Starting phenix.real_space_refine on Wed Feb 14 18:45:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/02_2024/7jr9_22444.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/02_2024/7jr9_22444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/02_2024/7jr9_22444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/02_2024/7jr9_22444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/02_2024/7jr9_22444.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/02_2024/7jr9_22444.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 37 5.16 5 C 6391 2.51 5 N 1706 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 205": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10021 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1970 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Chain: "B" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1946 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 1 Chain: "C" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2110 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 22, 'TRANS': 257} Chain breaks: 3 Chain: "D" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2574 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 301} Chain breaks: 2 Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1351 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.69, per 1000 atoms: 0.57 Number of scatterers: 10021 At special positions: 0 Unit cell: (88.92, 97.47, 164.16, 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 37 16.00 O 1887 8.00 N 1706 7.00 C 6391 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 155 " distance=2.02 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 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 18 sheets defined 23.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.755A pdb=" N HIS A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.531A pdb=" N GLN A 213 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 23 through 42 removed outlier: 3.567A pdb=" N ALA B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Proline residue: B 35 - end of helix Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.995A pdb=" N THR B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.913A pdb=" N ASN C 214 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 245 removed outlier: 3.647A pdb=" N ARG C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 283 removed outlier: 3.542A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 315 removed outlier: 4.006A pdb=" N ALA C 315 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 125 through 142 Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 246 through 263 removed outlier: 3.711A pdb=" N VAL D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.631A pdb=" N GLU D 292 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.686A pdb=" N ASP D 349 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 85 removed outlier: 3.536A pdb=" N GLU A 79 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 68 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 81 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TYR A 66 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 83 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU A 64 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER A 85 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL A 62 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU A 64 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 48 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TYR A 66 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A 46 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 16.418A pdb=" N TRP A 251 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N THR A 47 " --> pdb=" O TRP A 251 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N SER A 253 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TRP A 49 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR A 240 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 93 removed outlier: 5.798A pdb=" N ALA B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER B 71 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 77 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA B 69 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU B 79 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN B 67 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLU B 64 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU B 48 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TYR B 66 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU B 46 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 16.010A pdb=" N TRP B 251 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N THR B 47 " --> pdb=" O TRP B 251 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N SER B 253 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TRP B 49 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR B 240 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 229 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 123 Processing sheet with id=AA7, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AA8, first strand: chain 'B' and resid 172 through 174 Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 230 removed outlier: 6.458A pdb=" N