Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 06:38:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2023/8f7r_28908_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2023/8f7r_28908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2023/8f7r_28908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2023/8f7r_28908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2023/8f7r_28908_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2023/8f7r_28908_updated.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 98 5.16 5 C 7615 2.51 5 N 1900 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 97": "NH1" <-> "NH2" Residue "R ARG 181": "NH1" <-> "NH2" Residue "R ARG 213": "NH1" <-> "NH2" Residue "R ARG 260": "NH1" <-> "NH2" Residue "R ARG 265": "NH1" <-> "NH2" Residue "R ARG 275": "NH1" <-> "NH2" Residue "R ARG 278": "NH1" <-> "NH2" Residue "R ARG 282": "NH1" <-> "NH2" Residue "R ARG 347": "NH1" <-> "NH2" Residue "R ARG 350": "NH1" <-> "NH2" Residue "P PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M ARG 213": "NH1" <-> "NH2" Residue "M ARG 260": "NH1" <-> "NH2" Residue "M ARG 265": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M ARG 282": "NH1" <-> "NH2" Residue "M ARG 347": "NH1" <-> "NH2" Residue "M ARG 350": "NH1" <-> "NH2" Residue "Q PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11697 Number of models: 1 Model: "" Number of chains: 11 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PCIS': 1, 'TRANS': 2} Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2567 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain: "C" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 428 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PCIS': 1, 'TRANS': 2} Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 130 Classifications: {'peptide': 17} Modifications used: {'COO': 1} Link IDs: {'TRANS': 16} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.67, per 1000 atoms: 0.57 Number of scatterers: 11697 At special positions: 0 Unit cell: (104.8, 108, 147.2, 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 98 16.00 O 2084 8.00 N 1900 7.00 C 7615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " distance=2.03 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: 4.68 Conformation dependent library (CDL) restraints added in 1.8 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 16 sheets defined 44.6% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'R' and resid 69 through 97 Processing helix chain 'R' and resid 104 through 121 Processing helix chain 'R' and resid 123 through 132 Processing helix chain 'R' and resid 139 through 172 removed outlier: 3.852A pdb=" N PHE R 154 " --> pdb=" O TYR R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.889A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 207 removed outlier: 3.512A pdb=" N ALA R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 227 through 263 removed outlier: 5.538A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 271 through 307 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 314 through 338 removed outlier: 4.041A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 343 through 351 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.895A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 216 removed outlier: 4.706A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.524A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.753A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'M' and resid 69 through 97 Processing helix chain 'M' and resid 104 through 121 Processing helix chain 'M' and resid 123 through 132 Processing helix chain 'M' and resid 139 through 172 removed outlier: 3.851A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 180 removed outlier: 3.890A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 207 removed outlier: 3.512A pdb=" N ALA M 199 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 227 through 263 removed outlier: 5.538A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 271 through 307 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 314 through 338 removed outlier: 4.041A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 343 through 351 Processing helix chain 'F' and resid 339 through 351 Processing sheet with id= A, first strand: chain 'R' and resid 208 through 213 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.847A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.876A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.680A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.799A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.991A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.655A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.613A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.657A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.586A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.805A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER E 120 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 93 through 99 removed outlier: 3.527A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 147 through 149 removed outlier: 7.082A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 156 through 160 Processing sheet with id= O, first strand: chain 'E' and resid 227 through 232 removed outlier: 3.505A pdb=" N ILE E 190 " --> pdb=" O TRP E 177 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'M' and resid 208 through 213 598 hydrogen bonds defined for protein. 