Starting phenix.real_space_refine on Thu Mar 14 22:02:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/03_2024/7tyn_26188.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/03_2024/7tyn_26188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/03_2024/7tyn_26188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/03_2024/7tyn_26188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/03_2024/7tyn_26188.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyn_26188/03_2024/7tyn_26188.pdb" } resolution = 2.6 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 543 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 63 5.16 5 C 6025 2.51 5 N 1581 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 24": "NH1" <-> "NH2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R ARG 180": "NH1" <-> "NH2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R GLU 210": "OE1" <-> "OE2" Residue "R GLU 240": "OE1" <-> "OE2" Residue "R GLU 255": "OE1" <-> "OE2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R GLU 329": "OE1" <-> "OE2" Residue "R GLU 334": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9364 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 239 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 29} Chain: "R" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2892 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 17, 'TRANS': 355} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "A" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1881 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Unusual residues: {'NAG': 2, 'P42': 1, 'PLM': 13, 'Y01': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.59, per 1000 atoms: 0.60 Number of scatterers: 9364 At special positions: 0 Unit cell: (94.1673, 158.153, 90.5455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 1 15.00 O 1694 8.00 N 1581 7.00 C 6025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.6 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 41.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 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 21 Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.703A pdb=" N TYR R 56 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 137 removed outlier: 3.867A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE R 137 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.504A pdb=" N VAL R 205 " --> pdb=" O HIS R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.555A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 4.247A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (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 removed outlier: 3.652A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) 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 329 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 348 Processing helix chain 'R' and resid 348 through 353 Processing helix chain 'R' and resid 354 through 359 removed outlier: 3.539A pdb=" N PHE R 359 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 removed outlier: 3.854A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE R 409 " --> pdb=" O GLN R 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.500A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.635A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.677A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.575A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.650A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.757A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.668A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.530A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'R' and resid 89 through 94 removed outlier: 3.922A pdb=" N VAL R 89 " --> pdb=" O CYS R 112 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS R 112 " --> pdb=" O VAL R 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.967A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.274A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.867A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.682A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.573A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.784A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.498A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.696A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=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: 6.844A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1311 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: 2.75 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1551 1.32 - 1.45: 2578 1.45 - 1.57: 5340 1.57 - 1.70: 2 1.70 - 1.82: 88 Bond restraints: 9559 Sorted by residual: bond pdb=" C1 NAG R 502 " pdb=" O5 NAG R 502 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" N GLY P 28 " pdb=" CA GLY P 28 