TYR C 167 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS C 159 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 169 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N ARG C 155 " --> pdb=" O CYS C 414 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N TYR C 416 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE C 157 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY C 418 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LYS C 159 " --> pdb=" O GLY C 418 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA C 403 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AB2, first strand: chain 'C' and resid 290 through 292 Processing sheet with id=AB3, first strand: chain 'D' and resid 209 through 210 removed outlier: 6.515A pdb=" N TYR D 163 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS D 155 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL D 165 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR D 149 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 21.775A pdb=" N PHE D 400 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N THR D 149 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 14.927A pdb=" N SER D 402 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N ARG D 151 " --> pdb=" O SER D 402 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N TYR D 404 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE D 153 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY D 406 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS D 155 " --> pdb=" O GLY D 406 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 264 through 266 Processing sheet with id=AB5, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AB6, first strand: chain 'D' and resid 365 through 369 Processing sheet with id=AB7, first strand: chain 'G' and resid -3 through -1 removed outlier: 3.560A pdb=" N UNK G -3 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 29 " --> pdb=" O UNK G -3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 53 removed outlier: 5.893A pdb=" N THR E 51 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR E 58 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS E 84 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL E 77 " --> pdb=" O HIS E 82 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS E 82 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY E 97 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN E 107 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS E 130 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP E 123 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS E 128 " --> pdb=" O TRP E 123 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN E 141 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP E 156 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL E 143 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY E 154 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP E 145 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR E 152 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR E 178 " --> pdb=" O PHE E 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 50 through 53 removed outlier: 5.893A pdb=" N THR E 51 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR E 58 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS E 84 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL E 77 " --> pdb=" O HIS E 82 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS E 82 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY E 97 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN E 107 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS E 130 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP E 123 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS E 128 " --> pdb=" O TRP E 123 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN E 141 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP E 156 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL E 143 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY E 154 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP E 145 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR E 152 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR E 178 " --> pdb=" O PHE E 195 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 3.79 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: 3191 1.34 - 1.45: 1777 1.45 - 1.57: 5256 1.57 - 1.69: 0 1.69 - 1.80: 56 Bond restraints: 10280 Sorted by residual: bond pdb=" C ALA D 294 " pdb=" N LEU D 295 " ideal model delta sigma weight residual 1.332 1.289 0.042 1.92e-02 2.71e+03 4.89e+00 bond pdb=" CA GLY D 121 " pdb=" C GLY D 121 " ideal model delta sigma weight residual 1.514 1.489 0.025 1.41e-02 5.03e+03 3.25e+00 bond pdb=" CG LEU D 134 " pdb=" CD1 LEU D 134 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB ARG C 396 " pdb=" CG ARG C 396 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.52e+00 bond pdb=" C THR E 111 " pdb=" N TYR E 112 " ideal model delta sigma weight residual 1.329 1.300 0.029 1.86e-02 2.89e+03 2.36e+00 ... (remaining 10275 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.37: 401 106.37 - 113.29: 5379 113.29 - 120.21: 3724 120.21 - 127.13: 4333 127.13 - 134.05: 148 Bond angle restraints: 13985 Sorted by residual: angle