Starting phenix.real_space_refine (version: dev) on Tue Apr 5 10:34:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/04_2022/3jad_6344_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/04_2022/3jad_6344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/04_2022/3jad_6344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/04_2022/3jad_6344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/04_2022/3jad_6344_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/04_2022/3jad_6344_updated.pdb" } resolution = 3.9 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= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 337": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 12705 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "B" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "D" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "E" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'SY9': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'SY9': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'SY9': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'SY9': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'SY9': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.57, per 1000 atoms: 0.60 Number of scatterers: 12705 At special positions: 0 Unit cell: (98.98, 97.97, 126.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2245 8.00 N 2090 7.00 C 8305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " 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 BETA1-4 " NAG A 501 " - " NAG A 502 " " NAG B 402 " - " NAG B 403 " " NAG C 402 " - " NAG C 403 " " NAG D 402 " - " NAG D 403 " " NAG E 402 " - " NAG E 403 " Time building additional restraints: 5.47 Conformation dependent library (CDL) restraints added in 2.0 seconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3230 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 25 sheets defined 33.8% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.513A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 268 through 289 Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.959A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 361 Proline residue: A 347 - end of helix removed outlier: 3.841A pdb=" N ILE A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.514A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 268 through 289 Processing helix chain 'B' and resid 298 through 324 removed outlier: 3.959A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 361 Proline residue: B 347 - end of helix removed outlier: 3.841A pdb=" N ILE B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.513A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 268 through 289 Processing helix chain 'C' and resid 298 through 324 removed outlier: 3.960A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 361 Proline residue: C 347 - end of helix removed outlier: 3.841A pdb=" N ILE C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.514A pdb=" N LEU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 107 No H-bonds generated for 'chain 'D' and resid 105 through 107' Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 268 through 289 Processing helix chain 'D' and resid 298 through 324 removed outlier: 3.960A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 361 Proline residue: D 347 - end of helix removed outlier: 3.841A pdb=" N ILE D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 removed outlier: 3.514A pdb=" N LEU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 237 through 242 Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 268 through 289 Processing helix chain 'E' and resid 298 through 324 removed outlier: 3.959A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 361 Proline residue: E 347 - end of helix removed outlier: 3.841A pdb=" N ILE E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 185 removed outlier: 6.488A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 59 through 61 Processing sheet with id= C, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= D, first strand: chain 'A' and resid 209 through 218 Processing sheet with id= E, first strand: chain 'A' and resid 119 through 124 removed outlier: 7.011A pdb=" N VAL A 151 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA A 122 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 149 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 182 through 185 removed outlier: 6.488A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= H, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= I, first strand: chain 'B' and resid 209 through 218 Processing sheet with id= J, first strand: chain 'B' and resid 119 through 124 removed outlier: 7.012A pdb=" N VAL B 151 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA B 122 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR B 149 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 182 through 185 removed outlier: 6.488A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 59 through 61 Processing sheet with id= M, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= N, first strand: chain 'C' and resid 209 through 218 Processing sheet with id= O, first strand: chain 'C' and resid 119 through 124 removed outlier: 7.011A pdb=" N VAL C 151 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA