Starting phenix.real_space_refine on Fri Mar 15 20:19:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/03_2024/3jad_6344_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/03_2024/3jad_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_6344/03_2024/3jad_6344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/03_2024/3jad_6344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/03_2024/3jad_6344_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/03_2024/3jad_6344_updated.pdb" } resolution = 3.9 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= 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12705 Number of models: 1 Model: "" Number of chains: 15 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.00, per 1000 atoms: 0.55 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.4 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: 2.51 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: 4.02 Time building geometry restraints manager: 5.81 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: 7664 15.95 - 31.91: 187 31.91 - 47.86: 54 47.86 - 63.82: 40 63.82 - 79.77: 10 Dihedral angle restraints: 7955 sinusoidal: 2975 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 7952 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.430 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.950 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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= 0.520 Angle : 1.327 11.471 17935 Z= 0.854 Chirality : 0.062 0.728 2120 Planarity : 0.004 0.034 2235 Dihedral : 10.082 79.771 4710 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 % Allowed : 1.72 % Favored : 97.84 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 259 HIS 0.002 0.001 HIS C 217 PHE 0.075 0.003 PHE C 115 TYR 0.015 0.002 TYR D 144 ARG 0.006 0.001 ARG B 234 *********************** 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 : 1.475 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 REVERT: A 115 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7837 (p90) REVERT: A 239 TYR cc_start: 0.7194 (m-80) cc_final: 0.6984 (m-80) REVERT: A 255 TRP cc_start: 0.8111 (m-10) cc_final: 0.7412 (m-10) REVERT: A 262 MET cc_start: 0.7608 (mtm) cc_final: 0.7233 (mtm) REVERT: A 277 LEU cc_start: 0.8917 (tp) cc_final: 0.8686 (tp) REVERT: B 72 MET cc_start: 0.7714 (tpp) cc_final: 0.7499 (tpp) REVERT: B 255 TRP cc_start: 0.8038 (m-10) cc_final: 0.7314 (m-10) REVERT: B 302 TRP cc_start: 0.7996 (t60) cc_final: 0.7655 (t60) REVERT: C 255 TRP cc_start: 0.8073 (m-10) cc_final: 0.7462 (m-10) REVERT: D 80 LEU cc_start: 0.8622 (tp) cc_final: 0.8399 (tp) REVERT: D 255 TRP cc_start: 0.8072 (m-10) cc_final: 0.7500 (m-10) REVERT: D 277 LEU cc_start: 0.9028 (tp) cc_final: 0.8787 (tp) REVERT: E 255 TRP cc_start: 0.8029 (m-10) cc_final: 0.7476 (m-10) REVERT: E 302 TRP cc_start: 0.8033 (t60) cc_final: 0.7777 (t60) outliers start: 5 outliers final: 0 residues processed: 300 average time/residue: 0.2636 time to fit residues: 110.0748 Evaluate side-chains 157 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE 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 E 83 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13060 Z= 0.241 Angle : 0.695 8.816 17935 Z= 0.348 Chirality : 0.044 0.169 2120 Planarity : 0.004 0.051 2235 Dihedral : 8.034 51.877 2337 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.84 % Allowed : 7.16 % Favored : 90.00 % 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: -0.58 (0.20), residues: 1665 helix: 0.95 (0.21), residues: 575 sheet: -0.28 (0.23), residues: 410 loop : -1.61 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 259 HIS 0.002 0.001 HIS A 231 PHE 0.029 0.002 PHE E 115 TYR 0.020 0.002 TYR B 144 ARG 0.007 0.001 ARG E 147 *********************** 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 217 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TYR cc_start: 0.7270 (m-80) cc_final: 0.7004 (m-80) REVERT: A 255 TRP cc_start: 0.8097 (m-10) cc_final: 0.7783 (m-10) REVERT: A 274 THR cc_start: 0.8572 (m) cc_final: 0.7890 (t) REVERT: B 239 TYR cc_start: 0.7273 (m-80) cc_final: 0.7041 (m-80) REVERT: B 255 TRP cc_start: 0.8117 (m-10) cc_final: 0.7672 (m-10) REVERT: B 302 TRP cc_start: 0.7859 (t60) cc_final: 0.7410 (t60) REVERT: B 311 PHE cc_start: 0.8156 (t80) cc_final: 0.7789 (t80) REVERT: C 239 TYR cc_start: 0.7365 (m-80) cc_final: 0.6958 (m-80) REVERT: C 255 TRP cc_start: 0.8075 (m-10) cc_final: 0.7615 (m-10) REVERT: D 255 TRP cc_start: 0.8079 (m-10) cc_final: 0.7682 (m-10) REVERT: E 72 MET cc_start: 0.7050 (mmm) cc_final: 0.6733 (tpp) REVERT: E 255 TRP cc_start: 0.8043 (m-10) cc_final: 0.7621 (m-10) outliers start: 33 outliers final: 24 residues processed: 207 average time/residue: 0.2247 time to fit residues: 70.6649 Evaluate side-chains 173 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13060 Z= 0.301 Angle : 0.689 9.108 17935 Z= 0.351 Chirality : 0.044 0.162 2120 Planarity : 0.004 0.037 2235 Dihedral : 7.013 51.363 2335 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.88 % Allowed : 9.57 % Favored : 86.55 % 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: -0.38 (0.20), residues: 1665 helix: 1.35 (0.20), residues: 585 sheet: -0.52 (0.25), residues: 410 loop : -1.51 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 302 HIS 0.004 0.002 HIS E 231 PHE 0.016 0.002 PHE A 311 TYR 0.021 0.002 TYR B 144 ARG 0.004 0.001 ARG D 229 *********************** 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 202 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 157 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.7630 (tpp) cc_final: 0.7121 (tpp) REVERT: A 239 TYR cc_start: 0.7344 (m-80) cc_final: 0.7103 (m-80) REVERT: A 255 TRP cc_start: 0.8093 (m-10) cc_final: 0.7705 (m-10) REVERT: B 132 LYS cc_start: 0.8223 (mptt) cc_final: 0.7797 (mmtt) REVERT: B 255 TRP cc_start: 0.8132 (m-10) cc_final: 0.7840 (m-10) REVERT: B 302 TRP cc_start: 0.7866 (t60) cc_final: 0.7419 (t60) REVERT: C 255 TRP cc_start: 0.8140 (m-10) cc_final: 0.7791 (m-10) REVERT: D 255 TRP cc_start: 0.8173 (m-10) cc_final: 0.7829 (m-10) REVERT: E 255 TRP cc_start: 0.8101 (m-10) cc_final: 0.7711 (m-10) outliers start: 45 outliers final: 29 residues processed: 191 average time/residue: 0.2315 time to fit residues: 66.2487 Evaluate side-chains 168 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13060 Z= 0.250 Angle : 0.658 9.357 17935 Z= 0.326 Chirality : 0.043 0.150 2120 Planarity : 0.004 0.030 2235 Dihedral : 6.526 51.371 2335 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.53 % Allowed : 11.90 % Favored : 84.57 % 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: -0.19 (0.21), residues: 1665 helix: 1.77 (0.20), residues: 585 sheet: -0.75 (0.24), residues: 410 loop : -1.41 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP E 302 HIS 0.003 0.001 HIS B 217 PHE 0.018 0.002 PHE E 115 TYR 0.019 0.002 TYR D 295 ARG 0.004 0.001 ARG D 229 *********************** 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 185 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 1.515 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.7523 (tpp) cc_final: 0.7038 (tpp) REVERT: A 255 TRP cc_start: 0.8094 (m-10) cc_final: 0.7700 (m-10) REVERT: B 132 LYS cc_start: 0.8306 (mptt) cc_final: 0.7831 (mmtt) REVERT: B 252 ILE cc_start: 0.9244 (mm) cc_final: 0.8973 (mm) REVERT: B 255 TRP cc_start: 0.8144 (m-10) cc_final: 0.7937 (m-10) REVERT: C 255 TRP cc_start: 0.8151 (m-10) cc_final: 0.7816 (m-10) REVERT: D 255 TRP cc_start: 0.8253 (m-10) cc_final: 0.7913 (m-10) REVERT: E 132 LYS cc_start: 0.8226 (mmtm) cc_final: 0.7819 (mmtp) REVERT: E 252 ILE cc_start: 0.9247 (mm) cc_final: 0.8943 (mm) outliers start: 41 outliers final: 32 residues processed: 171 average time/residue: 0.2035 time to fit residues: 53.7470 Evaluate side-chains 169 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 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 123 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13060 Z= 0.343 Angle : 0.702 7.632 17935 Z= 0.357 Chirality : 0.044 0.190 2120 Planarity : 0.005 0.037 2235 Dihedral : 6.679 51.764 2335 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.22 % Allowed : 13.53 % Favored : 82.24 % 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: -0.47 (0.20), residues: 1665 helix: 1.55 (0.20), residues: 585 sheet: -1.02 (0.24), residues: 430 loop : -1.50 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 302 HIS 0.006 0.002 HIS B 217 PHE 0.021 0.002 PHE A 175 TYR 0.018 0.003 TYR A 144 ARG 0.004 0.001 ARG A 234 *********************** 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 191 