pdb=" C THR E 111 " pdb=" N TYR E 112 " pdb=" CA TYR E 112 " ideal model delta sigma weight residual 121.48 128.38 -6.90 2.04e+00 2.40e-01 1.14e+01 angle pdb=" C VAL B 157 " pdb=" N ASP B 158 " pdb=" CA ASP B 158 " ideal model delta sigma weight residual 121.58 115.41 6.17 1.95e+00 2.63e-01 1.00e+01 angle pdb=" CA TYR A 78 " pdb=" CB TYR A 78 " pdb=" CG TYR A 78 " ideal model delta sigma weight residual 113.90 119.52 -5.62 1.80e+00 3.09e-01 9.74e+00 angle pdb=" C GLY C 372 " pdb=" N GLU C 373 " pdb=" CA GLU C 373 " ideal model delta sigma weight residual 122.40 126.92 -4.52 1.45e+00 4.76e-01 9.73e+00 angle pdb=" C THR B 164 " pdb=" N SER B 165 " pdb=" CA SER B 165 " ideal model delta sigma weight residual 122.82 127.22 -4.40 1.42e+00 4.96e-01 9.60e+00 ... (remaining 13980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 5821 14.84 - 29.68: 186 29.68 - 44.52: 24 44.52 - 59.35: 1 59.35 - 74.19: 5 Dihedral angle restraints: 6037 sinusoidal: 2309 harmonic: 3728 Sorted by residual: dihedral pdb=" CA TYR C 260 " pdb=" C TYR C 260 " pdb=" N PRO C 261 " pdb=" CA PRO C 261 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA THR D 168 " pdb=" C THR D 168 " pdb=" N THR D 169 " pdb=" CA THR D 169 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA SER A 92 " pdb=" C SER A 92 " pdb=" N ASP A 93 " pdb=" CA ASP A 93 " ideal model delta harmonic sigma weight residual 180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 6034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1073 0.052 - 0.105: 355 0.105 - 0.157: 63 0.157 - 0.210: 9 0.210 - 0.262: 3 Chirality restraints: 1503 Sorted by residual: chirality pdb=" CB VAL E 71 " pdb=" CA VAL E 71 " pdb=" CG1 VAL E 71 " pdb=" CG2 VAL E 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB VAL E 88 " pdb=" CA VAL E 88 " pdb=" CG1 VAL E 88 " pdb=" CG2 VAL E 88 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE B 8 " pdb=" CA ILE B 8 " pdb=" CG1 ILE B 8 " pdb=" CG2 ILE B 8 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1500 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 184 " -0.022 2.00e-02 2.50e+03 1.97e-02 7.76e+00 pdb=" CG TYR E 184 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR E 184 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 184 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 184 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 184 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 184 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 184 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 168 " -0.010 2.00e-02 2.50e+03 1.93e-02 6.52e+00 pdb=" CG PHE E 168 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE E 168 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE E 168 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 168 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE E 168 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 168 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 78 " -0.018 2.00e-02 2.50e+03 1.79e-02 6.42e+00 pdb=" CG TYR B 78 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 78 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 78 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 78 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 78 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 78 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 78 " 0.001 2.00e-02 2.50e+03 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1999 2.77 - 3.30: 8334 3.30 - 3.83: 16447 3.83 - 4.37: 19983 4.37 - 4.90: 34353 Nonbonded interactions: 81116 Sorted by model distance: nonbonded pdb=" OG SER C 383 " pdb=" OE1 GLN C 391 " model vdw 2.235 2.440 nonbonded pdb=" OG SER A 234 " pdb=" O PHE A 237 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR A 255 " pdb=" O ASP A 258 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THR D 230 " pdb=" OE1 GLU D 247 " model vdw 2.300 2.440 nonbonded pdb=" OG1 THR C 250 " pdb=" OE1 GLU C 267 " model vdw 2.313 2.440 ... (remaining 81111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 124 or resid 142 through 269)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 7.440 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.880 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 0.057 10280 Z= 0.513 Angle : 0.815 7.675 13985 Z= 0.459 Chirality : 0.054 0.262 1503 Planarity : 0.008 0.055 1828 Dihedral : 8.260 74.192 3664 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -2.53 (0.20), residues: 1274 helix: -2.33 (0.23), residues: 266 sheet: -1.43 (0.26), residues: 310 loop : -1.46 (0.20), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 156 HIS 0.006 0.002 HIS C 321 PHE 0.040 0.004 PHE E 168 TYR 0.048 0.004 TYR E 184 ARG 0.015 0.002 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 325 HIS cc_start: 0.7901 (p-80) cc_final: 0.7218 (t-170) REVERT: E 87 MET cc_start: 0.7786 (tpt) cc_final: 0.6798 (tpt) REVERT: E 119 GLN cc_start: 0.7860 (mt0) cc_final: 0.7575 (mt0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.5450 time to fit residues: 287.6595 Evaluate side-chains 73 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN C 80 GLN C 238 GLN C 374 GLN C 391 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10280 Z= 0.176 Angle : 0.508 8.016 13985 Z= 0.266 Chirality : 0.040 0.140 