Starting phenix.real_space_refine (version: dev) on Mon Dec 12 09:58:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/12_2022/7tyn_26188_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/12_2022/7tyn_26188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/12_2022/7tyn_26188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/12_2022/7tyn_26188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/12_2022/7tyn_26188_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/12_2022/7tyn_26188_updated.pdb" } resolution = 2.6 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 543 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "P ARG 24": "NH1" <-> "NH2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R ARG 180": "NH1" <-> "NH2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R GLU 210": "OE1" <-> "OE2" Residue "R GLU 240": "OE1" <-> "OE2" Residue "R GLU 255": "OE1" <-> "OE2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R GLU 329": "OE1" <-> "OE2" Residue "R GLU 334": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9364 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 239 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 29} Chain: "R" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2892 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 17, 'TRANS': 355} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "A" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1881 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Unusual residues: {'NAG': 2, 'P42': 1, 'PLM': 13, 'Y01': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.90, per 1000 atoms: 0.63 Number of scatterers: 9364 At special positions: 0 Unit cell: (94.1673, 158.153, 90.5455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 1 15.00 O 1694 8.00 N 1581 7.00 C 6025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.8 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 11 sheets defined 37.0% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'P' and resid 5 through 20 removed outlier: 3.613A pdb=" N VAL P 8 " --> pdb=" O SER P 5 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU P 9 " --> pdb=" O THR P 6 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY P 10 " --> pdb=" O CYS P 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER P 13 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU P 15 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU P 16 " --> pdb=" O SER P 13 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS P 18 " --> pdb=" O GLU P 15 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU P 19 " --> pdb=" O LEU P 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 61 removed outlier: 3.703A pdb=" N TYR R 56 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 172 removed outlier: 4.535A pdb=" N PHE R 137 " --> pdb=" O MET R 133 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N THR R 138 " --> pdb=" O CYS R 134 " (cutoff:3.500A) Proline residue: R 139 - end of helix Processing helix chain 'R' and resid 179 through 204 Processing helix chain 'R' and resid 209 through 214 Processing helix chain 'R' and resid 217 through 248 removed outlier: 3.543A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 266 Processing helix chain 'R' and resid 269 through 283 Proline residue: R 273 - end of helix removed outlier: 3.632A pdb=" N ILE R 276 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG R 281 " --> pdb=" O ALA R 278 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 283 " --> pdb=" O THR R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 296 through 329 removed outlier: 3.920A pdb=" N HIS R 302 " --> pdb=" O TYR R 299 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY R 303 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Proline residue: R 304 - end of helix removed outlier: 3.649A pdb=" N ALA R 307 " --> pdb=" O PRO R 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL R 311 " --> pdb=" O ALA R 308 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL R 320 " --> pdb=" O LEU R 317 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL R 322 " --> pdb=" O ILE R 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL R 324 " --> pdb=" O ARG R 321 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG R 328 " --> pdb=" O THR R 325 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU R 329 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 347 Processing helix chain 'R' and resid 349 through 352 No H-bonds generated for 'chain 'R' and resid 349 through 352' Processing helix chain 'R' and resid 354 through 358 removed outlier: 4.061A pdb=" N VAL R 358 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 366 through 381 Processing helix chain 'R' and resid 383 through 391 Processing helix chain 'R' and resid 396 through 408 removed outlier: 3.854A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.500A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.635A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 300 removed outlier: 3.575A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.757A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.668A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.530A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 89 through 94 removed outlier: 3.922A pdb=" N VAL R 89 " --> pdb=" O CYS R 112 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS R 112 " --> pdb=" O VAL R 89 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.236A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.867A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.682A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.595A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.784A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.498A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.077A 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: 6.412A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.565A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.265A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1047 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: 2.74 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1551 1.32 - 1.45: 2578 1.45 - 1.57: 5340 1.57 - 1.70: 2 1.70 - 1.82: 88 Bond