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.40e-03 1.13e+04 9.31e+00 bond pdb=" N LEU R 80 " pdb=" CA LEU R 80 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.51e+00 bond pdb=" OBN P42 R 503 " pdb=" PBM P42 R 503 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.51e+00 ... (remaining 9554 not shown) Histogram of bond angle deviations from ideal: 90.04 - 101.55: 28 101.55 - 113.05: 5195 113.05 - 124.56: 7486 124.56 - 136.07: 177 136.07 - 147.58: 1 Bond angle restraints: 12887 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 90.04 21.96 1.40e+00 5.10e-01 2.46e+02 angle pdb=" C THR P 31 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 125.00 147.58 -22.58 4.10e+00 5.95e-02 3.03e+01 angle pdb=" C THR P 27 " pdb=" CA THR P 27 " pdb=" CB THR P 27 " ideal model delta sigma weight residual 111.80 119.64 -7.84 1.46e+00 4.69e-01 2.88e+01 angle pdb=" N GLY R 78 " pdb=" CA GLY R 78 " pdb=" C GLY R 78 " ideal model delta sigma weight residual 114.37 108.36 6.01 1.26e+00 6.30e-01 2.27e+01 angle pdb=" N TYR R 131 " pdb=" CA TYR R 131 " pdb=" C TYR R 131 " ideal model delta sigma weight residual 112.92 107.38 5.54 1.23e+00 6.61e-01 2.03e+01 ... (remaining 12882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.64: 5526 24.64 - 49.29: 233 49.29 - 73.93: 36 73.93 - 98.58: 16 98.58 - 123.22: 1 Dihedral angle restraints: 5812 sinusoidal: 2453 harmonic: 3359 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -27.30 -58.70 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 40.92 52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 5809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1400 0.120 - 0.239: 9 0.239 - 0.359: 3 0.359 - 0.479: 0 0.479 - 0.599: 1 Chirality restraints: 1413 Sorted by residual: chirality pdb=" C1 NAG R 501 " pdb=" ND2 ASN R 130 " pdb=" C2 NAG R 501 " pdb=" O5 NAG R 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CA THR P 27 " pdb=" N THR P 27 " pdb=" C THR P 27 " pdb=" CB THR P 27 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA TRP R 76 " pdb=" N TRP R 76 " pdb=" C TRP R 76 " pdb=" CB TRP R 76 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1410 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR P 31 " -0.049 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO P 32 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO R 304 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 236 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.018 5.00e-02 4.00e+02 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1097 2.75 - 3.29: 8785 3.29 - 3.83: 15304 3.83 - 4.36: 19777 4.36 - 4.90: 32888 Nonbonded interactions: 77851 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.216 2.440 nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.256 2.440 nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.262 2.440 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.264 2.520 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.279 2.440 ... (remaining 77846 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 1.760 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.910 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9559 Z= 0.256 Angle : 0.623 22.577 12887 Z= 0.363 Chirality : 0.045 0.599 1413 Planarity : 0.003 0.064 1621 Dihedral : 13.818 123.221 3621 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.01 % Allowed : 12.88 % Favored : 85.11 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.21), residues: 1138 helix: -3.02 (0.16), residues: 414 sheet: -0.75 (0.30), residues: 253 loop : -1.29 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 76 HIS 0.005 0.001 HIS R 302 PHE 0.012 0.001 PHE N 108 TYR 0.010 0.001 TYR R 98 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 1.061 Fit side-chains REVERT: P 32 PRO cc_start: 0.4510 (OUTLIER) cc_final: 0.4118 (Cg_exo) REVERT: R 143 LYS cc_start: 0.7422 (ttmt) cc_final: 0.7103 (ttmt) REVERT: R 174 ARG cc_start: 0.7704 (mmm-85) cc_final: 0.7389 (mtm-85) REVERT: R 229 MET cc_start: 0.8624 (tpp) cc_final: 0.8364 (tpp) REVERT: R 230 MET cc_start: 0.8015 (ttm) cc_final: 0.7812 (ttm) REVERT: R 337 MET cc_start: 0.7876 (ttp) cc_final: 0.7427 (ttm) REVERT: A 53 LYS cc_start: 0.7514 (ttpt) cc_final: 0.6784 (tttt) REVERT: A 221 MET cc_start: 0.8337 (ttp) cc_final: 0.7996 (ttp) REVERT: A 356 ARG cc_start: 0.7042 (mtm180) cc_final: 0.6839 (ptt180) REVERT: A 358 TYR cc_start: 0.8075 (m-80) cc_final: 0.7782 (m-80) REVERT: B 9 GLN cc_start: 0.7469 (tt0) cc_final: 0.7230 (tm-30) REVERT: B 19 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7710 (ttp80) REVERT: B 266 HIS cc_start: 0.7880 (t-170) cc_final: 0.7576 (t70) REVERT: G 14 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7518 (ptpt) REVERT: G 38 MET cc_start: 0.8421 (ttp) cc_final: 0.8092 (ttm) REVERT: N 19 ARG cc_start: 0.8694 (ttt90) cc_final: 0.8397 (ttt180) REVERT: N 46 GLU cc_start: 0.7742 (tt0) cc_final: 0.7448 (tt0) REVERT: N 50 ASP cc_start: 0.8635 (p0) cc_final: 0.8406 (p0) REVERT: N 123 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8554 (mm-40) outliers start: 19 outliers final: 5 residues processed: 204 average time/residue: 1.4092 time to fit residues: 303.7944 Evaluate side-chains 154 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 PRO Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain N residue 12 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.0470 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN R 227 GLN R 383 GLN B 132 ASN B 220 GLN G 24 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9559 Z= 0.192 Angle : 0.544 9.040 12887 Z= 0.282 Chirality : 0.042 0.216 1413 Planarity : 0.004 0.059 1621 Dihedral : 8.698 108.485 1606 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.06 % Allowed : 17.63 % Favored : 79.30 % 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: -0.74 (0.23), residues: 1138 helix: -0.06 (0.23), residues: 437 sheet: -0.30 (0.32), residues: 228 loop : -0.84 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE R 172 TYR 0.012 0.001 TYR R 149 ARG 0.005 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.018 Fit side-chains REVERT: R 140 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7364 (tp30) REVERT: R 204 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6330 (mm-30) REVERT: R 229 MET cc_start: 0.8396 (tpp) cc_final: 0.7947 (mmm) REVERT: A 221 MET cc_start: 0.8408 (ttp) cc_final: 0.8167 (ttp) REVERT: A 299 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6548 (pt0) REVERT: B 19 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7267 (ttp80) REVERT: B 61 MET cc_start: 0.8484 (ppp) cc_final: 0.8148 (ppp) REVERT: G 14 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7300 (ttmt) REVERT: G 38 MET cc_start: 0.8179 (ttp) cc_final: 0.7792 (ttm) REVERT: N 30 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8546 (p) REVERT: N 46 GLU cc_start: 0.7741 (tt0) cc_final: 0.7460 (tt0) REVERT: N 89 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: N 106 ASP cc_start: 0.8374 (p0) cc_final: 0.8155 (p0) REVERT: N 123 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8699 (mm-40) outliers start: 29 outliers final: 9 residues processed: 172 average time/residue: 1.3270 time to fit residues: 242.4492 Evaluate side-chains 154 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN A 19 GLN A 31 GLN A 213 GLN A 294 GLN B 17 GLN B 88 ASN N 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9559 Z= 0.277 Angle : 0.585 9.876 12887 Z= 0.302 Chirality : 0.044 0.176 1413 Planarity : 0.004 0.039 1621 Dihedral : 9.024 99.514 1598 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.22 % Allowed : 17.21 % Favored : 78.56 % 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: 0.01 (0.24), residues: 1138 helix: 0.84 (0.24), residues: 446 sheet: -0.06 (0.32), residues: 226 loop : -0.68 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.013 0.002 TYR R 391 ARG 0.006 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 0.774 Fit side-chains REVERT: R 196 MET cc_start: 0.7976 (mtt) cc_final: 0.7726 (mtm) REVERT: R 204 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6337 (mm-30) REVERT: R 256 LYS cc_start: 0.6457 (tmtt) cc_final: 0.6241 (tptt) REVERT: R 405 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7186 (tm-30) REVERT: A 221 MET cc_start: 0.8435 (ttp) cc_final: 0.8186 (ttp) REVERT: B 19 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7290 (ttp80) REVERT: B 61 MET cc_start: 0.8569 (ppp) cc_final: 0.8200 (ppp) REVERT: B 124 TYR cc_start: 0.8946 (m-80) cc_final: 0.8616 (m-80) REVERT: G 38 MET cc_start: 0.8242 (ttp) cc_final: 0.7888 (ttm) REVERT: N 89 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: N 123 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8606 (tp40) outliers start: 40 outliers final: 23 residues processed: 176 average time/residue: 1.2447 time to fit residues: 233.2007 Evaluate side-chains 167 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain R residue 378 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 19 GLN A 31 GLN A 357 HIS B 17 GLN N 1 GLN N 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9559 Z= 0.237 Angle : 0.560 9.138 12887 Z= 0.287 Chirality : 0.043 0.182 1413 Planarity : 0.004 0.039 1621 Dihedral : 8.935 91.451 1598 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.96 % Allowed : 17.74 % Favored : 77.30 % 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: 0.43 (0.24), residues: 1138 helix: 1.33 (0.25), residues: 447 sheet: 0.02 (0.33), residues: 226 loop : -0.52 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS R 381 PHE 0.014 0.001 PHE A 212 TYR 0.013 0.001 TYR R 391 ARG 0.003 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 145 time to evaluate : 1.078 Fit side-chains REVERT: R 140 