C 122 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR C 149 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 182 through 185 removed outlier: 6.488A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 59 through 61 Processing sheet with id= R, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= S, first strand: chain 'D' and resid 209 through 218 Processing sheet with id= T, first strand: chain 'D' and resid 119 through 124 removed outlier: 7.010A pdb=" N VAL D 151 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA D 122 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR D 149 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 182 through 185 removed outlier: 6.488A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= W, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= X, first strand: chain 'E' and resid 209 through 218 Processing sheet with id= Y, first strand: chain 'E' and resid 119 through 124 removed outlier: 7.012A pdb=" N VAL E 151 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA E 122 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR E 149 " --> pdb=" O ALA E 122 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1890 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: 3.66 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3870 1.34 - 1.46: 3345 1.46 - 1.59: 5730 1.59 - 1.71: 15 1.71 - 1.84: 100 Bond restraints: 13060 Sorted by residual: bond pdb=" CAR SY9 E 401 " pdb=" CAS SY9 E 401 " ideal model delta sigma weight residual 1.509 1.623 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" CAR SY9 B 401 " pdb=" CAS SY9 B 401 " ideal model delta sigma weight residual 1.509 1.623 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" CAR SY9 C 401 " pdb=" CAS SY9 C 401 " ideal model delta sigma weight residual 1.509 1.623 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" CAR SY9 A 503 " pdb=" CAS SY9 A 503 " ideal model delta sigma weight residual 1.509 1.623 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" CAR SY9 D 401 " pdb=" CAS SY9 D 401 " ideal model delta sigma weight residual 1.509 1.622 -0.113 2.00e-02 2.50e+03 3.21e+01 ... (remaining 13055 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.58: 370 105.58 - 112.75: 6712 112.75 - 119.92: 4198 119.92 - 127.09: 6510 127.09 - 134.26: 145 Bond angle restraints: 17935 Sorted by residual: angle pdb=" C TYR B 94 " pdb=" N PRO B 95 " pdb=" CA PRO B 95 " ideal model delta sigma weight residual 119.32 125.78 -6.46 1.14e+00 7.69e-01 3.21e+01 angle pdb=" C TYR C 94 " pdb=" N PRO C 95 " pdb=" CA PRO C 95 " ideal model delta sigma weight residual 119.32 125.78 -6.46 1.14e+00 7.69e-01 3.21e+01 angle pdb=" C TYR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta sigma weight residual 119.32 125.76 -6.44 1.14e+00 7.69e-01 3.20e+01 angle pdb=" C TYR A 94 " pdb=" N PRO A 95 " pdb=" CA PRO A 95 " ideal model delta sigma weight residual 119.32 125.76 -6.44 1.14e+00 7.69e-01 3.19e+01 angle pdb=" C TYR E 94 " pdb=" N PRO E 95 " pdb=" CA PRO E 95 " ideal model delta sigma weight residual 119.32 125.69 -6.37 1.14e+00 7.69e-01 3.13e+01 ... (remaining 17930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 7308 15.95 - 31.91: 143 31.91 - 47.86: 39 47.86 - 63.82: 0 63.82 - 79.77: 10 Dihedral angle restraints: 7500 sinusoidal: 2520 harmonic: 4980 Sorted by residual: dihedral pdb=" CB CYS E 214 " pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " pdb=" CB CYS E 225 " ideal model delta sinusoidal sigma weight residual -86.00 -152.09 66.09 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -152.09 66.09 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -152.09 66.09 1 1.00e+01 1.00e-02 5.71e+01 ... (remaining 7497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2086 0.146 - 0.291: 19 0.291 - 0.437: 10 0.437 - 0.583: 0 0.583 - 0.728: 5 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CAG SY9 D 401 " pdb=" CAB SY9 D 401 " pdb=" CAK SY9 D 401 " pdb=" CAV SY9 D 401 " both_signs ideal model delta sigma weight residual False -2.68 -1.96 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CAG SY9 A 503 " pdb=" CAB SY9 A 503 " pdb=" CAK SY9 A 503 " pdb=" CAV SY9 A 503 " both_signs ideal model delta sigma weight residual False -2.68 -1.96 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CAG SY9 C 401 " pdb=" CAB SY9 C 401 " pdb=" CAK SY9 C 401 " pdb=" CAV SY9 C 401 " both_signs ideal model delta sigma weight residual False -2.68 -1.96 -0.72 2.00e-01 2.50e+01 1.31e+01 ... (remaining 2117 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 115 " -0.030 2.00e-02 2.50e+03 3.40e-02 2.02e+01 pdb=" CG PHE C 115 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE C 115 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE C 115 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 115 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 115 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE C 115 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 115 " -0.030 2.00e-02 2.50e+03 3.40e-02 2.02e+01 pdb=" CG PHE E 115 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE E 115 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE E 115 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 115 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 