restraints: 9559 Sorted by residual: bond pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" N GLY P 28 " pdb=" CA GLY P 28 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.40e-03 1.13e+04 9.31e+00 bond pdb=" N LEU R 80 " pdb=" CA LEU R 80 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.51e+00 bond pdb=" OBN P42 R 503 " pdb=" PBM P42 R 503 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.51e+00 bond pdb=" N ARG R 126 " pdb=" CA ARG R 126 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.29e-02 6.01e+03 6.27e+00 ... (remaining 9554 not shown) Histogram of bond angle deviations from ideal: 90.04 - 101.55: 28 101.55 - 113.05: 5195 113.05 - 124.56: 7486 124.56 - 136.07: 177 136.07 - 147.58: 1 Bond angle restraints: 12887 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 90.04 21.96 1.40e+00 5.10e-01 2.46e+02 angle pdb=" C THR P 31 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 125.00 147.58 -22.58 4.10e+00 5.95e-02 3.03e+01 angle pdb=" C THR P 27 " pdb=" CA THR P 27 " pdb=" CB THR P 27 " ideal model delta sigma weight residual 111.80 119.64 -7.84 1.46e+00 4.69e-01 2.88e+01 angle pdb=" N GLY R 78 " pdb=" CA GLY R 78 " pdb=" C GLY R 78 " ideal model delta sigma weight residual 114.37 108.36 6.01 1.26e+00 6.30e-01 2.27e+01 angle pdb=" N TYR R 131 " pdb=" CA TYR R 131 " pdb=" C TYR R 131 " ideal model delta sigma weight residual 112.92 107.38 5.54 1.23e+00 6.61e-01 2.03e+01 ... (remaining 12882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 5372 22.05 - 44.10: 274 44.10 - 66.16: 46 66.16 - 88.21: 14 88.21 - 110.26: 1 Dihedral angle restraints: 5707 sinusoidal: 2348 harmonic: 3359 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -27.30 -58.70 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 40.92 52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 5704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1400 0.120 - 0.239: 9 0.239 - 0.359: 3 0.359 - 0.479: 0 0.479 - 0.599: 1 Chirality restraints: 1413 Sorted by residual: chirality pdb=" C1 NAG R 501 " pdb=" ND2 ASN R 130 " pdb=" C2 NAG R 501 " pdb=" O5 NAG R 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CA THR P 27 " pdb=" N THR P 27 " pdb=" C THR P 27 " pdb=" CB THR P 27 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA TRP R 76 " pdb=" N TRP R 76 " pdb=" C TRP R 76 " pdb=" CB TRP R 76 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1410 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR P 31 " -0.049 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO P 32 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO R 304 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 236 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.018 5.00e-02 4.00e+02 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1099 2.75 - 3.29: 8848 3.29 - 3.83: 15322 3.83 - 4.36: 19923 4.36 - 4.90: 32907 Nonbonded interactions: 78099 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.216 2.440 nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.256 2.440 nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.262 2.440 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.264 2.520 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.279 2.440 ... (remaining 78094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 63 5.16 5 C 6025 2.51 5 N 1581 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 2.110 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 28.130 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 0.051 9559 Z= 0.255 Angle : 0.619 22.577 12887 Z= 0.363 Chirality : 0.045 0.599 1413 Planarity : 0.003 0.064 1621 Dihedral : 13.413 110.261 3516 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -2.90 (0.21), residues: 1138 helix: -3.02 (0.16), residues: 414 sheet: -0.75 (0.30), residues: 253 loop : -1.29 (0.25), residues: 471 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 1.053 Fit side-chains outliers start: 19 outliers final: 5 residues processed: 204 average time/residue: 1.3852 time to fit residues: 299.9208 Evaluate side-chains 151 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0847 time to fit residues: 1.6939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 0.0670 chunk 28 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 GLN R 179 GLN R 302 HIS R 383 GLN A 294 GLN B 132 ASN B 220 GLN B 266 HIS G 24 ASN N 77 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 9559 Z= 0.341 Angle : 0.639 10.456 12887 Z= 0.333 Chirality : 0.046 0.197 1413 Planarity : 0.005 0.063 1621 Dihedral : 8.577 111.389 1492 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 4.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.32 (0.22), residues: 1138 helix: -0.85 (0.22), residues: 441 sheet: -0.36 (0.31), residues: 233 loop : -0.98 (0.26), residues: 464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 146 time to evaluate : 1.155 Fit side-chains outliers start: 47 outliers final: 23 residues processed: 179 average time/residue: 1.2299 time to fit residues: 235.6166 Evaluate side-chains 169 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.7787 time to fit residues: 5.7938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.0270 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 19 GLN A 31 GLN N 1 GLN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 9559 Z= 0.142 Angle : 0.491 10.576 12887 Z= 0.255 Chirality : 0.040 0.139 1413 Planarity : 0.003 0.040 1621 Dihedral : 7.569 111.099 1492 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 4.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1138 helix: 0.47 (0.25), residues: 433 sheet: -0.12 (0.32), residues: 233 loop : -0.56 (0.27), residues: 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 1.175 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 180 average time/residue: 1.2370 time to fit residues: 237.7689 Evaluate side-chains 164 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 6 average time/residue: 0.7994 time to fit residues: 6.7118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN A 19 GLN A 31 GLN A 213 GLN A 357 HIS B 17 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 9559 Z= 0.221 Angle : 0.536 8.773 12887 Z= 0.279 Chirality : 0.043 0.143 1413 Planarity : 0.004 0.042 1621 Dihedral : 8.132 110.994 1492 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 4.