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7082 (tp30) REVERT: R 196 MET cc_start: 0.7949 (mtt) cc_final: 0.7551 (mtp) REVERT: R 204 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6315 (mm-30) REVERT: R 284 TYR cc_start: 0.7292 (m-80) cc_final: 0.7033 (m-80) REVERT: R 327 MET cc_start: 0.8445 (mtm) cc_final: 0.8233 (mtt) REVERT: B 19 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7279 (ttp80) REVERT: B 57 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8513 (pttp) REVERT: B 59 TYR cc_start: 0.9177 (OUTLIER) cc_final: 0.8959 (m-80) REVERT: B 61 MET cc_start: 0.8568 (ppp) cc_final: 0.8284 (ppp) REVERT: B 124 TYR cc_start: 0.8939 (m-80) cc_final: 0.8649 (m-80) REVERT: B 219 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7526 (mtm180) REVERT: G 38 MET cc_start: 0.8235 (ttp) cc_final: 0.7766 (ttm) REVERT: N 89 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: N 105 ARG cc_start: 0.7685 (mpp80) cc_final: 0.7433 (ttp-110) REVERT: N 123 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8631 (tp40) outliers start: 47 outliers final: 23 residues processed: 177 average time/residue: 1.2990 time to fit residues: 244.8613 Evaluate side-chains 171 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 377 HIS A 19 GLN A 31 GLN A 357 HIS B 17 GLN N 1 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.005 0.049 9559 Z= 0.301 Angle : 0.602 10.855 12887 Z= 0.310 Chirality : 0.045 0.166 1413 Planarity : 0.004 0.039 1621 Dihedral : 9.448 82.582 1598 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.96 % Allowed : 17.74 % Favored : 77.30 % 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: 0.45 (0.24), residues: 1138 helix: 1.37 (0.25), residues: 446 sheet: -0.11 (0.32), residues: 237 loop : -0.45 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 236 HIS 0.004 0.001 HIS R 381 PHE 0.015 0.002 PHE A 212 TYR 0.015 0.002 TYR R 391 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 1.035 Fit side-chains REVERT: R 140 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7094 (tp30) REVERT: R 196 MET cc_start: 0.7964 (mtt) cc_final: 0.7585 (mtp) REVERT: R 204 GLU cc_start: 0.6719 (mm-30) cc_final: 0.6319 (mm-30) REVERT: R 284 TYR cc_start: 0.7253 (m-80) cc_final: 0.6971 (m-80) REVERT: R 405 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 17 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7100 (ttmm) REVERT: A 299 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6606 (tt0) REVERT: B 19 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7220 (ttp80) REVERT: B 61 MET cc_start: 0.8637 (ppp) cc_final: 0.8229 (ppp) REVERT: B 124 TYR cc_start: 0.8923 (m-80) cc_final: 0.8646 (m-80) REVERT: G 38 MET cc_start: 0.8232 (ttp) cc_final: 0.7909 (ttm) REVERT: N 89 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: N 105 ARG cc_start: 0.7664 (mpp80) cc_final: 0.7375 (ttp-110) REVERT: N 123 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8617 (tp40) outliers start: 47 outliers final: 31 residues processed: 174 average time/residue: 1.2388 time to fit residues: 230.0259 Evaluate side-chains 175 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain R residue 378 SER Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 31 GLN A 357 HIS B 17 GLN N 1 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9559 Z= 0.221 Angle : 0.550 9.326 12887 Z= 0.282 Chirality : 0.043 0.169 1413 Planarity : 0.004 0.040 1621 Dihedral : 9.071 79.021 1598 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.33 % Allowed : 19.01 % Favored : 76.66 % 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: 0.63 (0.25), residues: 1138 helix: 1.61 (0.25), residues: 446 sheet: -0.16 (0.32), residues: 238 loop : -0.38 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 236 HIS 0.004 0.001 HIS R 381 PHE 0.013 0.001 PHE B 253 TYR 0.013 0.001 TYR R 391 ARG 0.003 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 1.094 Fit side-chains REVERT: R 196 MET cc_start: 0.7956 (mtt) cc_final: 0.7560 (mtp) REVERT: R 204 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6313 (mm-30) REVERT: R 284 TYR cc_start: 0.7353 (m-80) cc_final: 0.7032 (m-80) REVERT: A 17 LYS cc_start: 0.7571 (ttmm) cc_final: 0.7049 (pttt) REVERT: A 299 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6610 (tt0) REVERT: B 19 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7277 (ttp80) REVERT: B 38 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: B 61 MET cc_start: 0.8600 (ppp) cc_final: 0.8285 (ppp) REVERT: B 124 TYR cc_start: 0.8913 (m-80) cc_final: 0.8638 (m-80) REVERT: B 219 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7510 (mtm180) REVERT: G 38 MET cc_start: 0.8264 (ttp) cc_final: 0.7907 (ttm) REVERT: N 89 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7584 (pt0) REVERT: N 105 ARG cc_start: 0.7578 (mpp80) cc_final: 0.7366 (ttp-110) REVERT: N 123 