115 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE E 115 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 115 " -0.030 2.00e-02 2.50e+03 3.39e-02 2.01e+01 pdb=" CG PHE A 115 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE A 115 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 115 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 115 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 115 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 115 " 0.005 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2544 2.78 - 3.31: 12872 3.31 - 3.84: 21224 3.84 - 4.37: 24153 4.37 - 4.90: 40617 Nonbonded interactions: 101410 Sorted by model distance: nonbonded pdb=" OH TYR E 91 " pdb=" O SER E 98 " model vdw 2.250 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" O SER B 98 " model vdw 2.250 2.440 nonbonded pdb=" OH TYR D 91 " pdb=" O SER D 98 " model vdw 2.250 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" O SER A 98 " model vdw 2.251 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" O SER C 98 " model vdw 2.251 2.440 ... (remaining 101405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 364 or resid 502)) selection = (chain 'B' and (resid 25 through 364 or resid 402)) selection = (chain 'C' and (resid 25 through 364 or resid 402)) selection = (chain 'D' and (resid 25 through 364 or resid 402)) selection = (chain 'E' and (resid 25 through 364 or resid 402)) } 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8305 2.51 5 N 2090 2.21 5 O 2245 1.98 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 group one per residue 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: 3.880 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: 0.000 Extract box with map and model: 6.510 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.110 Process input model: 35.130 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.008 0.114 13060 Z= 0.519 Angle : 1.322 11.471 17935 Z= 0.855 Chirality : 0.062 0.728 2120 Planarity : 0.004 0.034 2235 Dihedral : 8.458 79.771 4255 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.43 % 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: -2.13 (0.18), residues: 1665 helix: -1.20 (0.19), residues: 575 sheet: -0.41 (0.22), residues: 385 loop : -2.11 (0.20), residues: 705 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 295 time to evaluate : 1.482 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: symmetry clash outliers start: 5 outliers final: 0 residues processed: 300 average time/residue: 0.2688 time to fit residues: 112.4029 Evaluate side-chains 155 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.503 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 0.0270 overall best weight: 2.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN D 123 ASN E 83 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 13060 Z= 0.235 Angle : 0.695 9.165 17935 Z= 0.352 Chirality : 0.045 0.261 2120 Planarity : 0.004 0.041 2235 Dihedral : 5.647 22.945 1880 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 2.84 % 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: -0.65 (0.20), residues: 1665 helix: 0.88 (0.21), residues: 580 sheet: -0.26 (0.23), residues: 410 loop : -1.68 (0.23), residues: 675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 208 average time/residue: 0.2093 time to fit residues: 66.0704 Evaluate side-chains 170 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.397 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1256 time to fit residues: 7.5211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 13060 Z= 0.306 Angle : 0.691 12.539 17935 Z= 0.351 Chirality : 0.044 0.169 2120 Planarity : 0.004 0.027 2235 Dihedral : 5.461 23.066 1880 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 2.07 % 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: -0.39 (0.20), residues: 1665 helix: 1.32 (0.20), residues: 585 sheet: -0.55 (0.24), residues: 410 loop : -1.47 (0.24), residues: 670 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 1.605 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 173 average time/residue: 0.2220 time to fit residues: 57.6934 Evaluate side-chains 146 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.474 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1064 time to fit residues: 3.8917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13060 Z= 0.224 Angle : 0.640 10.839 17935 Z= 0.318 Chirality : 0.042 0.132 2120 Planarity : 0.004 0.034 2235 Dihedral : 5.159 22.093 1880 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 2.24 % 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: -0.15 (0.21), residues: 1665 helix: 1.72 (0.20), residues: 585 sheet: -0.71 (0.24), residues: 410 loop : -1.33 (0.25), residues: 670 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 167 average time/residue: 0.2271 time to fit residues: 59.0971 Evaluate side-chains 151 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1312 time to fit residues: 5.3447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.2980 chunk 90 optimal weight: 5.9990 chunk 2 optimal weight: 0.0980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 136 optimal weight: 0.0770 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13060 Z= 0.172 Angle : 0.631 13.764 17935 Z= 0.304 