Starting phenix.real_space_refine on Thu Mar 14 18:46:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/03_2024/7tyh_26179_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/03_2024/7tyh_26179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/03_2024/7tyh_26179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/03_2024/7tyh_26179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/03_2024/7tyh_26179_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/03_2024/7tyh_26179_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 68 5.16 5 C 6015 2.51 5 N 1663 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R GLU 210": "OE1" <-> "OE2" Residue "R GLU 240": "OE1" <-> "OE2" Residue "R GLU 397": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9492 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2598 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 514 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 186 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: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2867 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 122 Time building chain proxies: 5.09, per 1000 atoms: 0.54 Number of scatterers: 9492 At special positions: 0 Unit cell: (89.88, 102.72, 156.648, 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 68 16.00 O 1746 8.00 N 1663 7.00 C 6015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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=2.01 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 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 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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: 3.04 Conformation dependent library (CDL) restraints added in 1.8 seconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 12 sheets defined 35.6% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.797A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 27 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.583A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.611A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 removed outlier: 3.843A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 332 through 351 removed outlier: 4.248A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.556A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 removed outlier: 3.518A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.821A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 33 No H-bonds generated for 'chain 'G' and resid 30 through 33' Processing helix chain 'G' and resid 35 through 43 removed outlier: 3.582A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 76 removed outlier: 3.608A pdb=" N GLN E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 73 " --> pdb=" O TRP E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 103 removed outlier: 4.193A pdb=" N LEU E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG E 97 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 100 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 126 removed outlier: 3.602A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 165 removed outlier: 3.531A pdb=" N ALA E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Proline residue: E 153 - end of helix removed outlier: 3.603A pdb=" N ILE E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Proline residue: E 158 - end of helix removed outlier: 3.551A pdb=" N LEU E 163 " --> pdb=" O PHE E 159 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 21 removed outlier: 3.659A pdb=" N ASN P 17 " --> pdb=" O THR P 13 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE P 19 " --> pdb=" O ASP P 15 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS P 20 " --> pdb=" O PHE P 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 61 removed outlier: 3.753A pdb=" N ASP R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 135 No H-bonds generated for 'chain 'R' and resid 132 through 135' Processing helix chain 'R' and resid 138 through 170 removed outlier: 3.572A pdb=" N LYS R 143 " --> pdb=" O PRO R 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU R 148 " --> pdb=" O ASN R 144 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER R 159 " --> pdb=" O GLY R 155 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE R 160 " --> pdb=" O HIS R 156 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE R 170 " --> pdb=" O SER R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 204 removed outlier: 3.720A pdb=" N ILE R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 213 Processing helix chain 'R' and resid 217 through 248 removed outlier: 3.620A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU R 244 " --> pdb=" O GLU R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 267 removed outlier: 3.584A pdb=" N TRP R 267 " --> pdb=" O TYR R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 283 Proline residue: R 273 - end of helix removed outlier: 3.749A pdb=" N ILE R 276 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE R 279 " --> pdb=" O ILE R 276 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR R 280 " --> pdb=" O HIS R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 316 removed outlier: 3.687A pdb=" N HIS R 302 " --> pdb=" O TYR R 299 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY R 303 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Proline residue: R 304 - end of helix removed outlier: 4.126A pdb=" N LEU R 309 " --> pdb=" O MET R 306 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL R 310 " --> pdb=" O ALA R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 328 Processing helix chain 'R' and resid 334 through 337 No H-bonds generated for 'chain 'R' and resid 334 through 337' Processing helix chain 'R' and resid 339 through 343 removed outlier: 3.798A pdb=" N LYS R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 339 through 343' Processing helix chain 'R' and resid 345 through 352 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 366 through 388 removed outlier: 4.666A pdb=" N ILE R 371 " --> pdb=" O MET R 367 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR R 374 " --> pdb=" O LYS R 370 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS R 377 " --> pdb=" O ASP R 373 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU R 379 " --> pdb=" O VAL R 375 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLY R 384 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE R 385 " --> pdb=" O HIS R 381 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 399 No H-bonds generated for 'chain 'R' and resid 396 through 399' Processing helix chain 'R' and resid 401 through 404 No H-bonds generated for 'chain 'R' and resid 401 through 404' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.339A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.919A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.924A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.299A 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: 6.959A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.965A 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: 7.155A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.614A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 284 through 288 removed outlier: 3.553A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.927A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 5 Processing sheet with id= K, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.515A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.515A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 894 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: 2.48 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1556 1.31 - 1.44: 2704 1.44 - 1.56: 5345 1.56 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 9700 Sorted by residual: bond pdb=" C PRO N 100 " pdb=" O PRO N 100 " ideal model delta sigma weight residual 1.237 1.189 0.049 1.26e-02 6.30e+03 1.49e+01 bond pdb=" N ARG N 98 " pdb=" CA ARG N 98 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.21e-02 6.83e+03 1.36e+01 bond pdb=" N ASP N 106 " pdb=" CA ASP N 106 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.22e-02 6.72e+03 1.24e+01 bond pdb=" N ILE A 276 " pdb=" CA ILE A 276 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.65e+00 bond pdb=" N CYS P 7 " pdb=" CA CYS P 7 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.22e+00 ... (remaining 9695 not shown) Histogram of bond angle deviations from ideal: 100.21 - 107.12: 273 107.12 - 114.04: 5448 114.04 - 120.95: 4505 120.95 - 127.86: 2864 127.86 - 134.78: 89 Bond angle restraints: 13179 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 112.00 100.21 11.79 1.40e+00 5.10e-01 7.09e+01 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 111.77 120.11 -8.34 1.67e+00 3.59e-01 2.49e+01 angle pdb=" CA PRO N 102 " pdb=" C PRO N 102 " pdb=" O PRO N 102 " ideal model delta sigma weight residual 122.13 116.49 5.64 1.23e+00 6.61e-01 2.10e+01 angle pdb=" CA VAL N 110 " pdb=" C VAL N 110 " pdb=" O VAL N 110 " ideal model delta sigma weight residual 120.85 116.37 4.48 1.06e+00 8.90e-01 1.78e+01 angle pdb=" CA PRO N 102 " pdb=" C PRO N 102 " pdb=" N PHE N 103 " ideal model delta sigma weight residual 114.58 119.39 -4.81 1.16e+00 7.43e-01 1.72e+01 ... (remaining 13174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5337 17.98 - 35.97: 336 35.97 - 53.95: 58 53.95 - 71.93: 12 71.93 - 89.91: 6 Dihedral angle restraints: 5749 sinusoidal: 2117 harmonic: 3632 Sorted by residual: 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 93.00 154.15 -61.15 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -127.86 41.86 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " pdb=" CG ASP N 106 " pdb=" OD1 ASP N 106 " ideal model delta sinusoidal sigma weight residual -30.00 -87.44 57.44 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1085 0.041 - 0.081: 274 0.081 - 0.122: 104 0.122 - 0.163: 14 0.163 - 0.204: 5 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" C PRO P 32 " pdb=" CB PRO P 32 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA MET P 8 " pdb=" N MET P 8 " pdb=" C MET P 8 " pdb=" CB MET P 8 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA LEU P 4 " pdb=" N