1503 Planarity : 0.005 0.040 1828 Dihedral : 4.353 16.988 1422 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.96 % Allowed : 8.51 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -1.19 (0.22), residues: 1274 helix: -0.57 (0.29), residues: 276 sheet: -0.92 (0.28), residues: 303 loop : -0.72 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 415 HIS 0.002 0.001 HIS B 200 PHE 0.012 0.001 PHE A 267 TYR 0.018 0.002 TYR B 255 ARG 0.004 0.001 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 325 HIS cc_start: 0.7912 (p-80) cc_final: 0.7269 (t-170) REVERT: C 366 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: E 87 MET cc_start: 0.7728 (tpt) cc_final: 0.6995 (tpt) outliers start: 20 outliers final: 6 residues processed: 92 average time/residue: 1.4173 time to fit residues: 139.5384 Evaluate side-chains 78 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 200 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10280 Z= 0.304 Angle : 0.547 6.621 13985 Z= 0.284 Chirality : 0.041 0.153 1503 Planarity : 0.004 0.036 1828 Dihedral : 4.353 18.883 1422 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.35 % Allowed : 9.10 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.67 (0.22), residues: 1274 helix: 0.07 (0.31), residues: 277 sheet: -0.66 (0.29), residues: 267 loop : -0.49 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 99 HIS 0.003 0.001 HIS B 200 PHE 0.012 0.002 PHE A 186 TYR 0.029 0.002 TYR D 198 ARG 0.004 0.001 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 1.176 Fit side-chains REVERT: C 325 HIS cc_start: 0.7958 (p-80) cc_final: 0.7237 (t-170) REVERT: C 366 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: E 82 HIS cc_start: 0.8714 (t70) cc_final: 0.7567 (t-90) outliers start: 24 outliers final: 9 residues processed: 86 average time/residue: 1.4726 time to fit residues: 135.5097 Evaluate side-chains 74 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 200 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10280 Z= 0.401 Angle : 0.579 6.885 13985 Z= 0.301 Chirality : 0.043 0.160 1503 Planarity : 0.005 0.045 1828 Dihedral : 4.427 19.450 1422 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.35 % Allowed : 10.37 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.43 (0.23), residues: 1274 helix: 0.14 (0.31), residues: 277 sheet: -0.29 (0.29), residues: 281 loop : -0.36 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 99 HIS 0.003 0.001 HIS D 301 PHE 0.013 0.002 PHE E 168 TYR 0.028 0.002 TYR E 184 ARG 0.006 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 67 time to evaluate : 1.177 Fit side-chains REVERT: A 90 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7588 (ptm-80) REVERT: A 213 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8597 (mp10) REVERT: C 303 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7112 (pm20) REVERT: C 325 HIS cc_start: 0.8065 (p-80) cc_final: 0.7154 (t-170) REVERT: C 366 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: D 193 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8884 (t) outliers start: 24 outliers final: 11 residues processed: 85 average time/residue: 1.5011 time to fit residues: 136.2354 Evaluate side-chains 77 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 188 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.0370 chunk 105 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.0370 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 0.4980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10280 Z= 0.119 Angle : 0.458 6.058 13985 Z= 0.236 Chirality : 0.038 0.135 1503 Planarity : 0.004 0.035 1828 Dihedral : 3.859 16.091 1422 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.57 % Allowed : 11.84 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.09 (0.23), residues: 1274 helix: 0.81 (0.32), residues: 272 sheet: -0.15 (0.29), residues: 297 loop : -0.04 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 99 HIS 0.003 0.001 HIS A 14 PHE 0.009 0.001 PHE E 122 TYR 0.010 0.001 TYR E 76 ARG 0.008 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 1.199 Fit side-chains REVERT: A 145 PHE cc_start: 0.8172 (m-80) cc_final: 0.7947 (m-80) REVERT: C 325 HIS cc_start: 0.7952 (p-80) cc_final: 0.7122 (t-170) outliers start: 16 outliers final: 7 residues processed: 82 average time/residue: 1.3937 time to fit residues: 122.6201 Evaluate side-chains 72 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 181 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10280 Z= 0.183 Angle : 0.479 5.746 13985 Z= 0.245 Chirality : 0.039 0.137 1503 Planarity : 0.004 0.032 1828 Dihedral : 3.839 17.738 1422 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.27 % Allowed : 12.52 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1274 helix: 1.03 (0.32), residues: 271 sheet: -0.12 (0.31), residues: 265 loop : 0.01 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 99 HIS 0.003 0.001 HIS A 32 PHE 0.009 0.001 PHE B 242 TYR 0.012 0.001 TYR B 255 ARG 0.006 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 145 PHE cc_start: 0.8153 (m-80) cc_final: 0.7941 (m-80) REVERT: A 147 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8647 (mm) REVERT: C 325 HIS cc_start: 0.7962 (p-80) cc_final: 0.7123 (t-170) outliers start: 13 outliers final: 8 residues processed: 74 