Chirality : 0.042 0.195 2120 Planarity : 0.003 0.035 2235 Dihedral : 4.885 21.070 1880 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.47 % 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: 1665 helix: 2.08 (0.20), residues: 585 sheet: -0.75 (0.23), residues: 440 loop : -1.24 (0.26), residues: 640 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.586 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 167 average time/residue: 0.2154 time to fit residues: 55.0821 Evaluate side-chains 143 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1158 time to fit residues: 3.2297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 0.0040 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13060 Z= 0.169 Angle : 0.619 13.000 17935 Z= 0.299 Chirality : 0.042 0.139 2120 Planarity : 0.003 0.035 2235 Dihedral : 4.726 21.228 1880 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.03 % 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: 1665 helix: 2.28 (0.20), residues: 585 sheet: -0.72 (0.23), residues: 440 loop : -1.19 (0.26), residues: 640 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 154 average time/residue: 0.2068 time to fit residues: 49.6927 Evaluate side-chains 141 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1078 time to fit residues: 3.1480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 116 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 13060 Z= 0.256 Angle : 0.651 11.892 17935 Z= 0.323 Chirality : 0.043 0.308 2120 Planarity : 0.004 0.035 2235 Dihedral : 4.920 21.824 1880 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 1.90 % 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 (0.21), residues: 1665 helix: 2.10 (0.20), residues: 585 sheet: -0.89 (0.23), residues: 440 loop : -1.22 (0.26), residues: 640 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.548 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 158 average time/residue: 0.1967 time to fit residues: 48.7047 Evaluate side-chains 149 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.517 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1148 time to fit residues: 4.3502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 13060 Z= 0.368 Angle : 0.748 13.072 17935 Z= 0.375 Chirality : 0.045 0.195 2120 Planarity : 0.005 0.042 2235 Dihedral : 5.389 22.598 1880 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 1.12 % 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: -0.36 (0.21), residues: 1665 helix: 1.73 (0.20), residues: 585 sheet: -1.12 (0.24), residues: 430 loop : -1.40 (0.24), residues: 650 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.481 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 151 average time/residue: 0.2062 time to fit residues: 48.3933 Evaluate side-chains 141 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1132 time to fit residues: 3.5092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13060 Z= 0.199 Angle : 0.684 12.916 17935 Z= 0.327 Chirality : 0.044 0.464 2120 Planarity : 0.004 0.045 2235 Dihedral : 5.087 22.977 1880 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.26 % 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: -0.01 (0.21), residues: 1665 helix: 2.23 (0.20), residues: 585 sheet: -1.15 (0.23), residues: 440 loop : -1.25 (0.26), residues: 640 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.515 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 158 average time/residue: 0.2121 time to fit residues: 51.8182 Evaluate side-chains 138 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1100 time to fit residues: 2.3882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 13060 Z= 0.203 Angle : 0.664 12.895 17935 Z= 0.319 Chirality : 0.044 0.424 2120 Planarity : 0.004 0.046 2235 Dihedral : 5.003 22.878 1880 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1665 helix: 2.50 (0.20), residues: 575 sheet: -1.05 (0.23), residues: 460 loop : -1.18 (0.26), residues: 630 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.507 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 143 average time/residue: 0.2084 time to fit residues: 46.9156 Evaluate side-chains 141 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1265 time to fit residues: 2.8915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 0.0020 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 overall best weight: 3.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.041179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.034723 restraints weight = 99229.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.035523 restraints weight = 62116.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035980 restraints weight = 43910.661| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 13060 Z= 0.255 Angle : 0.681 12.770 17935 Z= 0.334 Chirality : 0.044 0.429 2120 Planarity : 0.004 0.059 2235 Dihedral : 5.086 23.764 1880 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.34 % 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: 1665 helix: 2.26 (0.20), residues: 580 sheet: -1.13 (0.23), residues: 460 loop : -1.19 (0.26), residues: 625 =============================================================================== Job complete usr+sys time: 2064.06 seconds wall clock time: 38 minutes 57.83 seconds (2337.83 seconds total)