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 142 time to evaluate : 1.399 Fit side-chains REVERT: A 255 TRP cc_start: 0.8175 (m-10) cc_final: 0.7787 (m-10) REVERT: B 132 LYS cc_start: 0.8297 (mptt) cc_final: 0.7862 (mptt) REVERT: B 255 TRP cc_start: 0.8156 (m-10) cc_final: 0.7806 (m-10) REVERT: C 132 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7857 (mmtp) REVERT: C 230 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6920 (m-80) REVERT: C 255 TRP cc_start: 0.8108 (m-10) cc_final: 0.7783 (m-10) REVERT: D 255 TRP cc_start: 0.8276 (m-10) cc_final: 0.7990 (m-10) REVERT: E 132 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7747 (mmtp) REVERT: E 290 LEU cc_start: 0.8199 (tp) cc_final: 0.7927 (pp) REVERT: E 296 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.7990 (p) outliers start: 49 outliers final: 33 residues processed: 181 average time/residue: 0.1960 time to fit residues: 55.4736 Evaluate side-chains 165 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 0.0070 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 overall best weight: 3.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 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** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 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: 0.7569 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13060 Z= 0.254 Angle : 0.655 9.754 17935 Z= 0.326 Chirality : 0.043 0.142 2120 Planarity : 0.004 0.035 2235 Dihedral : 6.376 52.327 2335 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.79 % Allowed : 14.40 % Favored : 81.81 % 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: -0.26 (0.21), residues: 1665 helix: 1.79 (0.20), residues: 590 sheet: -1.05 (0.23), residues: 460 loop : -1.35 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 302 HIS 0.004 0.001 HIS C 217 PHE 0.012 0.002 PHE D 124 TYR 0.013 0.002 TYR E 357 ARG 0.003 0.001 ARG D 229 *********************** 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 182 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 138 time to evaluate : 1.570 Fit side-chains REVERT: A 255 TRP cc_start: 0.8126 (m-10) cc_final: 0.7743 (m-10) REVERT: B 132 LYS cc_start: 0.8363 (mptt) cc_final: 0.7716 (mmtp) REVERT: B 296 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7888 (p) REVERT: C 132 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7774 (mmtp) REVERT: C 230 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: C 255 TRP cc_start: 0.8096 (m-10) cc_final: 0.7752 (m-10) REVERT: E 72 MET cc_start: 0.7866 (tpt) cc_final: 0.7643 (tpp) REVERT: E 132 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7616 (mmtp) REVERT: E 290 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7818 (pp) outliers start: 44 outliers final: 34 residues processed: 174 average time/residue: 0.1966 time to fit residues: 53.8015 Evaluate side-chains 167 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 0.0870 chunk 98 optimal weight: 8.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 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** ** C 118 ASN ** 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 ** 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: 0.7540 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13060 Z= 0.184 Angle : 0.644 14.271 17935 Z= 0.308 Chirality : 0.042 0.140 2120 Planarity : 0.003 0.033 2235 Dihedral : 6.002 52.347 2335 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.02 % Allowed : 15.26 % Favored : 81.72 % 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: 0.01 (0.21), residues: 1665 helix: 2.22 (0.21), residues: 590 sheet: -1.10 (0.23), residues: 440 loop : -1.27 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP E 302 HIS 0.003 0.001 HIS B 217 PHE 0.014 0.001 PHE D 230 TYR 0.016 0.002 TYR E 144 ARG 0.002 0.000 ARG D 229 *********************** 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 184 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.469 Fit side-chains REVERT: A 118 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7249 (p0) REVERT: A 255 TRP cc_start: 0.8100 (m-10) cc_final: 0.7639 (m-10) REVERT: B 132 LYS cc_start: 0.8366 (mptt) cc_final: 0.7688 (mmtp) REVERT: C 132 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7733 (mmtp) REVERT: C 255 TRP cc_start: 0.8080 (m-10) cc_final: 0.7700 (m-10) REVERT: C 303 MET cc_start: 0.7885 (mmm) cc_final: 0.7532 (mmt) REVERT: D 255 TRP cc_start: 0.8216 (m-10) cc_final: 0.7622 (m-10) REVERT: E 132 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7620 (mmtp) REVERT: E 274 THR cc_start: 0.8387 (p) cc_final: 0.8042 (t) outliers start: 35 outliers final: 30 residues processed: 174 average time/residue: 0.2003 time to fit residues: 54.3813 Evaluate side-chains 174 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 108 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 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** ** C 118 ASN ** 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: 0.7552 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13060 Z= 0.221 Angle : 0.666 11.453 17935 Z= 0.319 Chirality : 0.042 0.192 2120 Planarity : 0.004 0.039 2235 Dihedral : 5.982 52.581 2335 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.45 % Allowed : 16.81 % Favored : 79.74 % 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: 0.11 (0.21), residues: 1665 helix: 2.18 (0.20), residues: 590 sheet: -0.88 (0.23), residues: 450 loop : -1.22 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 302 HIS 0.003 0.001 HIS A 217 PHE 0.014 0.001 PHE D 230 TYR 0.014 0.002 TYR E 244 ARG 0.003 0.000 ARG C 234 *********************** 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 182 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 1.478 Fit side-chains REVERT: A 118 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7240 (p0) REVERT: A 255 TRP cc_start: 0.8117 (m-10) cc_final: 0.7744 (m-10) REVERT: A 274 THR cc_start: 0.8376 (p) cc_final: 0.8175 (t) REVERT: A 303 MET cc_start: 0.8049 (mmm) cc_final: 0.7791 (mmm) REVERT: B 132 LYS cc_start: 0.8373 (mptt) cc_final: 0.7702 (mmtp) REVERT: B 296 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7874 (p) REVERT: C 132 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7733 (mmtp) REVERT: C 230 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6919 (m-80) REVERT: C 255 TRP cc_start: 0.8041 (m-10) cc_final: 0.7655 (m-10) REVERT: D 72 MET cc_start: 0.7654 (tpp) cc_final: 0.7111 (tpp) REVERT: D 255 TRP cc_start: 0.8265 (m-10) cc_final: 0.7711 (m-10) REVERT: E 132 LYS cc_start: 0.8055 (mmtm) cc_final: 0.7628 (mmtp) REVERT: E 296 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.7979 (p) outliers start: 40 outliers final: 30 residues processed: 172 average time/residue: 0.1948 time to fit residues: 52.2201 Evaluate side-chains 172 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 9.9990 chunk 139 optimal weight: 0.0040 chunk 148 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 overall best weight: 4.6000 ------------------------------------------------------------------------------- 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 202 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** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 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: 0.7593 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13060 Z= 0.319 Angle : 0.724 12.807 17935 Z= 0.354 Chirality : 0.043 0.157 2120 Planarity : 0.005 0.049 2235 Dihedral : 6.362 53.730 2335 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.19 % Allowed : 17.16 % Favored : 79.66 % 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: -0.27 (0.21), residues: 1665 helix: 1.75 (0.20), residues: 595 sheet: -1.00 (0.24), residues: 420 loop : -1.41 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 255 HIS 0.006 0.002 HIS B 217 PHE 0.016 0.002 PHE D 230 TYR 0.016 0.002 TYR A 357 ARG 0.006 0.001 ARG C 234 *********************** 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 175 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 1.403 Fit side-chains REVERT: A 118 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7483 (p0) REVERT: A 255 TRP cc_start: 0.8144 (m-10) cc_final: 0.7821 (m-10) REVERT: B 132 LYS cc_start: 0.8366 (mptt) cc_final: 0.7720 (mmtp) REVERT: B 296 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7881 (p) REVERT: C 132 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7840 (mmtp) REVERT: C 230 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6997 (m-80) REVERT: C 255 TRP cc_start: 0.8124 (m-10) cc_final: 0.7717 (m-10) REVERT: D 72 MET cc_start: 0.7593 (tpp) cc_final: 0.7282 (tpp) REVERT: D 255 TRP cc_start: 0.8304 (m-10) cc_final: 0.7813 (m-10) REVERT: E 72 MET cc_start: 0.7724 (tpt) cc_final: 0.7053 (tpp) REVERT: E 132 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7567 (mmtp) REVERT: E 156 MET cc_start: 0.7300 (mpp) cc_final: 0.6461 (mpp) REVERT: E 255 TRP cc_start: 0.8197 (m-10) cc_final: 0.7732 (m-10) REVERT: E 276 VAL cc_start: 0.9203 (t) cc_final: 0.8950 (p) REVERT: E 296 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7919 (p) outliers start: 37 outliers final: 29 residues processed: 167 average time/residue: 0.2042 time to fit residues: 52.5414 Evaluate side-chains 169 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 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** ** C 118 ASN ** 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: 0.7556 moved from start: 0.4924 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= 0.207 Angle : 0.685 13.846 17935 Z= 0.322 Chirality : 0.043 0.162 2120 Planarity : 0.003 0.048 2235 Dihedral : 6.046 53.008 2335 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.84 % Allowed : 17.84 % Favored : 79.31 % 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: 0.07 (0.21), residues: 1665 helix: 2.23 (0.20), residues: 590 sheet: -0.97 (0.23), residues: 450 loop : -1.26 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 255 HIS 0.003 0.001 HIS B 217 PHE 0.014 0.001 PHE D 230 TYR 0.011 0.002 TYR E 144 ARG 0.006 0.000 ARG E 234 ********************** 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 173 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.396 Fit side-chains REVERT: A 118 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7223 (p0) REVERT: A 255 TRP cc_start: 0.8063 (m-10) cc_final: 0.7723 (m-10) REVERT: A 303 MET cc_start: 0.8018 (mmm) cc_final: 0.7813 (mmm) REVERT: B 132 LYS cc_start: 0.8361 (mptt) cc_final: 0.7693 (mmtp) REVERT: B 296 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7908 (p) REVERT: C 132 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7714 (mmtp) REVERT: C 230 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: C 255 TRP cc_start: 0.8048 (m-10) cc_final: 0.7603 (m-10) REVERT: D 255 TRP cc_start: 0.8270 (m-10) cc_final: 0.7755 (m-10) REVERT: E 72 MET cc_start: 0.7746 (tpt) cc_final: 0.7117 (tpp) REVERT: E 132 LYS cc_start: 0.8001 (mmtm) cc_final: 0.7546 (mmtp) REVERT: E 156 MET cc_start: 0.7182 (mpp) cc_final: 0.6498 (mpp) REVERT: E 255 TRP cc_start: 0.8216 (m-10) cc_final: 0.7720 (m-10) REVERT: E 276 VAL cc_start: 0.9174 (t) cc_final: 0.8905 (p) REVERT: E 296 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7843 (p) REVERT: E 302 TRP cc_start: 0.8224 (t-100) cc_final: 0.7847 (t-100) outliers start: 33 outliers final: 28 residues processed: 167 average time/residue: 0.2019 time to fit residues: 51.8295 Evaluate side-chains 168 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 296 VAL 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: 6.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 54 optimal weight: 0.3980 chunk 134 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 24 optimal weight: 0.0270 chunk 115 optimal weight: 4.9990 overall best weight: 2.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 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** ** C 118 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.040544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.034107 restraints weight = 99248.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.034936 restraints weight = 63648.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.035307 restraints weight = 45822.357| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13060 Z= 0.235 Angle : 0.688 13.444 17935 Z= 0.327 Chirality : 0.043 0.158 2120 Planarity : 0.004 0.049 2235 Dihedral : 6.074 53.708 2335 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.36 % Allowed : 17.50 % Favored : 79.14 % 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: 1665 helix: 2.14 (0.20), residues: 595 sheet: -0.99 (0.24), residues: 420 loop : -1.25 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 255 HIS 0.004 0.001 HIS B 217 PHE 0.014 0.002 PHE D 230 TYR 0.013 0.002 TYR D 357 ARG 0.005 0.001 ARG E 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2251.27 seconds wall clock time: 41 minutes 53.81 seconds (2513.81 seconds total)