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8691 (tp40) outliers start: 41 outliers final: 29 residues processed: 170 average time/residue: 1.2538 time to fit residues: 226.9832 Evaluate side-chains 176 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain R residue 378 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 50.0000 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 0.0020 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 31 GLN A 357 HIS B 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9559 Z= 0.173 Angle : 0.525 11.922 12887 Z= 0.267 Chirality : 0.041 0.170 1413 Planarity : 0.003 0.040 1621 Dihedral : 8.547 77.528 1598 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.01 % Allowed : 19.01 % Favored : 76.98 % 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: 0.79 (0.25), residues: 1138 helix: 1.81 (0.25), residues: 447 sheet: -0.19 (0.32), residues: 237 loop : -0.30 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 PHE 0.012 0.001 PHE B 253 TYR 0.012 0.001 TYR R 149 ARG 0.004 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 1.128 Fit side-chains REVERT: R 140 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7152 (tp30) REVERT: R 143 LYS cc_start: 0.7245 (ttmt) cc_final: 0.7006 (mtpt) REVERT: R 196 MET cc_start: 0.7956 (mtt) cc_final: 0.7594 (mtp) REVERT: R 204 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6315 (mm-30) REVERT: R 284 TYR cc_start: 0.7467 (m-80) cc_final: 0.7206 (m-80) REVERT: A 17 LYS cc_start: 0.7540 (ttmm) cc_final: 0.7039 (pttt) REVERT: A 299 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6637 (tt0) REVERT: B 19 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7244 (ttp80) REVERT: B 38 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7538 (m-30) REVERT: B 61 MET cc_start: 0.8580 (ppp) cc_final: 0.8256 (ppp) REVERT: B 124 TYR cc_start: 0.8870 (m-80) cc_final: 0.8624 (m-80) REVERT: B 219 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7535 (mtm180) REVERT: B 314 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8073 (ttm-80) REVERT: G 38 MET cc_start: 0.8244 (ttp) cc_final: 0.7880 (ttm) REVERT: N 89 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7568 (pt0) outliers start: 38 outliers final: 24 residues processed: 176 average time/residue: 1.3402 time to fit residues: 250.5837 Evaluate side-chains 171 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 378 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 9.9990 chunk 32 optimal weight: 0.0670 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 50.0000 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 31 GLN A 357 HIS A 390 GLN B 17 GLN N 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9559 Z= 0.306 Angle : 0.602 10.502 12887 Z= 0.312 Chirality : 0.045 0.183 1413 Planarity : 0.004 0.064 1621 Dihedral : 9.306 81.032 1598 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.75 % Allowed : 18.37 % Favored : 76.87 % 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 (0.25), residues: 1138 helix: 1.62 (0.25), residues: 446 sheet: -0.20 (0.32), residues: 238 loop : -0.33 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 236 HIS 0.004 0.001 HIS B 311 PHE 0.018 0.002 PHE R 172 TYR 0.019 0.002 TYR B 59 ARG 0.010 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 140 time to evaluate : 1.137 Fit side-chains REVERT: R 140 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: R 196 MET cc_start: 0.7957 (mtt) cc_final: 0.7579 (mtp) REVERT: R 204 GLU cc_start: 0.6671 (mm-30) cc_final: 0.6226 (mm-30) REVERT: R 284 TYR cc_start: 0.7384 (m-80) cc_final: 0.7086 (m-80) REVERT: R 405 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7308 (tm-30) REVERT: A 17 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7090 (ttmm) REVERT: A 299 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6651 (tt0) REVERT: B 19 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7229 (ttp80) REVERT: B 38 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: B 61 MET cc_start: 0.8646 (ppp) cc_final: 0.8204 (ppp) REVERT: B 124 TYR cc_start: 0.8909 (m-80) cc_final: 0.8644 (m-80) REVERT: B 219 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7479 (mtm180) REVERT: G 38 MET cc_start: 0.8279 (ttp) cc_final: 0.7971 (ttm) REVERT: N 89 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7591 (pt0) outliers start: 45 outliers final: 29 residues processed: 171 average time/residue: 1.3278 time to fit residues: 241.8181 Evaluate side-chains 173 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain R residue 378 SER Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 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: 2.9990 chunk 60 optimal weight: 0.0370 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 0.0370 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 31 GLN A 357 HIS A 390 