Starting phenix.real_space_refine on Thu Jan 18 22:46:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/01_2024/8f0j_28758.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/01_2024/8f0j_28758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/01_2024/8f0j_28758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/01_2024/8f0j_28758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/01_2024/8f0j_28758.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0j_28758/01_2024/8f0j_28758.pdb" } resolution = 2.0 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= 0.006 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 67 5.16 5 C 6237 2.51 5 N 1605 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 11": "NH1" <-> "NH2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R GLU 329": "OE1" <-> "OE2" Residue "R GLU 332": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9678 Number of models: 1 Model: "" Number of chains: 11 Chain: "P" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 278 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Chain: "R" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3058 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 354} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1844 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 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: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 444 Unusual residues: {'NAG': 2, 'P42': 1, 'PLM': 8, 'PTY': 3, 'Y01': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.07, per 1000 atoms: 0.63 Number of scatterers: 9678 At special positions: 0 Unit cell: (109.85, 100.1, 143.65, 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 67 16.00 P 4 15.00 O 1765 8.00 N 1605 7.00 C 6237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS P 2 " - 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.7 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 13 sheets defined 43.1% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 removed outlier: 3.727A pdb=" N HIS P 18 " --> pdb=" O ASN P 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 62 removed outlier: 3.643A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 135 removed outlier: 3.911A pdb=" N ASN R 135 " --> pdb=" O THR R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.748A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.572A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 408 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.571A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.504A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.792A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.505A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.345A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.957A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.474A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.528A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.688A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.509A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 89 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.396A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.605A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.592A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.780A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.559A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.266A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.534A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.764A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.798A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1507 1.31 - 1.43: 2699 1.43 - 1.56: 5551 1.56 - 1.69: 9 1.69 - 1.81: 96 Bond restraints: 9862 Sorted by residual: bond pdb=" C TYR P 37 " pdb=" N NH2 P 38 " ideal model delta sigma weight residual 2.329 1.325 1.004 1.40e-02 5.10e+03 5.14e+03 bond pdb=" C LYS P 21 " pdb=" O LYS P 21 " ideal model delta sigma weight residual 1.242 1.182 0.059 1.00e-02 1.00e+04 3.54e+01 bond pdb=" C02 D6M P 101 " pdb=" N03 D6M P 101 " ideal model delta sigma weight residual 1.339 1.452 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" N VAL R 250 " pdb=" CA VAL R 250 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.15e-02 