1746 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: 3.35 Time building geometry restraints manager: 5.06 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: 3511 1.34 - 1.46: 2327 1.46 - 1.58: 5996 1.58 - 1.70: 0 1.70 - 1.82: 145 Bond restraints: 11979 Sorted by residual: bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.34e+00 bond pdb=" C5 CLR R 404 " pdb=" C6 CLR R 404 " ideal model delta sigma weight residual 1.332 1.296 0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" C5 CLR M 405 " pdb=" C6 CLR M 405 " ideal model delta sigma weight residual 1.332 1.296 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C THR M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" C10 CLR M 401 " pdb=" C9 CLR M 401 " ideal model delta sigma weight residual 1.551 1.518 0.033 2.00e-02 2.50e+03 2.64e+00 ... (remaining 11974 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.22: 308 106.22 - 113.18: 6678 113.18 - 120.14: 4172 120.14 - 127.10: 5019 127.10 - 134.06: 126 Bond angle restraints: 16303 Sorted by residual: angle pdb=" N PRO A 288 " pdb=" CA PRO A 288 " pdb=" CB PRO A 288 " ideal model delta sigma weight residual 103.44 109.80 -6.36 1.12e+00 7.97e-01 3.22e+01 angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 131.25 -9.71 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" CA PHE P 4 " pdb=" CB PHE P 4 " pdb=" CG PHE P 4 " ideal model delta sigma weight residual 113.80 116.70 -2.90 1.00e+00 1.00e+00 8.39e+00 angle pdb=" CA PHE Q 4 " pdb=" CB PHE Q 4 " pdb=" CG PHE Q 4 " ideal model delta sigma weight residual 113.80 116.68 -2.88 1.00e+00 1.00e+00 8.29e+00 ... (remaining 16298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.61: 6227 9.61 - 19.23: 660 19.23 - 28.84: 72 28.84 - 38.45: 33 38.45 - 48.06: 7 Dihedral angle restraints: 6999 sinusoidal: 2780 harmonic: 4219 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA HIS B 266 " pdb=" C HIS B 266 " pdb=" N ASP B 267 " pdb=" CA ASP B 267 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 6996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1706 0.092 - 0.183: 162 0.183 - 0.275: 15 0.275 - 0.367: 11 0.367 - 0.459: 9 Chirality restraints: 1903 Sorted by residual: chirality pdb=" C14 CLR M 401 " pdb=" C13 CLR M 401 " pdb=" C15 CLR M 401 " pdb=" C8 CLR M 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C14 CLR R 405 " pdb=" C13 CLR R 405 " pdb=" C15 CLR R 405 " pdb=" C8 CLR R 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1900 not shown) Planarity restraints: 1964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO B 236 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 334 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO R 335 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 335 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 335 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 334 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO M 335 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO M 335 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO M 335 " 0.029 5.00e-02 4.00e+02 ... (remaining 1961 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2369 2.79 - 3.32: 10403 3.32 - 3.84: 19441 3.84 - 4.37: 21903 4.37 - 4.90: 39180 Nonbonded interactions: 93296 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.260 2.440 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.260 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.261 2.440 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.282 2.440 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.329 2.440 ... (remaining 93291 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 'M' selection = chain 'R' } ncs_group { reference = chain 'P' selection = chain 'Q' } 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: 1.940 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: 0.020 Extract box with map and model: 6.990 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 32.170 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 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 : 0.004 0.049 11979 Z= 0.282 Angle : 0.839 9.710 16303 Z= 0.443 Chirality : 0.065 0.459 1903 Planarity : 0.006 0.064 1964 Dihedral : 7.821 43.643 4262 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -0.71 (0.19), residues: 1421 helix: 0.10 (0.16), residues: 653 sheet: 0.12 (0.31), residues: 276 loop : -1.47 (0.24), residues: 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2736 time to fit residues: 108.5786 Evaluate side-chains 188 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 7.9990 chunk 106 optimal weight: 0.0370 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.0670 chunk 127 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN A 188 HIS B 88 ASN B 91 HIS B 183 HIS B 266 HIS C 44 HIS E 168 HIS E 184 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 321 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 11979 Z= 0.154 Angle : 0.494 5.456 16303 Z= 0.257 Chirality : 0.039 0.139 1903 Planarity : 0.004 0.051 1964 Dihedral : 4.334 38.452 1655 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 0.81 (0.21), residues: 1421 helix: 1.77 (0.18), residues: 657 sheet: 0.23 (0.31), residues: 277 loop : -0.96 (0.25), residues: 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 216 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 229 average time/residue: 0.2770 time to fit residues: 88.1487 Evaluate side-chains 197 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 1.355 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1061 time to fit residues: 3.5499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 321 HIS R 334 ASN A 188 HIS B 230 ASN E 82 GLN M 173 HIS ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 11979 Z= 0.280 Angle : 0.583 6.388 16303 Z= 0.301 Chirality : 0.041 0.145 1903 Planarity : 0.004 0.047 1964 Dihedral : 4.625 26.525 1655 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.08 (0.22), residues: 1421 helix: 1.91 (0.19), residues: 658 sheet: 0.43 (0.32), residues: 286 loop : -0.77 (0.26), residues: 477 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 221 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 231 average time/residue: 0.2771 time to fit residues: 88.8756 Evaluate side-chains 188 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1027 time to fit residues: 3.6877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 135 optimal weight: 0.2980 chunk 121 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 176 GLN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 ASN M 299 HIS M 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 11979 Z= 0.167 Angle : 0.488 7.685 16303 Z= 0.250 Chirality : 0.039 0.135 1903 Planarity : 0.003 0.043 1964 Dihedral : 4.396 34.233 1655 