: 3.5867 time to fit residues: 732.5653 Evaluate side-chains 175 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 355 GLU 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: 6.9990 chunk 103 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 0.3980 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13624 Z= 0.269 Angle : 0.622 15.364 18496 Z= 0.339 Chirality : 0.047 0.230 2040 Planarity : 0.004 0.048 2352 Dihedral : 7.721 58.923 2016 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.52 % Favored : 94.37 % Rotamer: Outliers : 2.66 % Allowed : 8.19 % Favored : 89.15 % 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: -0.04 (0.21), residues: 1704 helix: -0.65 (0.45), residues: 120 sheet: 0.70 (0.21), residues: 568 loop : -0.33 (0.22), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 169 HIS 0.005 0.001 HIS F 358 PHE 0.014 0.002 PHE C 323 TYR 0.016 0.002 TYR C 239 ARG 0.010 0.001 ARG D 266 *********************** 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 204 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 2.108 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: B 203 ARG cc_start: 0.7809 (ttt-90) cc_final: 0.7343 (ttt90) REVERT: B 254 ASN cc_start: 0.8056 (m110) cc_final: 0.7701 (m110) REVERT: B 280 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7976 (tt) REVERT: A 255 LYS cc_start: 0.8201 (mttm) cc_final: 0.7960 (mtmm) REVERT: D 254 ASN cc_start: 0.8158 (m110) cc_final: 0.7877 (m110) REVERT: C 254 ASN cc_start: 0.8084 (m110) cc_final: 0.7830 (m110) REVERT: H 280 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7932 (tt) REVERT: G 231 ARG cc_start: 0.7579 (mpt180) cc_final: 0.7367 (mmt-90) REVERT: F 172 ARG cc_start: 0.6881 (ptt-90) cc_final: 0.6675 (ptm-80) REVERT: F 173 SER cc_start: 0.7931 (t) cc_final: 0.7697 (p) REVERT: F 243 GLN cc_start: 0.6153 (OUTLIER) cc_final: 0.5762 (pp30) REVERT: F 262 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7340 (t) REVERT: F 355 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6844 (tp30) outliers start: 37 outliers final: 20 residues processed: 183 average time/residue: 3.5124 time to fit residues: 691.4838 Evaluate side-chains 181 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 355 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 0.0060 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 13624 Z= 0.209 Angle : 0.556 15.887 18496 Z= 0.299 Chirality : 0.046 0.198 2040 Planarity : 0.003 0.047 2352 Dihedral : 7.174 59.758 2016 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.28 % Favored : 94.60 % Rotamer: Outliers : 2.87 % Allowed : 8.55 % Favored : 88.58 % 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: -0.30 (0.46), residues: 128 sheet: 0.61 (0.21), residues: 584 loop : -0.25 (0.22), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 284 HIS 0.002 0.001 HIS F 358 PHE 0.009 0.001 PHE A 225 TYR 0.013 0.002 TYR C 239 ARG 0.012 0.000 ARG D 266 *********************** 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 206 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 2.129 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: B 203 ARG cc_start: 0.7780 (ttt-90) cc_final: 0.7312 (ttt90) REVERT: B 254 ASN cc_start: 0.8133 (m110) cc_final: 0.7790 (m110) REVERT: B 280 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7948 (tt) REVERT: D 254 ASN cc_start: 0.8156 (m110) cc_final: 0.7870 (m110) REVERT: C 254 ASN cc_start: 0.8135 (m110) cc_final: 0.7847 (m110) REVERT: E 254 ASN cc_start: 0.8052 (m110) cc_final: 0.7820 (m110) REVERT: H 355 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: F 173 SER cc_start: 0.7923 (t) cc_final: 0.7709 (p) REVERT: F 243 GLN cc_start: 0.6217 (OUTLIER) cc_final: 0.5979 (pp30) outliers start: 40 outliers final: 25 residues processed: 187 average time/residue: 3.6040 time to fit residues: 726.1948 Evaluate side-chains 190 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 355 GLU Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 359 ILE 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: 2.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN G 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 13624 Z= 0.290 Angle : 0.618 16.102 18496 Z= 0.335 Chirality : 0.047 0.215 2040 Planarity : 0.004 0.055 2352 Dihedral : 7.542 59.954 2016 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % Rotamer: Outliers : 3.02 % Allowed : 9.27 % Favored : 87.72 % 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: -0.08 (0.21), residues: 1704 helix: -0.53 (0.48), residues: 120 sheet: 0.56 (0.21), residues: 584 loop : -0.31 (0.22), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 339 HIS 0.006 0.002 HIS B 358 PHE 0.011 0.002 PHE C 323 TYR 0.015 0.002 TYR B 239 ARG 0.013 0.001 ARG H 266 *********************** 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 204 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 2.130 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: B 203 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7335 (ttt90) REVERT: B 254 ASN cc_start: 0.8122 (m110) cc_final: 0.7776 (m110) REVERT: B 280 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7977 (tt) REVERT: A 243 GLN cc_start: 0.6044 (OUTLIER) cc_final: 0.5828 (pp30) REVERT: A 355 GLU cc_start: 0.7239 (tp30) cc_final: 0.7025 (mp0) REVERT: C 254 ASN cc_start: 0.8106 (m110) cc_final: 0.7873 (m110) REVERT: E 280 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7934 (tt) REVERT: H 355 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6876 (tp30) REVERT: F 173 SER cc_start: 0.7950 (t) cc_final: 0.7733 (p) REVERT: F 243 GLN cc_start: 0.5941 (OUTLIER) cc_final: 0.5593 (pp30) outliers start: 42 outliers final: 23 residues processed: 183 average time/residue: 3.6962 time to fit residues: 725.5107 Evaluate side-chains 183 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 355 GLU Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.8480 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 13624 Z= 0.342 Angle : 0.659 16.241 18496 Z= 0.357 Chirality : 0.048 0.222 2040 Planarity : 0.004 0.060 2352 Dihedral : 7.571 58.574 2016 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 3.23 % Allowed : 9.20 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1704 helix: -0.87 (0.48), residues: 120 sheet: 0.36 (0.19), residues: 648 loop : -0.43 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 339 HIS 0.008 0.002 HIS B 358 PHE 0.011 0.002 PHE H 323 TYR 0.016 0.002 TYR B 239 ARG 0.016 0.001 ARG D 266 *********************** 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 193 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 148 time to evaluate : 2.256 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: B 254 ASN cc_start: 0.8131 (m110) cc_final: 0.7824 (m110) REVERT: B 280 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7993 (tt) REVERT: A 243 GLN cc_start: 0.6148 (OUTLIER) cc_final: 0.5861 (pp30) REVERT: C 254 ASN cc_start: 0.8131 (m110) cc_final: 0.7883 (m110) REVERT: E 280 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7940 (tt) REVERT: H 355 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6966 (tp30) REVERT: F 173 SER cc_start: 0.7952 (t) cc_final: 0.7703 (p) REVERT: F 243 GLN cc_start: 0.6027 (OUTLIER) cc_final: 0.5801 (pp30) REVERT: F 343 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7766 (mp) outliers start: 45 outliers final: 26 residues processed: 174 average time/residue: 3.4132 time to fit residues: 641.1346 Evaluate side-chains 179 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 355 GLU Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 118 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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: 0.8444 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13624 Z= 0.199 Angle : 0.549 14.619 18496 Z= 0.296 Chirality : 0.046 0.184 2040 Planarity : 0.003 0.081 2352 Dihedral : 7.054 59.970 2016 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 2.73 % Allowed : 9.84 % Favored : 87.43 % 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: -0.32 (0.50), residues: 120 sheet: 0.60 (0.20), residues: 608 loop : -0.42 (0.22), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.001 HIS D 197 PHE 0.010 0.001 PHE E 225 TYR 0.014 0.002 TYR B 239 ARG 0.015 0.001 ARG D 266 *********************** 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 195 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 2.469 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 revert: symmetry clash REVERT: B 203 ARG cc_start: 0.7759 (ttt-90) cc_final: 0.7427 (ttt90) REVERT: B 254 ASN cc_start: 0.8037 (m110) cc_final: 0.7735 (m110) REVERT: A 243 GLN cc_start: 0.6181 (OUTLIER) cc_final: 0.5880 (pp30) REVERT: C 254 ASN cc_start: 0.8103 (m110) cc_final: 0.7804 (m110) REVERT: F 173 SER cc_start: 0.7936 (t) cc_final: 0.7716 (p) outliers start: 38 outliers final: 20 residues processed: 177 average time/residue: 3.3079 time to fit residues: 634.1125 Evaluate side-chains 173 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 262 VAL 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: 2.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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: 0.8469 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 13624 Z= 0.291 Angle : 0.610 15.070 18496 Z= 0.330 Chirality : 0.047 0.201 2040 Planarity : 0.004 0.084 2352 Dihedral : 7.312 59.565 2016 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 2.73 % Allowed : 9.91 % Favored : 87.36 % 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: -0.19 (0.21), residues: 1704 helix: -0.63 (0.49), residues: 120 sheet: 0.58 (0.20), residues: 608 loop : -0.49 (0.22), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 339 HIS 0.006 0.001 HIS B 358 PHE 0.010 0.002 PHE D 323 TYR 0.015 0.002 TYR B 239 ARG 0.017 0.001 ARG D 266 *********************** 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 189 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 2.098 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: B 254 ASN cc_start: 0.8073 (m110) cc_final: 0.7758 (m110) REVERT: C 254 ASN cc_start: 0.8139 (m110) cc_final: 0.7885 (m110) REVERT: E 231 ARG cc_start: 0.7563 (mmt-90) cc_final: 0.7142 (mmt-90) REVERT: F 173 SER cc_start: 0.7942 (t) cc_final: 0.7713 (p) REVERT: F 243 GLN cc_start: 0.5994 (OUTLIER) cc_final: 0.5664 (pp30) outliers start: 38 outliers final: 23 residues processed: 172 average time/residue: 3.2384 time to fit residues: 603.4772 Evaluate side-chains 173 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 262 VAL 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: 0.7980 chunk 150 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 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: 1.9990 chunk 159 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.8461 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= 0.254 Angle : 0.586 14.841 18496 Z= 0.316 Chirality : 0.046 0.192 2040 Planarity : 0.004 0.093 2352 Dihedral : 7.188 59.984 2016 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.96 % Rotamer: Outliers : 2.87 % Allowed : 9.84 % Favored : 87.28 % 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: -0.17 (0.21), residues: 1704 helix: -0.54 (0.50), residues: 120 sheet: 0.59 (0.20), residues: 608 loop : -0.48 (0.22), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 169 HIS 0.005 0.001 HIS F 358 PHE 0.009 0.002 PHE B 225 TYR 0.015 0.002 TYR B 239 ARG 0.019 0.001 ARG D 266 *********************** 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 191 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 2.083 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: B 254 ASN cc_start: 0.8093 (m110) cc_final: 0.7774 (m110) REVERT: C 254 ASN cc_start: 0.8134 (m110) cc_final: 0.7854 (m110) REVERT: E 231 ARG cc_start: 0.7546 (mmt-90) cc_final: 0.6882 (mpt180) REVERT: H 266 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7555 (ttm110) REVERT: H 355 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6973 (tp30) REVERT: F 173 SER cc_start: 0.7927 (t) cc_final: 0.7689 (p) REVERT: F 255 LYS cc_start: 0.8177 (mttp) cc_final: 0.7903 (mtmm) outliers start: 40 outliers final: 23 residues processed: 174 average time/residue: 3.2634 time to fit residues: 616.2516 Evaluate side-chains 172 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 355 GLU Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 262 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 13624 Z= 0.228 Angle : 0.565 14.497 18496 Z= 0.305 Chirality : 0.046 0.185 2040 Planarity : 0.004 0.090 2352 Dihedral : 7.015 59.998 2016 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 2.16 % Allowed : 10.92 % Favored : 86.93 % 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: -0.17 (0.21), residues: 1704 helix: -0.64 (0.48), residues: 128 sheet: 0.58 (0.20), residues: 608 loop : -0.45 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 169 HIS 0.004 0.001 HIS B 358 PHE 0.009 0.001 PHE E 225 TYR 0.014 0.002 TYR B 239 ARG 0.017 0.001 ARG D 266 ********************** 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 176 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 2.293 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: B 254 ASN cc_start: 0.8119 (m110) cc_final: 0.7784 (m110) REVERT: C 254 ASN cc_start: 0.8139 (m110) cc_final: 0.7855 (m110) REVERT: E 231 ARG cc_start: 0.7531 (mmt-90) cc_final: 0.6877 (mpt180) REVERT: H 254 ASN cc_start: 0.7910 (m110) cc_final: 0.7709 (m110) REVERT: H 355 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6978 (tp30) REVERT: F 173 SER cc_start: 0.7926 (t) cc_final: 0.7688 (p) REVERT: F 255 LYS cc_start: 0.8164 (mttp) cc_final: 0.7900 (mtmm) outliers start: 30 outliers final: 23 residues processed: 167 average time/residue: 3.2362 time to fit residues: 588.1532 Evaluate side-chains 170 residues out of total 1392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 355 GLU Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 317 CYS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 262 VAL 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: 1.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105445 restraints weight = 39896.707| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.76 r_work: 0.3074 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13624 Z= 0.268 Angle : 0.598 14.966 18496 Z= 0.323 Chirality : 0.047 0.195 2040 Planarity : 0.004 0.098 2352 Dihedral : 7.231 59.831 2016 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 2.44 % Allowed : 10.78 % Favored : 86.78 % 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: -0.24 (0.21), residues: 1704 helix: -0.81 (0.47), residues: 128 sheet: 0.56 (0.20), residues: 608 loop : -0.51 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 339 HIS 0.007 0.001 HIS B 358 PHE 0.008 0.002 PHE H 323 TYR 0.015 0.002 TYR B 239 ARG 0.019 0.001 ARG D 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11101.06 seconds wall clock time: 194 minutes 7.25 seconds (11647.25 seconds total)