7.56e+03 1.21e+01 bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.185 0.062 2.00e-02 2.50e+03 9.68e+00 ... (remaining 9857 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.82: 184 105.82 - 112.86: 5149 112.86 - 119.91: 3387 119.91 - 126.96: 4434 126.96 - 134.00: 125 Bond angle restraints: 13279 Sorted by residual: angle pdb=" N ILE R 248 " pdb=" CA ILE R 248 " pdb=" C ILE R 248 " ideal model delta sigma weight residual 110.72 115.31 -4.59 1.01e+00 9.80e-01 2.06e+01 angle pdb=" N VAL R 293 " pdb=" CA VAL R 293 " pdb=" C VAL R 293 " ideal model delta sigma weight residual 112.17 107.88 4.29 9.50e-01 1.11e+00 2.04e+01 angle pdb=" N SER P 19 " pdb=" CA SER P 19 " pdb=" C SER P 19 " ideal model delta sigma weight residual 110.53 104.74 5.79 1.32e+00 5.74e-01 1.93e+01 angle pdb=" N ILE R 319 " pdb=" CA ILE R 319 " pdb=" C ILE R 319 " ideal model delta sigma weight residual 111.58 106.98 4.60 1.06e+00 8.90e-01 1.89e+01 angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 122.28 118.30 3.98 1.00e+00 1.00e+00 1.58e+01 ... (remaining 13274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.13: 5696 24.13 - 48.26: 293 48.26 - 72.39: 58 72.39 - 96.52: 19 96.52 - 120.65: 5 Dihedral angle restraints: 6071 sinusoidal: 2696 harmonic: 3375 Sorted by residual: dihedral pdb=" C THR R 254 " pdb=" N THR R 254 " pdb=" CA THR R 254 " pdb=" CB THR R 254 " ideal model delta harmonic sigma weight residual -122.00 -136.85 14.85 0 2.50e+00 1.60e-01 3.53e+01 dihedral pdb=" N THR R 254 " pdb=" C THR R 254 " pdb=" CA THR R 254 " pdb=" CB THR R 254 " ideal model delta harmonic sigma weight residual 123.40 134.35 -10.95 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" CAM P42 R 509 " pdb=" CAN P42 R 509 " pdb=" CAO P42 R 509 " pdb=" CAP P42 R 509 " ideal model delta sinusoidal sigma weight residual 179.85 -59.50 -120.65 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 6068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1352 0.095 - 0.190: 81 0.190 - 0.284: 4 0.284 - 0.379: 1 0.379 - 0.474: 2 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA THR R 254 " pdb=" N THR R 254 " pdb=" C THR R 254 " pdb=" CB THR R 254 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" C6 PTY R 504 " pdb=" C1 PTY R 504 " pdb=" C5 PTY R 504 " pdb=" O7 PTY R 504 " both_signs ideal model delta sigma weight residual False 2.49 2.04 0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" C6 PTY R 508 " pdb=" C1 PTY R 508 " pdb=" C5 PTY R 508 " pdb=" O7 PTY R 508 " both_signs ideal model delta sigma weight residual False 2.49 2.18 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 1437 not shown) Planarity restraints: 1649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 17 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL P 17 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL P 17 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS P 18 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO R 304 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 254 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C THR R 254 " 0.021 2.00e-02 2.50e+03 pdb=" O THR R 254 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU R 255 " -0.007 2.00e-02 2.50e+03 ... (remaining 1646 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1829 2.78 - 3.31: 9039 3.31 - 3.84: 16058 3.84 - 4.37: 20380 4.37 - 4.90: 33984 Nonbonded interactions: 81290 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.246 2.440 nonbonded pdb=" OE1 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.317 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.319 2.440 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.352 2.520 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.376 2.440 ... (remaining 81285 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.650 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.120 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 : 0.011 1.004 9862 Z= 0.796 Angle : 0.613 10.024 13279 Z= 0.373 Chirality : 0.048 0.474 1440 Planarity : 0.003 0.038 1647 Dihedral : 15.417 120.653 3872 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.40 % Allowed : 5.36 % Favored : 94.23 % Cbeta Deviations : 0.09 % 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: -1.49 (0.22), residues: 1141 helix: -1.49 (0.19), residues: 439 sheet: -0.12 (0.32), residues: 231 loop : -0.70 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 302 PHE 0.010 0.001 PHE R 235 TYR 0.013 0.001 TYR P 37 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: R 59 MET cc_start: 0.2331 (mtm) cc_final: 0.1359 (ttt) REVERT: R 295 THR cc_start: 0.6162 (t) cc_final: 0.5960 (t) REVERT: R 306 MET cc_start: 0.7539 (mmm) cc_final: 0.7337 (mmm) REVERT: A 60 MET cc_start: 0.3732 (mtm) cc_final: 0.3141 (mmt) REVERT: N 87 LYS cc_start: 0.7713 (mttt) cc_final: 0.7451 (mttm) outliers start: 4 outliers final: 3 residues processed: 171 average time/residue: 1.4992 time to fit residues: 272.3426 Evaluate side-chains 141 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 GLN P 18 HIS R 60 GLN ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN R 226 HIS R 257 GLN R 288 ASN A 218 ASN B 13 GLN B 16 ASN B 340 ASN G 11 GLN G 24 ASN N 13 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9862 Z= 0.239 Angle : 0.636 7.868 13279 Z= 0.339 Chirality : 0.045 0.156 1440 Planarity : 0.005 0.050 1647 Dihedral : 12.866 101.113 1763 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.33 % Allowed : 10.02 % Favored : 87.65 % 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: 0.52 (0.24), residues: 1141 helix: 1.08 (0.23), residues: 443 sheet: 0.23 (0.32), residues: 235 loop : -0.18 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 234 HIS 0.006 0.002 HIS B 266 PHE 0.024 0.002 PHE N 29 TYR 0.013 0.002 TYR R 391 ARG 0.005 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.029 Fit side-chains REVERT: R 59 MET cc_start: 0.2375 (mtm) cc_final: 0.1053 (ptm) REVERT: R 143 LYS cc_start: 0.5239 (ttpt) cc_final: 0.4863 (tttt) REVERT: R 346 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6607 (mmm) REVERT: R 367 MET cc_start: 0.4978 (tpp) cc_final: 0.4652 (tpp) REVERT: R 386 PHE cc_start: 0.7193 (m-80) cc_final: 0.6966 (m-80) REVERT: A 19 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: A 38 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6967 (mpt-90) outliers start: 23 outliers final: 10 residues processed: 154 average time/residue: 1.4294 time to fit residues: 233.6112 Evaluate side-chains 152 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 346 MET Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9862 Z= 0.156 Angle : 0.520 6.601 13279 Z= 0.279 Chirality : 0.041 0.153 1440 Planarity : 0.004 0.037 1647 Dihedral : 12.061 89.975 1763 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.13 % Allowed : 10.63 % Favored : 87.25 % 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: 1.17 (0.25), residues: 1141 helix: 1.91 (0.24), residues: 443 sheet: 0.40 (0.33), residues: 234 loop : -0.06 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.018 0.001 PHE R 235 TYR 0.013 0.001 TYR R 149 ARG 0.003 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.053 Fit side-chains REVERT: R 59 MET cc_start: 0.2462 (mtm) cc_final: 0.1132 (ptm) REVERT: R 346 MET cc_start: 0.6970 (mmp) cc_final: 0.6538 (mmm) REVERT: R 367 MET cc_start: 0.4919 (tpp) cc_final: 0.4681 (tpp) outliers start: 21 outliers final: 10 residues processed: 142 average time/residue: 1.4017 time to fit residues: 211.6027 Evaluate side-chains 139 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9862 Z= 0.199 Angle : 0.578 6.793 13279 Z= 0.308 Chirality : 0.043 0.152 1440 Planarity : 0.004 0.040 1647 Dihedral : 12.494 89.244 1760 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.33 % Allowed : 11.64 % Favored : 86.03 % 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: 1.26 (0.25), residues: 1141 helix: 2.01 (0.24), residues: 443 sheet: 0.36 (0.32), residues: 240 loop : 0.02 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.022 0.002 PHE R 235 TYR 0.012 0.002 TYR R 149 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.130 Fit side-chains REVERT: R 59 MET cc_start: 0.2570 (mtm) cc_final: 0.1184 (ptm) REVERT: R 102 PHE cc_start: 0.5499 (OUTLIER) cc_final: 0.4203 (m-10) REVERT: R 143 LYS cc_start: 0.5116 (tttt) cc_final: 0.4914 (pttt) REVERT: R 208 ASN cc_start: 0.5203 (t0) cc_final: 0.4757 (m110) REVERT: R 300 ILE cc_start: 0.7203 (mt) cc_final: 0.6972 (mp) REVERT: R 367 MET cc_start: 