Starting phenix.real_space_refine on Fri Nov 15 02:49:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/11_2024/8iw1_35761.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/11_2024/8iw1_35761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/11_2024/8iw1_35761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/11_2024/8iw1_35761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/11_2024/8iw1_35761.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/11_2024/8iw1_35761.cif" } resolution = 3.4 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= 0.004 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5307 2.51 5 N 1412 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8327 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1761 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2483 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 327} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 328 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 43} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1984 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 8, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 128 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1771 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.08, per 1000 atoms: 0.61 Number of scatterers: 8327 At special positions: 0 Unit cell: (120.7, 93.5, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1557 8.00 N 1412 7.00 C 5307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 33.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.646A pdb=" N GLN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.754A pdb=" N ILE A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.511A pdb=" N ASP A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.764A pdb=" N ARG A 270 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 4.035A pdb=" N GLU A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.711A pdb=" N ILE A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 365 removed outlier: 4.402A pdb=" N ARG A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 378 Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.552A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 36 removed outlier: 3.584A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 32 through 36' Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.673A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'R' and resid 33 through 38 removed outlier: 4.472A pdb=" N GLY R 37 " --> pdb=" O ALA R 33 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 33 through 38' Processing helix chain 'R' and resid 42 through 48 Processing helix chain 'R' and resid 50 through 59 removed outlier: 3.979A pdb=" N ILE R 54 " --> pdb=" O ASN R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 96 removed outlier: 3.509A pdb=" N PHE R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU R 70 " --> pdb=" O PRO R 66 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA R 72 " --> pdb=" O ASN R 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU R 74 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) Proline residue: R 87 - end of helix removed outlier: 4.773A pdb=" N VAL R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 135 removed outlier: 4.209A pdb=" N CYS R 105 " --> pdb=" O GLY R 101 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR R 113 " --> pdb=" O THR R 109 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER R 114 " --> pdb=" O CYS R 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE R 117 " --> pdb=" O THR R 113 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N CYS R 125 " --> pdb=" O PHE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 198 through 226 removed outlier: 3.590A pdb=" N PHE R 206 " --> pdb=" O CYS R 202 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 3.684A pdb=" N TYR R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 284 removed outlier: 3.801A pdb=" N ALA R 263 " --> pdb=" O THR R 259 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 291 through 304 removed outlier: 4.670A pdb=" N ILE R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL R 297 " --> pdb=" O TYR R 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 311 removed outlier: 4.033A pdb=" N TYR R 311 " --> pdb=" O ASN R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 327 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.739A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 197 Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 197 removed outlier: 6.767A pdb=" N HIS A 43 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE A 209 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A 45 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG A 44 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE A 232 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU A 46 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL A 234 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE A 277 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR A 233 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASN A 279 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA A 235 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.822A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.617A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.230A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.399A 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: 3.812A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.598A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.814A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.687A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.790A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.790A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG S 98 " --> pdb=" O PHE S 110 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.091A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1011 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: 2.21 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1349 1.29 - 1.42: 2320 1.42 - 1.55: 4765 1.55 - 1.68: 5 1.68 - 1.81: 72 Bond restraints: 8511 Sorted by residual: bond pdb=" C LEU S 178 " pdb=" O LEU S 178 " ideal model delta sigma weight residual 1.235 1.156 0.079 1.13e-02 7.83e+03 4.93e+01 bond pdb=" C TYR R 226 " pdb=" O TYR R 226 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.33e-02 5.65e+03 2.72e+01 bond pdb=" C LYS R 230 " pdb=" O LYS R 230 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.19e-02 7.06e+03 2.65e+01 bond pdb=" CA ASP A 258 " pdb=" C ASP A 258 " ideal model delta sigma weight residual 1.524 1.459 0.064 1.26e-02 6.30e+03 2.62e+01 bond pdb=" CA LEU A 28 " pdb=" C LEU A 28 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.24e-02 6.50e+03 2.50e+01 ... (remaining 8506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 11300 2.51 - 5.03: 242 5.03 - 7.54: 31 7.54 - 10.06: 11 10.06 - 12.57: 1 Bond angle restraints: 11585 Sorted by residual: angle pdb=" N THR A 356 " pdb=" CA THR A 356 " pdb=" C THR A 356 " ideal model delta sigma weight residual 110.97 119.90 -8.93 1.09e+00 8.42e-01 6.71e+01 angle pdb=" N ASN A 358 " pdb=" CA ASN A 358 " pdb=" C ASN A 358 " ideal model delta sigma weight residual 112.59 103.36 9.23 1.22e+00 6.72e-01 5.73e+01 angle pdb=" N VAL A 354 " pdb=" CA VAL A 354 " pdb=" C VAL A 354 " ideal model delta sigma weight residual 110.62 118.32 -7.70 1.02e+00 9.61e-01 5.70e+01 angle pdb=" N HIS R 59 " pdb=" CA HIS R 59 " pdb=" C HIS R 59 " ideal model delta sigma weight residual 111.14 118.12 -6.98 1.08e+00 8.57e-01 4.18e+01 angle pdb=" N LEU A 28 " pdb=" CA LEU A 28 " pdb=" C LEU A 28 " ideal model delta sigma weight residual 111.03 103.87 7.16 1.11e+00 8.12e-01 4.16e+01 ... (remaining 11580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 4321 16.80 - 33.59: 496 33.59 - 50.39: 129 50.39 - 67.18: 19 67.18 - 83.98: 10 Dihedral angle restraints: 4975 sinusoidal: 1762 harmonic: 3213 Sorted by residual: dihedral pdb=" CA CYS A 366 " pdb=" C CYS A 366 " pdb=" N ARG A 367 " pdb=" CA ARG A 367 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLN R 227 " pdb=" C GLN R 227 " pdb=" N ALA R 228 " pdb=" CA ALA R 228 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C PHE R 60 " pdb=" N PHE R 60 " pdb=" CA PHE R 60 " pdb=" CB PHE R 60 " ideal model delta harmonic sigma weight residual -122.60 -132.80 10.20 0 2.50e+00 1.60e-01 1.66e+01 ... (remaining 4972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1250 0.103 - 0.205: 62 0.205 - 0.307: 12 0.307 - 0.410: 4 0.410 - 0.512: 5 Chirality restraints: 1333 Sorted by residual: chirality pdb=" CA TYR R 226 " pdb=" N TYR R 226 " pdb=" C TYR R 226 " pdb=" CB TYR R 226 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CA PHE R 60 " pdb=" N PHE R 60 " pdb=" C PHE R 60 " pdb=" CB PHE R 60 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CA PHE R 207 " pdb=" N PHE R 207 " pdb=" C PHE R 207 " pdb=" CB PHE R 207 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 1330 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 352 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C CYS A 352 " 0.068 2.00e-02 2.50e+03 pdb=" O CYS A 352 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA A 353 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 257 " -0.013 2.00e-02 2.50e+03 2.77e-02 7.70e+00 pdb=" C LEU A 257 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU A 257 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP A 258 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 260 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C PHE A 260 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE A 260 