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1138 helix: 0.68 (0.25), residues: 439 sheet: -0.07 (0.32), residues: 227 loop : -0.48 (0.27), residues: 472 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 1.155 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 25 residues processed: 181 average time/residue: 1.2730 time to fit residues: 245.5550 Evaluate side-chains 177 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 8 average time/residue: 0.7379 time to fit residues: 8.0421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.0170 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 31 GLN A 357 HIS B 17 GLN N 1 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 9559 Z= 0.193 Angle : 0.511 8.823 12887 Z= 0.267 Chirality : 0.042 0.139 1413 Planarity : 0.004 0.041 1621 Dihedral : 8.107 110.844 1492 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1138 helix: 0.92 (0.25), residues: 441 sheet: -0.11 (0.32), residues: 231 loop : -0.37 (0.27), residues: 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 1.013 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 178 average time/residue: 1.4198 time to fit residues: 268.6296 Evaluate side-chains 172 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 0.4924 time to fit residues: 6.1156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN A 31 GLN A 357 HIS B 17 GLN N 1 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 9559 Z= 0.188 Angle : 0.515 10.705 12887 Z= 0.267 Chirality : 0.042 0.139 1413 Planarity : 0.004 0.047 1621 Dihedral : 8.147 110.756 1492 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 4.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1138 helix: 1.05 (0.26), residues: 441 sheet: -0.20 (0.31), residues: 238 loop : -0.26 (0.28), residues: 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 1.103 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 26 residues processed: 177 average time/residue: 1.2682 time to fit residues: 239.2714 Evaluate side-chains 171 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.5183 time to fit residues: 5.5737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 30.0000 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9559 Z= 0.186 Angle : 0.512 10.492 12887 Z= 0.265 Chirality : 0.041 0.140 1413 Planarity : 0.003 0.041 1621 Dihedral : 8.190 110.752 1492 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 4.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1138 helix: 1.16 (0.26), residues: 441 sheet: -0.28 (0.31), residues: 240 loop : -0.22 (0.28), residues: 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 1.138 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 29 residues processed: 182 average time/residue: 1.2976 time to fit residues: 252.1476 Evaluate side-chains 180 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.6031 time to fit residues: 6.9244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 chunk 10 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN A 31 GLN A 357 HIS B 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9559 Z= 0.182 Angle : 0.514 11.315 12887 Z= 0.265 Chirality : 0.041 0.139 1413 Planarity : 0.004 0.061 1621 Dihedral : 8.203 110.773 1492 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1138 helix: 1.23 (0.26), residues: 441 sheet: -0.26 (0.31), residues: 240 loop : -0.19 (0.28), residues: 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 1.143 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 26 residues processed: 177 average time/residue: 1.2916 time to fit residues: 244.1924 Evaluate side-chains 176 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 0.7642 time to fit residues: 5.7547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 0.0270 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN A 31 GLN A 35 GLN A 357 HIS B 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 9559 Z= 0.138 Angle : 0.483 13.110 12887 Z= 0.247 Chirality : 0.040 0.139 1413 Planarity : 0.003 0.040 1621 Dihedral : 7.866 110.756 1492 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1138 helix: 1.43 (0.26), residues: 438 sheet: -0.28 (0.31), residues: 240 loop : -0.06 (0.28), residues: 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.074 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 22 residues processed: 178 average time/residue: 1.4001 time to fit residues: 267.0716 Evaluate side-chains 172 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.1019 time to fit residues: 2.3737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN A 14 ASN A 31 GLN A 35 GLN A 357 HIS B 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 9559 Z= 0.153 Angle : 0.501 13.268 12887 Z= 0.254 Chirality : 0.041 0.140 1413 Planarity : 0.004 0.063 1621 Dihedral : 7.872 110.731 1492 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1138 helix: 1.45 (0.26), residues: 440 sheet: -0.27 (0.32), residues: 240 loop : -0.03 (0.28), residues: 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.210 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 20 residues processed: 170 average time/residue: 1.2932 time to fit residues: 234.3924 Evaluate side-chains 169 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.0876 time to fit residues: 1.8628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 40.0000 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN A 31 GLN A 35 GLN A 357 HIS B 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.172132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123420 restraints weight = 9573.859| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.96 r_work: 0.3127 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 9559 Z= 0.135 Angle : 0.481 13.344 12887 Z= 0.244 Chirality : 0.040 0.138 1413 Planarity : 0.003 0.039 1621 Dihedral : 7.660 110.710 1492 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1138 helix: 1.68 (0.26), residues: 432 sheet: -0.23 (0.32), residues: 240 loop : 0.07 (0.29), residues: 466 =============================================================================== Job complete usr+sys time: 4288.22 seconds wall clock time: 76 minutes 19.86 seconds (4579.86 seconds total)