average time/residue: 1.4149 time to fit residues: 112.3786 Evaluate side-chains 71 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 181 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10280 Z= 0.283 Angle : 0.521 6.607 13985 Z= 0.269 Chirality : 0.040 0.150 1503 Planarity : 0.004 0.037 1828 Dihedral : 4.023 18.320 1422 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.05 % Allowed : 11.74 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1274 helix: 0.80 (0.32), residues: 277 sheet: 0.03 (0.30), residues: 274 loop : -0.03 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 99 HIS 0.002 0.001 HIS E 134 PHE 0.010 0.001 PHE B 242 TYR 0.016 0.002 TYR E 184 ARG 0.006 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 90 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7548 (ptm-80) REVERT: A 145 PHE cc_start: 0.8210 (m-80) cc_final: 0.7963 (m-80) REVERT: A 147 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8712 (mm) REVERT: C 325 HIS cc_start: 0.8010 (p-80) cc_final: 0.7139 (t-170) REVERT: C 373 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7603 (mp0) outliers start: 21 outliers final: 10 residues processed: 77 average time/residue: 1.5095 time to fit residues: 124.7694 Evaluate side-chains 75 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 188 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10280 Z= 0.141 Angle : 0.463 6.938 13985 Z= 0.237 Chirality : 0.038 0.132 1503 Planarity : 0.004 0.034 1828 Dihedral : 3.770 16.954 1422 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.27 % Allowed : 12.92 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.46 (0.23), residues: 1274 helix: 1.14 (0.32), residues: 272 sheet: 0.10 (0.30), residues: 275 loop : 0.18 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 99 HIS 0.002 0.001 HIS E 134 PHE 0.008 0.001 PHE D 240 TYR 0.011 0.001 TYR E 76 ARG 0.005 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 145 PHE cc_start: 0.8156 (m-80) cc_final: 0.7923 (m-80) REVERT: C 325 HIS cc_start: 0.7941 (p-80) cc_final: 0.7116 (t-170) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 1.3626 time to fit residues: 104.3826 Evaluate side-chains 69 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 75 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10280 Z= 0.202 Angle : 0.488 7.240 13985 Z= 0.252 Chirality : 0.039 0.138 1503 Planarity : 0.004 0.034 1828 Dihedral : 3.815 17.861 1422 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.27 % Allowed : 13.11 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.40 (0.23), residues: 1274 helix: 1.16 (0.32), residues: 271 sheet: -0.01 (0.31), residues: 265 loop : 0.13 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 99 HIS 0.002 0.001 HIS E 134 PHE 0.009 0.001 PHE B 242 TYR 0.012 0.001 TYR B 255 ARG 0.005 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.117 Fit side-chains REVERT: A 145 PHE cc_start: 0.8175 (m-80) cc_final: 0.7953 (m-80) REVERT: C 325 HIS cc_start: 0.7958 (p-80) cc_final: 0.7095 (t-170) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 1.4222 time to fit residues: 106.8250 Evaluate side-chains 72 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 75 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 127 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10280 Z= 0.175 Angle : 0.473 7.497 13985 Z= 0.243 Chirality : 0.039 0.135 1503 Planarity : 0.004 0.035 1828 Dihedral : 3.752 16.994 1422 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.08 % Allowed : 13.31 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.23), residues: 1274 helix: 1.18 (0.32), residues: 272 sheet: 0.03 (0.31), residues: 265 loop : 0.21 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 99 HIS 0.002 0.001 HIS E 134 PHE 0.009 0.001 PHE B 242 TYR 0.012 0.001 TYR E 76 ARG 0.007 0.000 ARG A 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 1.312 Fit side-chains REVERT: A 90 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7462 (ptm-80) REVERT: A 145 PHE cc_start: 0.8167 (m-80) cc_final: 0.7936 (m-80) REVERT: C 325 HIS cc_start: 0.7987 (p-80) cc_final: 0.7095 (t-170) outliers start: 11 outliers final: 10 residues processed: 70 average time/residue: 1.5297 time to fit residues: 114.5459 Evaluate side-chains 73 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 75 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.0060 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.089635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.067198 restraints weight = 17216.274| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.21 r_work: 0.2698 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10280 Z= 0.140 Angle : 0.458 6.793 13985 Z= 0.234 Chirality : 0.039 0.131 1503 Planarity : 0.003 0.033 1828 Dihedral : 3.615 16.719 1422 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.08 % Allowed : 13.60 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.62 (0.24), residues: 1274 helix: 1.28 (0.33), residues: 272 sheet: 0.16 (0.30), residues: 275 loop : 0.29 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 99 HIS 0.002 0.001 HIS E 134 PHE 0.008 0.001 PHE B 242 TYR 0.010 0.001 TYR B 255 ARG 0.009 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3231.06 seconds wall clock time: 58 minutes 22.47 seconds (3502.47 seconds total)