LEU P 4 " pdb=" C LEU P 4 " pdb=" CB LEU P 4 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 1479 not shown) Planarity restraints: 1699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 31 " -0.117 5.00e-02 4.00e+02 1.67e-01 4.47e+01 pdb=" N PRO P 32 " 0.289 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO N 100 " -0.009 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C PRO N 100 " 0.034 2.00e-02 2.50e+03 pdb=" O PRO N 100 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA N 101 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 234 " 0.018 2.00e-02 2.50e+03 1.19e-02 3.54e+00 pdb=" CG TRP A 234 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 234 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 234 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 234 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 234 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 234 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 234 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 234 " -0.001 2.00e-02 2.50e+03 ... (remaining 1696 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2612 2.80 - 3.32: 8594 3.32 - 3.85: 15104 3.85 - 4.37: 18671 4.37 - 4.90: 31288 Nonbonded interactions: 76269 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.306 2.440 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.315 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.321 2.440 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.328 2.440 ... (remaining 76264 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.130 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.200 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 : 0.003 0.053 9700 Z= 0.204 Angle : 0.605 11.790 13179 Z= 0.407 Chirality : 0.043 0.204 1482 Planarity : 0.005 0.167 1699 Dihedral : 12.285 89.913 3375 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.05 % Allowed : 7.96 % Favored : 90.99 % 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: -4.28 (0.19), residues: 1226 helix: -3.18 (0.18), residues: 442 sheet: -3.15 (0.31), residues: 197 loop : -2.32 (0.22), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 234 HIS 0.002 0.000 HIS R 302 PHE 0.024 0.001 PHE N 108 TYR 0.021 0.001 TYR N 115 ARG 0.002 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: R 230 MET cc_start: 0.7125 (ttp) cc_final: 0.6373 (ttm) REVERT: R 255 GLU cc_start: 0.3382 (mt-10) cc_final: 0.3129 (tt0) REVERT: R 340 LYS cc_start: 0.7578 (mmmm) cc_final: 0.7312 (mmtm) outliers start: 10 outliers final: 7 residues processed: 200 average time/residue: 0.2351 time to fit residues: 63.3658 Evaluate side-chains 152 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 230 ASN N 31 ASN E 124 HIS P 17 ASN R 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9700 Z= 0.232 Angle : 0.507 6.216 13179 Z= 0.271 Chirality : 0.042 0.152 1482 Planarity : 0.004 0.056 1699 Dihedral : 4.639 59.335 1356 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.51 % Allowed : 13.09 % Favored : 84.40 % 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: -3.04 (0.21), residues: 1226 helix: -1.63 (0.22), residues: 466 sheet: -2.51 (0.31), residues: 228 loop : -1.98 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.005 0.001 HIS R 381 PHE 0.017 0.001 PHE N 108 TYR 0.020 0.001 TYR N 80 ARG 0.009 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 0.996 Fit side-chains REVERT: B 264 TYR cc_start: 0.7439 (m-80) cc_final: 0.6975 (m-80) REVERT: N 87 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7874 (ttmt) REVERT: R 230 MET cc_start: 0.7012 (ttp) cc_final: 0.6580 (ttm) outliers start: 24 outliers final: 13 residues processed: 185 average time/residue: 0.2236 time to fit residues: 56.8010 Evaluate side-chains 153 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 0.0970 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9700 Z= 0.128 Angle : 0.442 7.352 13179 Z= 0.233 Chirality : 0.040 0.145 1482 Planarity : 0.003 0.043 1699 Dihedral : 3.986 57.536 1353 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.68 % Allowed : 16.65 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.22), residues: 1226 helix: -0.68 (0.24), residues: 470 sheet: -2.23 (0.31), residues: 230 loop : -1.66 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.000 HIS B 225 PHE 0.018 0.001 PHE R 161 TYR 0.016 0.001 TYR N 80 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.116 Fit side-chains REVERT: A 209 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6662 (mt-10) REVERT: B 264 TYR cc_start: 0.7214 (m-80) cc_final: 0.6868 (m-80) REVERT: P 8 MET cc_start: 0.6996 (tpt) cc_final: 0.6712 (tpp) REVERT: R 230 MET cc_start: 0.6983 (ttp) cc_final: 0.6553 (ttm) outliers start: 16 outliers final: 9 residues processed: 172 average time/residue: 0.2113 time to fit residues: 51.1621 Evaluate side-chains 156 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN N 123 GLN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9700 Z= 0.166 Angle : 0.456 7.559 13179 Z= 0.241 Chirality : 0.040 0.155 1482 Planarity : 0.003 0.043 1699 Dihedral : 4.008 56.733 1351 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.04 % Allowed : 17.70 % Favored : 79.27 % 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: -1.75 (0.23), residues: 1226 helix: -0.16 (0.24), residues: 471 sheet: -2.06 (0.31), residues: 230 loop : -1.54 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 381 PHE 0.021 0.001 PHE R 161 TYR 0.012 0.001 TYR N 80 ARG 0.006 0.000 ARG R 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 1.134 Fit side-chains REVERT: A 209 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6760 (mt-10) REVERT: B 264 TYR cc_start: 0.7309 (m-80) cc_final: 0.6930 (m-80) REVERT: P 8 MET cc_start: 0.6941 (tpt) cc_final: 0.6727 (tpp) REVERT: R 204 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5532 (tt0) REVERT: R 230 MET cc_start: 0.6995 (ttp) cc_final: 0.6575 (ttm) outliers start: 29 outliers final: 20 residues processed: 169 average time/residue: 0.2139 time to fit residues: 51.0529 Evaluate side-chains 160 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 375 VAL Chi-restraints excluded: chain R residue 394 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9700 Z= 0.149 Angle : 0.443 7.734 13179 Z= 0.232 Chirality : 0.040 0.153 1482 Planarity : 0.003 0.043 1699 Dihedral : 3.954 55.973 1351 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.72 % Allowed : 18.43 % Favored : 78.85 % 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: -1.41 (0.23), residues: 1226 helix: 0.23 (0.25), residues: 471 sheet: -1.97 (0.31), residues: 231 loop : -1.42 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.023 0.001 PHE R 161 TYR 0.012 0.001 TYR N 80 ARG 0.006 0.000 ARG R 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6568 (mt-10) REVERT: B 264 TYR cc_start: 0.7297 (m-80) cc_final: 0.6961 (m-80) REVERT: N 108 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: P 8 MET cc_start: 0.6929 (tpt) cc_final: 0.6504 (ttm) REVERT: R 213 ARG cc_start: 0.6868 (mtp85) cc_final: 0.6584 (mtp180) REVERT: R 230 MET cc_start: 0.6988 (ttp) cc_final: 0.6709 (ttm) outliers start: 26 outliers final: 22 residues processed: 167 average time/residue: 0.2081 time to fit residues: 49.0895 Evaluate side-chains 164 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 375 VAL Chi-restraints excluded: chain R residue 394 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.0970 chunk 104 optimal weight: 0.9980 chunk 22 optimal weight: 0.0040 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 0.0980 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.1928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 377 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9700 Z= 0.107 Angle : 0.424 8.517 13179 Z= 0.220 Chirality : 0.039 0.158 1482 Planarity : 0.003 0.041 1699 Dihedral : 3.713 54.046 1351 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.09 % Allowed : 19.58 % Favored : 78.32 % 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: -1.04 (0.24), residues: 1226 helix: 0.59 (0.25), residues: 467 sheet: -1.84 (0.32), residues: 225 loop : -1.25 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 PHE 0.026 0.001 PHE R 161 TYR 0.011 0.001 TYR N 60 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.149 Fit side-chains REVERT: A 35 GLN cc_start: 0.7775 (tp40) cc_final: 0.7213 (mp10) REVERT: B 264 TYR cc_start: 0.7107 (m-80) cc_final: 0.6770 (m-80) REVERT: P 8 MET cc_start: 0.6797 (tpt) cc_final: 0.6440 (ttm) REVERT: R 204 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5268 (tt0) REVERT: R 230 MET cc_start: 0.6893 (ttp) cc_final: 0.6637 (ttm) outliers start: 20 outliers final: 14 residues processed: 161 average time/residue: 0.1881 time to fit residues: 43.4086 Evaluate side-chains 156 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 252 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 115 optimal weight: 0.0670 chunk 72 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 31 ASN R 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9700 Z= 0.126 Angle : 0.443 11.799 13179 Z= 0.227 Chirality : 0.040 0.158 1482 Planarity : 0.003 0.040 1699 Dihedral : 3.711 53.557 1351 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.62 % Allowed : 19.58 % Favored : 77.80 % 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: -0.86 (0.24), residues: 1226 helix: 0.77 (0.26), residues: 468 sheet: -1.74 (0.32), residues: 229 loop : -1.17 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.001 0.000 HIS R 381 PHE 0.023 0.001 PHE R 161 TYR 0.011 0.001 TYR N 60 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 1.130 Fit side-chains REVERT: B 264 TYR cc_start: 0.7226 (m-80) cc_final: 0.6850 (m-80) REVERT: N 108 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: P 8 MET cc_start: 0.6761 (tpt) cc_final: 0.6425 (ttm) REVERT: R 204 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5295 (tt0) REVERT: R 295 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7535 (p) REVERT: R 306 MET cc_start: 0.8652 (tpt) cc_final: 0.8342 (tpt) outliers start: 25 outliers final: 21 residues processed: 162 average time/residue: 0.2072 time to fit residues: 47.4366 Evaluate side-chains 164 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9700 