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU A 261 " -0.015 2.00e-02 2.50e+03 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 516 2.72 - 3.27: 8090 3.27 - 3.81: 12826 3.81 - 4.36: 15138 4.36 - 4.90: 26997 Nonbonded interactions: 63567 Sorted by model distance: nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.179 3.120 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.180 3.040 nonbonded pdb=" O CYS R 110 " pdb=" OG SER R 164 " model vdw 2.203 3.040 nonbonded pdb=" O SER S 52 " pdb=" NH1 ARG S 72 " model vdw 2.224 3.120 nonbonded pdb=" NE1 TRP S 47 " pdb=" O ALA S 49 " model vdw 2.244 3.120 ... (remaining 63562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.120 Find NCS groups from input model: 0.090 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 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 : 0.007 0.079 8511 Z= 0.453 Angle : 0.860 12.572 11585 Z= 0.558 Chirality : 0.063 0.512 1333 Planarity : 0.005 0.048 1472 Dihedral : 15.677 83.981 2897 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.59 % Allowed : 15.13 % Favored : 84.28 % Cbeta Deviations : 0.10 % 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: -1.82 (0.25), residues: 1085 helix: -0.67 (0.29), residues: 343 sheet: -0.51 (0.32), residues: 267 loop : -1.98 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 271 HIS 0.008 0.001 HIS R 59 PHE 0.026 0.002 PHE R 60 TYR 0.024 0.002 TYR S 235 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 341 ASP cc_start: 0.7237 (t0) cc_final: 0.6929 (t0) REVERT: B 61 MET cc_start: 0.7411 (ppp) cc_final: 0.6855 (ppp) REVERT: R 220 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7860 (tt) outliers start: 5 outliers final: 2 residues processed: 190 average time/residue: 0.2598 time to fit residues: 64.0500 Evaluate side-chains 160 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain R residue 220 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 0.0170 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 358 ASN A 377 GLN B 176 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8511 Z= 0.158 Angle : 0.552 6.200 11585 Z= 0.296 Chirality : 0.042 0.176 1333 Planarity : 0.004 0.040 1472 Dihedral : 4.788 33.493 1195 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.84 % Allowed : 17.85 % Favored : 79.31 % 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: -1.20 (0.25), residues: 1085 helix: 0.16 (0.29), residues: 346 sheet: -0.21 (0.32), residues: 269 loop : -1.87 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 271 HIS 0.003 0.001 HIS A 349 PHE 0.013 0.001 PHE B 234 TYR 0.023 0.001 TYR S 235 ARG 0.010 0.001 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.7537 (ppp) cc_final: 0.6781 (ppp) REVERT: B 124 TYR cc_start: 0.7292 (m-80) cc_final: 0.7045 (m-80) REVERT: R 220 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7791 (mt) REVERT: R 302 TYR cc_start: 0.6571 (t80) cc_final: 0.6354 (t80) REVERT: S 34 MET cc_start: 0.6215 (mmm) cc_final: 0.5594 (mmt) outliers start: 24 outliers final: 14 residues processed: 174 average time/residue: 0.2578 time to fit residues: 58.5206 Evaluate side-chains 171 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 237 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8511 Z= 0.202 Angle : 0.555 6.433 11585 Z= 0.294 Chirality : 0.042 0.180 1333 Planarity : 0.004 0.047 1472 Dihedral : 4.585 32.871 1193 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.66 % Allowed : 19.62 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1085 helix: 0.61 (0.30), residues: 341 sheet: 0.00 (0.32), residues: 271 loop : -1.87 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.008 0.001 HIS R 122 PHE 0.015 0.002 PHE B 180 TYR 0.024 0.002 TYR S 235 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.7518 (ppp) cc_final: 0.6876 (ppp) REVERT: B 234 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: B 308 LEU cc_start: 0.6941 (mp) cc_final: 0.6703 (mp) REVERT: R 220 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7786 (mt) REVERT: R 302 TYR cc_start: 0.6766 (t80) cc_final: 0.6552 (t80) REVERT: S 34 MET cc_start: 0.6220 (mmm) cc_final: 0.5675 (mmt) outliers start: 31 outliers final: 18 residues processed: 178 average time/residue: 0.2433 time to fit residues: 56.9571 Evaluate side-chains 172 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 268 ASN C 44 HIS ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8511 Z= 0.302 Angle : 0.621 8.645 11585 Z= 0.327 Chirality : 0.045 0.226 1333 Planarity : 0.005 0.051 1472 Dihedral : 4.910 38.226 1193 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.37 % Allowed : 22.58 % Favored : 73.05 % 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: -0.91 (0.25), residues: 1085 helix: 0.39 (0.29), residues: 355 sheet: 0.14 (0.32), residues: 265 loop : -1.85 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.009 0.002 HIS R 122 