GLN B 17 GLN N 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9559 Z= 0.175 Angle : 0.522 12.006 12887 Z= 0.267 Chirality : 0.041 0.172 1413 Planarity : 0.003 0.040 1621 Dihedral : 8.537 76.952 1598 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.59 % Allowed : 20.06 % Favored : 76.35 % 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 (0.25), residues: 1138 helix: 1.89 (0.25), residues: 447 sheet: -0.19 (0.32), residues: 237 loop : -0.25 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 381 PHE 0.012 0.001 PHE B 253 TYR 0.012 0.001 TYR R 149 ARG 0.004 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.059 Fit side-chains REVERT: R 140 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7143 (tp30) REVERT: R 196 MET cc_start: 0.7962 (mtt) cc_final: 0.7598 (mtp) REVERT: R 204 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6236 (mm-30) REVERT: R 284 TYR cc_start: 0.7475 (m-80) cc_final: 0.7213 (m-80) REVERT: A 17 LYS cc_start: 0.7543 (ttmm) cc_final: 0.7042 (pttt) REVERT: A 299 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6634 (tt0) REVERT: B 19 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7257 (ttp80) REVERT: B 38 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: B 61 MET cc_start: 0.8547 (ppp) cc_final: 0.8203 (ppp) REVERT: B 124 TYR cc_start: 0.8859 (m-80) cc_final: 0.8624 (m-80) REVERT: B 219 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7512 (mtm180) REVERT: B 314 ARG cc_start: 0.8479 (ttt180) cc_final: 0.8053 (ttm-80) REVERT: G 38 MET cc_start: 0.8240 (ttp) cc_final: 0.7885 (ttm) REVERT: N 89 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: N 105 ARG cc_start: 0.7483 (mpp80) cc_final: 0.7245 (ttp-110) outliers start: 34 outliers final: 25 residues processed: 164 average time/residue: 1.3364 time to fit residues: 232.8880 Evaluate side-chains 173 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 378 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 31 GLN A 357 HIS A 390 GLN B 17 GLN N 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9559 Z= 0.173 Angle : 0.516 12.600 12887 Z= 0.265 Chirality : 0.041 0.175 1413 Planarity : 0.003 0.040 1621 Dihedral : 8.139 76.557 1598 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.48 % Allowed : 20.38 % Favored : 76.14 % 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: 1.01 (0.25), residues: 1138 helix: 2.03 (0.25), residues: 446 sheet: -0.15 (0.32), residues: 242 loop : -0.15 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 PHE 0.022 0.001 PHE R 172 TYR 0.013 0.001 TYR R 149 ARG 0.004 0.000 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.075 Fit side-chains REVERT: R 140 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: R 196 MET cc_start: 0.7947 (mtt) cc_final: 0.7624 (mtp) REVERT: R 204 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6238 (mm-30) REVERT: R 284 TYR cc_start: 0.7455 (m-80) cc_final: 0.7207 (m-80) REVERT: A 17 LYS cc_start: 0.7534 (ttmm) cc_final: 0.7041 (pttt) REVERT: A 299 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6659 (tt0) REVERT: B 19 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7242 (ttp80) REVERT: B 38 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: B 124 TYR cc_start: 0.8916 (m-80) cc_final: 0.8656 (m-80) REVERT: B 219 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7537 (mtm180) REVERT: B 325 MET cc_start: 0.8159 (mmt) cc_final: 0.7796 (mmm) REVERT: G 38 MET cc_start: 0.8236 (ttp) cc_final: 0.7875 (ttm) REVERT: N 89 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: N 105 ARG cc_start: 0.7481 (mpp80) cc_final: 0.7232 (ttp-110) outliers start: 33 outliers final: 20 residues processed: 166 average time/residue: 1.3226 time to fit residues: 233.2112 Evaluate side-chains 164 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 378 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 50.0000 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 31 GLN A 357 HIS A 390 GLN B 17 GLN N 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120487 restraints weight = 9578.374| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.11 r_work: 0.3063 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9559 Z= 0.200 Angle : 0.533 11.446 12887 Z= 0.274 Chirality : 0.042 0.171 1413 Planarity : 0.004 0.040 1621 Dihedral : 8.213 77.019 1598 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.17 % Allowed : 20.70 % Favored : 76.14 % 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: 0.99 (0.25), residues: 1138 helix: 2.04 (0.25), residues: 446 sheet: -0.18 (0.32), residues: 237 loop : -0.19 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.003 0.001 HIS R 381 PHE 0.013 0.001 PHE B 253 TYR 0.014 0.001 TYR N 80 ARG 0.004 0.000 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4247.77 seconds wall clock time: 75 minutes 14.85 seconds (4514.85 seconds total)