Z= 0.179 Angle : 0.478 12.499 13179 Z= 0.248 Chirality : 0.041 0.324 1482 Planarity : 0.003 0.041 1699 Dihedral : 3.972 54.044 1351 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.35 % Allowed : 19.37 % Favored : 77.28 % 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: -0.89 (0.24), residues: 1226 helix: 0.75 (0.25), residues: 469 sheet: -1.74 (0.31), residues: 234 loop : -1.20 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS B 142 PHE 0.022 0.001 PHE R 161 TYR 0.012 0.001 TYR N 80 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.109 Fit side-chains REVERT: B 264 TYR cc_start: 0.7316 (m-80) cc_final: 0.6946 (m-80) REVERT: N 108 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: P 8 MET cc_start: 0.6822 (tpt) cc_final: 0.6480 (ttm) REVERT: R 204 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5341 (tt0) REVERT: R 295 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7576 (p) REVERT: R 306 MET cc_start: 0.8699 (tpt) cc_final: 0.8325 (tpt) outliers start: 32 outliers final: 25 residues processed: 159 average time/residue: 0.2042 time to fit residues: 45.9875 Evaluate side-chains 160 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 375 VAL Chi-restraints excluded: chain R residue 394 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9700 Z= 0.163 Angle : 0.474 12.337 13179 Z= 0.245 Chirality : 0.041 0.271 1482 Planarity : 0.003 0.041 1699 Dihedral : 3.943 53.627 1351 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.72 % Allowed : 20.21 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.24), residues: 1226 helix: 0.77 (0.26), residues: 469 sheet: -1.61 (0.33), residues: 219 loop : -1.25 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS B 142 PHE 0.021 0.001 PHE R 161 TYR 0.011 0.001 TYR N 80 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.015 Fit side-chains REVERT: A 222 PHE cc_start: 0.7865 (m-80) cc_final: 0.7657 (m-80) REVERT: B 264 TYR cc_start: 0.7236 (m-80) cc_final: 0.6900 (m-80) REVERT: N 108 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: P 8 MET cc_start: 0.6849 (tpt) cc_final: 0.6504 (ttm) REVERT: R 204 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5329 (tt0) REVERT: R 229 MET cc_start: 0.6569 (mmm) cc_final: 0.6365 (mmm) REVERT: R 295 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7560 (p) REVERT: R 306 MET cc_start: 0.8679 (tpt) cc_final: 0.8297 (tpt) outliers start: 26 outliers final: 22 residues processed: 156 average time/residue: 0.1998 time to fit residues: 44.0991 Evaluate side-chains 158 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 375 VAL Chi-restraints excluded: chain R residue 394 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.6980 chunk 79 optimal weight: 0.0370 chunk 119 optimal weight: 0.7980 chunk 110 optimal weight: 0.0980 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 73 optimal weight: 20.0000 chunk 58 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 9700 Z= 0.114 Angle : 0.456 11.965 13179 Z= 0.235 Chirality : 0.040 0.267 1482 Planarity : 0.003 0.041 1699 Dihedral : 3.746 52.562 1351 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.83 % Allowed : 20.00 % Favored : 77.17 % 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: -0.69 (0.24), residues: 1226 helix: 0.94 (0.26), residues: 468 sheet: -1.55 (0.32), residues: 219 loop : -1.17 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.001 0.000 HIS E 124 PHE 0.021 0.001 PHE R 161 TYR 0.011 0.001 TYR N 60 ARG 0.007 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.185 Fit side-chains REVERT: A 35 GLN cc_start: 0.7717 (tp40) cc_final: 0.7123 (mp10) REVERT: B 264 TYR cc_start: 0.7124 (m-80) cc_final: 0.6766 (m-80) REVERT: N 108 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: P 8 MET cc_start: 0.6756 (tpt) cc_final: 0.6477 (ttm) REVERT: R 204 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5329 (tt0) REVERT: R 295 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7530 (p) REVERT: R 306 MET cc_start: 0.8566 (tpt) cc_final: 0.8255 (tpt) outliers start: 27 outliers final: 22 residues processed: 160 average time/residue: 0.2066 time to fit residues: 47.1336 Evaluate side-chains 162 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 8.9990 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.188425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156591 restraints weight = 11009.617| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.95 r_work: 0.3691 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 9700 Z= 0.138 Angle : 0.462 11.877 13179 Z= 0.239 Chirality : 0.040 0.300 1482 Planarity : 0.003 0.041 1699 Dihedral : 3.773 52.174 1351 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.72 % Allowed : 20.94 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1226 helix: 0.98 (0.26), residues: 468 sheet: -1.57 (0.33), residues: 217 loop : -1.13 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS R 226 PHE 0.021 0.001 PHE R 161 TYR 0.011 0.001 TYR N 60 ARG 0.007 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2392.59 seconds wall clock time: 43 minutes 28.60 seconds (2608.60 seconds total)