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.45 (0.22), residues: 1421 helix: 2.29 (0.19), residues: 654 sheet: 0.43 (0.32), residues: 289 loop : -0.56 (0.27), residues: 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 194 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 208 average time/residue: 0.2825 time to fit residues: 81.5733 Evaluate side-chains 192 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1104 time to fit residues: 5.0977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 299 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 11979 Z= 0.251 Angle : 0.541 5.945 16303 Z= 0.278 Chirality : 0.040 0.135 1903 Planarity : 0.004 0.052 1964 Dihedral : 4.714 31.623 1655 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.29 (0.22), residues: 1421 helix: 2.20 (0.20), residues: 646 sheet: 0.23 (0.31), residues: 282 loop : -0.57 (0.27), residues: 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 192 average time/residue: 0.2863 time to fit residues: 75.9032 Evaluate side-chains 178 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1191 time to fit residues: 4.1160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 75 GLN B 259 GLN E 168 HIS ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 334 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 11979 Z= 0.241 Angle : 0.528 6.761 16303 Z= 0.270 Chirality : 0.040 0.136 1903 Planarity : 0.004 0.040 1964 Dihedral : 4.732 32.527 1655 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.31 (0.22), residues: 1421 helix: 2.20 (0.20), residues: 646 sheet: 0.27 (0.31), residues: 283 loop : -0.54 (0.27), residues: 492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 192 average time/residue: 0.2759 time to fit residues: 73.7462 Evaluate side-chains 176 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1565 time to fit residues: 3.7392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 0.0870 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 82 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN E 39 GLN E 168 HIS E 180 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 334 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.063 11979 Z= 0.161 Angle : 0.478 6.265 16303 Z= 0.247 Chirality : 0.038 0.143 1903 Planarity : 0.003 0.039 1964 Dihedral : 4.528 40.249 1655 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.49 (0.22), residues: 1421 helix: 2.42 (0.20), residues: 646 sheet: 0.24 (0.30), residues: 286 loop : -0.48 (0.28), residues: 489 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 187 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 196 average time/residue: 0.2729 time to fit residues: 75.0462 Evaluate side-chains 179 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1107 time to fit residues: 3.1155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 0.0770 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 75 GLN E 39 GLN E 82 GLN E 168 HIS ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 11979 Z= 0.248 Angle : 0.537 6.140 16303 Z= 0.278 Chirality : 0.041 0.339 1903 Planarity : 0.004 0.046 1964 Dihedral : 4.821 43.569 1655 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.37 (0.22), residues: 1421 helix: 2.27 (0.20), residues: 645 sheet: 0.33 (0.30), residues: 281 loop : -0.55 (0.27), residues: 495 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 1.415 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 182 average time/residue: 0.2792 time to fit residues: 71.0194 Evaluate side-chains 178 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1625 time to fit residues: 3.9903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 113 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN E 39 GLN E 168 HIS ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11979 Z= 0.177 Angle : 0.497 6.778 16303 Z= 0.257 Chirality : 0.039 0.279 1903 Planarity : 0.004 0.043 1964 Dihedral : 4.674 44.116 1655 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.41 (0.22), residues: 1421 helix: 2.30 (0.20), residues: 652 sheet: 0.23 (0.30), residues: 286 loop : -0.49 (0.28), residues: 483 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 178 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 181 average time/residue: 0.2809 time to fit residues: 70.9727 Evaluate side-chains 177 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1307 time to fit residues: 2.9656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 0.0050 chunk 92 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 306 GLN B 75 GLN B 259 GLN E 82 GLN E 168 HIS ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 11979 Z= 0.240 Angle : 0.533 7.088 16303 Z= 0.275 Chirality : 0.040 0.293 1903 Planarity : 0.004 0.043 1964 Dihedral : 4.870 44.496 1655 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.29 (0.22), residues: 1421 helix: 2.17 (0.20), residues: 651 sheet: 0.14 (0.30), residues: 286 loop : -0.48 (0.28), residues: 484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 174 average time/residue: 0.2952 time to fit residues: 70.6065 Evaluate side-chains 170 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1081 time to fit residues: 2.3442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.0270 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 75 GLN B 259 GLN E 168 HIS ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 334 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.181863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147340 restraints weight = 13249.040| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.93 r_work: 0.3631 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 11979 Z= 0.160 Angle : 0.496 7.243 16303 Z= 0.256 Chirality : 0.039 0.228 1903 Planarity : 0.003 0.041 1964 Dihedral : 4.670 45.080 1655 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.41 (0.22), residues: 1421 helix: 2.31 (0.20), residues: 652 sheet: 0.13 (0.30), residues: 288 loop : -0.45 (0.28), residues: 481 =============================================================================== Job complete usr+sys time: 2706.25 seconds wall clock time: 49 minutes 56.12 seconds (2996.12 seconds total)