PHE 0.023 0.002 PHE B 241 TYR 0.029 0.002 TYR S 235 ARG 0.007 0.001 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.7504 (ppp) cc_final: 0.6899 (ppp) REVERT: B 117 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 234 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6974 (m-80) REVERT: B 308 LEU cc_start: 0.6941 (mp) cc_final: 0.6661 (mp) REVERT: R 205 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6397 (tp) REVERT: R 220 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7820 (mt) REVERT: R 264 MET cc_start: 0.7286 (tpt) cc_final: 0.7042 (tpt) REVERT: R 302 TYR cc_start: 0.6938 (t80) cc_final: 0.6673 (t80) REVERT: S 34 MET cc_start: 0.6251 (mmm) cc_final: 0.5711 (mmt) outliers start: 37 outliers final: 22 residues processed: 184 average time/residue: 0.2449 time to fit residues: 59.1549 Evaluate side-chains 182 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 226 TYR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8511 Z= 0.248 Angle : 0.583 8.806 11585 Z= 0.306 Chirality : 0.043 0.207 1333 Planarity : 0.004 0.050 1472 Dihedral : 4.781 38.874 1193 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.96 % Allowed : 22.34 % Favored : 72.70 % 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: -0.84 (0.25), residues: 1085 helix: 0.45 (0.29), residues: 354 sheet: 0.10 (0.32), residues: 274 loop : -1.79 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.007 0.001 HIS S 35 PHE 0.025 0.002 PHE B 241 TYR 0.027 0.002 TYR S 235 ARG 0.007 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.7430 (ppp) cc_final: 0.6897 (ppp) REVERT: B 234 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6744 (m-80) REVERT: B 308 LEU cc_start: 0.6989 (mp) cc_final: 0.6731 (mp) REVERT: R 205 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6371 (tp) REVERT: R 220 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7815 (mt) REVERT: R 302 TYR cc_start: 0.6944 (t80) cc_final: 0.6669 (t80) REVERT: R 314 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6551 (t80) REVERT: S 34 MET cc_start: 0.6249 (mmm) cc_final: 0.5656 (mmt) REVERT: S 80 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.5338 (p90) outliers start: 42 outliers final: 27 residues processed: 194 average time/residue: 0.2317 time to fit residues: 59.7130 Evaluate side-chains 193 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 226 TYR Chi-restraints excluded: chain R residue 259 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 237 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 0.0670 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 0.0870 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN R 303 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8511 Z= 0.155 Angle : 0.532 8.121 11585 Z= 0.276 Chirality : 0.041 0.179 1333 Planarity : 0.004 0.044 1472 Dihedral : 4.394 31.728 1193 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.31 % Allowed : 24.47 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1085 helix: 0.84 (0.29), residues: 349 sheet: 0.23 (0.32), residues: 267 loop : -1.70 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 317 HIS 0.003 0.001 HIS B 91 PHE 0.028 0.001 PHE B 241 TYR 0.020 0.001 TYR S 235 ARG 0.007 0.001 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.4442 (mtm) cc_final: 0.4163 (ptp) REVERT: B 45 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6162 (mtp) REVERT: B 61 MET cc_start: 0.7354 (ppp) cc_final: 0.6809 (ppp) REVERT: B 234 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6694 (m-80) REVERT: R 220 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7850 (mt) REVERT: R 302 TYR cc_start: 0.6816 (t80) cc_final: 0.6580 (t80) REVERT: R 314 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.6602 (t80) REVERT: S 34 MET cc_start: 0.6182 (mmm) cc_final: 0.5660 (mmt) outliers start: 28 outliers final: 18 residues processed: 177 average time/residue: 0.2370 time to fit residues: 55.1888 Evaluate side-chains 176 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 226 TYR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 0.0470 chunk 88 optimal weight: 0.9980 chunk 58 optimal weight: 0.0370 chunk 105 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 75 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8511 Z= 0.174 Angle : 0.545 8.573 11585 Z= 0.281 Chirality : 0.042 0.178 1333 Planarity : 0.004 0.043 1472 Dihedral : 4.431 28.936 1193 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.14 % Allowed : 24.11 % Favored : 71.75 % 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: -0.40 (0.25), residues: 1085 helix: 0.98 (0.29), residues: 348 sheet: 0.39 (0.31), residues: 264 loop : -1.65 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.021 0.001 PHE B 241 TYR 0.023 0.001 TYR S 235 ARG 0.011 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7817 (mtt-85) REVERT: B 234 