0.4970 (tpp) cc_final: 0.4698 (tpp) REVERT: A 390 GLN cc_start: 0.7394 (mt0) cc_final: 0.7170 (mt0) outliers start: 23 outliers final: 15 residues processed: 146 average time/residue: 1.4277 time to fit residues: 221.7641 Evaluate side-chains 150 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 92 optimal weight: 0.0170 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9862 Z= 0.121 Angle : 0.472 5.867 13279 Z= 0.255 Chirality : 0.040 0.145 1440 Planarity : 0.003 0.038 1647 Dihedral : 11.877 89.128 1760 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.11 % Allowed : 13.16 % Favored : 85.73 % 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: 1.60 (0.25), residues: 1141 helix: 2.42 (0.24), residues: 444 sheet: 0.53 (0.33), residues: 234 loop : 0.08 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 234 HIS 0.006 0.001 HIS B 266 PHE 0.013 0.001 PHE R 235 TYR 0.012 0.001 TYR R 149 ARG 0.003 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.078 Fit side-chains REVERT: R 59 MET cc_start: 0.2565 (mtm) cc_final: 0.1266 (ptm) REVERT: R 102 PHE cc_start: 0.5489 (OUTLIER) cc_final: 0.4249 (m-10) REVERT: R 208 ASN cc_start: 0.5150 (t0) cc_final: 0.4717 (m110) REVERT: R 346 MET cc_start: 0.7048 (mmp) cc_final: 0.6495 (mmm) REVERT: A 390 GLN cc_start: 0.7325 (mt0) cc_final: 0.7057 (mt0) outliers start: 11 outliers final: 5 residues processed: 144 average time/residue: 1.4087 time to fit residues: 215.7015 Evaluate side-chains 142 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9862 Z= 0.147 Angle : 0.503 5.966 13279 Z= 0.271 Chirality : 0.040 0.146 1440 Planarity : 0.004 0.039 1647 Dihedral : 11.933 89.512 1760 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.02 % Allowed : 12.85 % Favored : 85.12 % 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: 1.64 (0.25), residues: 1141 helix: 2.45 (0.24), residues: 444 sheet: 0.53 (0.33), residues: 235 loop : 0.10 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.004 0.001 HIS R 336 PHE 0.017 0.001 PHE R 235 TYR 0.012 0.001 TYR R 149 ARG 0.006 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.097 Fit side-chains REVERT: R 59 MET cc_start: 0.2574 (mtm) cc_final: 0.1260 (ptm) REVERT: R 102 PHE cc_start: 0.5532 (OUTLIER) cc_final: 0.4233 (m-10) REVERT: R 208 ASN cc_start: 0.5160 (t0) cc_final: 0.4687 (m110) REVERT: A 38 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7061 (mpt-90) REVERT: A 390 GLN cc_start: 0.7385 (mt0) cc_final: 0.7127 (mt0) outliers start: 20 outliers final: 10 residues processed: 148 average time/residue: 1.4108 time to fit residues: 222.2548 Evaluate side-chains 147 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 0.0980 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9862 Z= 0.144 Angle : 0.506 6.175 13279 Z= 0.271 Chirality : 0.040 0.145 1440 Planarity : 0.004 0.042 1647 Dihedral : 11.865 89.211 1760 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.62 % Allowed : 13.66 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1141 helix: 2.49 (0.24), residues: 444 sheet: 0.54 (0.33), residues: 234 loop : 0.12 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.004 0.001 HIS R 336 PHE 0.016 0.001 PHE R 235 TYR 0.011 0.001 TYR R 149 ARG 0.012 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.092 Fit side-chains REVERT: R 59 MET cc_start: 0.2649 (mtm) cc_final: 0.1243 (ptm) REVERT: R 102 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.4250 (m-10) REVERT: R 208 ASN cc_start: 0.5141 (t0) cc_final: 0.4659 (m110) REVERT: R 346 MET cc_start: 0.7104 (mmp) cc_final: 0.6585 (mmm) REVERT: A 38 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7058 (mpt-90) REVERT: A 390 GLN cc_start: 0.7376 (mt0) cc_final: 0.7111 (mt0) outliers start: 16 outliers final: 11 residues processed: 147 average time/residue: 1.4068 time to fit residues: 220.3021 Evaluate side-chains 150 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.0570 chunk 103 optimal weight: 0.6980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN R 233 ASN B 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9862 Z= 0.117 Angle : 0.465 5.835 13279 Z= 0.250 Chirality : 0.039 0.143 1440 Planarity : 0.003 0.048 1647 Dihedral : 11.425 89.200 1760 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.32 % Allowed : 14.07 % Favored : 84.62 % 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: 1.83 (0.25), residues: 1141 helix: 2.68 (0.24), residues: 444 sheet: 0.58 (0.33), residues: 234 loop : 0.16 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.002 0.001 HIS R 336 PHE 0.012 0.001 PHE R 235 TYR 0.017 0.001 TYR R 191 ARG 0.013 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.146 Fit side-chains REVERT: R 59 MET cc_start: 0.2640 (mtm) cc_final: 0.1325 (ptm) REVERT: R 102 PHE cc_start: 0.5484 (OUTLIER) cc_final: 0.4273 (m-10) REVERT: R 208 ASN cc_start: 0.5104 (t0) cc_final: 0.4657 (m110) REVERT: R 346 MET cc_start: 0.7066 (mmp) cc_final: 0.6544 (mmm) REVERT: A 38 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6899 (mpt-90) outliers start: 13 outliers final: 8 residues processed: 141 average time/residue: 1.4240 time to fit residues: 213.5070 Evaluate side-chains 141 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN R 277 HIS B 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9862 Z= 0.341 Angle : 0.745 8.219 13279 Z= 0.388 Chirality : 0.048 0.258 1440 Planarity : 0.006 0.070 1647 Dihedral : 12.991 87.509 1760 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.92 % Allowed : 13.97 % Favored : 84.11 % 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: 1.07 (0.24), residues: 1141 helix: 1.73 (0.23), residues: 443 sheet: 0.40 (0.33), residues: 240 loop : -0.02 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 234 HIS 0.009 0.002 HIS B 54 PHE 0.035 0.003 PHE R 235 TYR 0.020 0.003 TYR B 59 ARG 0.011 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.071 Fit side-chains REVERT: R 59 MET cc_start: 0.2604 (mtm) cc_final: 0.1190 (ptm) REVERT: R 102 PHE cc_start: 0.5569 (OUTLIER) cc_final: 0.4212 (m-10) outliers start: 19 outliers final: 11 residues processed: 156 average time/residue: 1.3929 time to fit residues: 230.9013 Evaluate side-chains 154 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN A 213 GLN B 13 GLN N 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9862 Z= 0.162 Angle : 0.542 6.740 13279 Z= 0.290 Chirality : 0.041 0.147 1440 Planarity : 0.004 0.060 1647 Dihedral : 12.348 88.655 1760 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.21 % Allowed : 14.68 % Favored : 84.11 % 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: 1.46 (0.25), residues: 1141 helix: 2.21 (0.24), residues: 443 sheet: 0.54 (0.34), residues: 235 loop : 0.04 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.003 0.001 HIS A 41 PHE 0.017 0.002 PHE R 235 TYR 0.018 0.002 TYR R 191 ARG 0.013 0.001 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.100 Fit side-chains REVERT: R 59 MET cc_start: 0.2610 (mtm) cc_final: 0.1208 (ptm) REVERT: R 102 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.4231 (m-10) REVERT: R 346 MET cc_start: 0.7118 (mmp) cc_final: 0.6608 (mmm) REVERT: R 370 LYS cc_start: 0.5557 (ptmt) cc_final: 0.5341 (pttt) REVERT: A 38 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7080 (mpt-90) outliers start: 12 outliers final: 9 residues processed: 144 average time/residue: 1.4033 time to fit residues: 215.4780 Evaluate side-chains 145 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN A 213 GLN B 13 GLN N 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.206445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.180507 restraints weight = 7398.033| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 0.55 r_work: 0.3812 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.3633 rms_B_bonded: 3.67 restraints_weight: 0.1250 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9862 Z= 0.169 Angle : 0.552 7.524 13279 Z= 0.294 Chirality : 0.042 0.147 1440 Planarity : 0.004 0.061 1647 Dihedral : 12.275 89.437 1760 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.42 % Allowed : 14.57 % Favored : 84.01 % 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: 1.53 (0.25), residues: 1141 helix: 2.27 (0.24), residues: 443 sheet: 0.66 (0.34), residues: 230 loop : 0.03 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.019 0.002 PHE R 235 TYR 0.019 0.002 TYR R 191 ARG 0.014 0.001 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4527.60 seconds wall clock time: 80 minutes 51.71 seconds (4851.71 seconds total)