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: R 220 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7772 (mt) REVERT: R 314 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6545 (t80) REVERT: S 34 MET cc_start: 0.6242 (mmm) cc_final: 0.5696 (mmt) REVERT: S 80 PHE cc_start: 0.5557 (OUTLIER) cc_final: 0.5131 (p90) outliers start: 35 outliers final: 21 residues processed: 183 average time/residue: 0.2315 time to fit residues: 56.4420 Evaluate side-chains 186 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 226 TYR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 0.0060 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8511 Z= 0.154 Angle : 0.542 8.769 11585 Z= 0.276 Chirality : 0.041 0.189 1333 Planarity : 0.004 0.041 1472 Dihedral : 4.373 27.246 1193 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.66 % Allowed : 24.59 % Favored : 71.75 % 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: -0.28 (0.25), residues: 1085 helix: 1.08 (0.29), residues: 349 sheet: 0.56 (0.31), residues: 262 loop : -1.62 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE B 241 TYR 0.021 0.001 TYR S 235 ARG 0.009 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 208 MET cc_start: 0.7110 (ttm) cc_final: 0.6855 (ttp) REVERT: B 45 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6081 (mtp) REVERT: B 61 MET cc_start: 0.7348 (ppp) cc_final: 0.6781 (ppp) REVERT: B 234 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6698 (m-80) REVERT: R 220 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7724 (mt) REVERT: S 34 MET cc_start: 0.6218 (mmm) cc_final: 0.5665 (mmt) REVERT: S 78 THR cc_start: 0.7289 (t) cc_final: 0.6988 (m) REVERT: S 80 PHE cc_start: 0.5509 (OUTLIER) cc_final: 0.5117 (p90) outliers start: 31 outliers final: 23 residues processed: 170 average time/residue: 0.2413 time to fit residues: 53.9020 Evaluate side-chains 174 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 226 TYR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 75 GLN ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8511 Z= 0.203 Angle : 0.567 9.379 11585 Z= 0.290 Chirality : 0.042 0.208 1333 Planarity : 0.004 0.041 1472 Dihedral : 4.459 32.592 1193 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.66 % Allowed : 25.41 % Favored : 70.92 % 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: -0.28 (0.26), residues: 1085 helix: 0.96 (0.29), residues: 356 sheet: 0.59 (0.31), residues: 273 loop : -1.63 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.006 0.001 HIS S 35 PHE 0.019 0.001 PHE B 241 TYR 0.024 0.002 TYR S 235 ARG 0.009 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6055 (mtp) REVERT: B 61 MET cc_start: 0.7315 (ppp) cc_final: 0.6795 (ppp) REVERT: B 234 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6696 (m-80) REVERT: B 251 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.6032 (mtt-85) REVERT: R 205 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6181 (tp) REVERT: R 220 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7653 (mt) REVERT: S 34 MET cc_start: 0.6235 (mmm) cc_final: 0.5700 (mmt) REVERT: S 78 THR cc_start: 0.7317 (t) cc_final: 0.6997 (m) REVERT: S 80 PHE cc_start: 0.5526 (OUTLIER) cc_final: 0.5118 (p90) outliers start: 31 outliers final: 20 residues processed: 180 average time/residue: 0.2386 time to fit residues: 56.6120 Evaluate side-chains 186 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 226 TYR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 53 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8511 Z= 0.150 Angle : 0.539 9.169 11585 Z= 0.274 Chirality : 0.041 0.175 1333 Planarity : 0.004 0.040 1472 Dihedral : 4.277 30.046 1193 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.07 % Allowed : 26.12 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1085 helix: 1.19 (0.29), residues: 350 sheet: 0.81 (0.32), residues: 264 loop : -1.61 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE B 241 TYR 0.020 0.001 TYR S 235 ARG 0.010 0.001 ARG R 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.896 Fit side-chains REVERT: B 45 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6100 (mtp) REVERT: B 61 MET cc_start: 0.7327 (ppp) cc_final: 0.6734 (ppp) REVERT: B 234 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: R 220 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7642 (mt) REVERT: S 34 MET cc_start: 0.6233 (mmm) cc_final: 0.5693 (mmt) REVERT: S 78 THR cc_start: 0.7234 (t) cc_final: 0.6952 (m) REVERT: S 80 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.5101 (p90) outliers start: 26 outliers final: 19 residues processed: 171 average time/residue: 0.2237 time to fit residues: 51.1995 Evaluate side-chains 176 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 220 ILE Chi-restraints excluded: chain R residue 226 TYR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.0270 chunk 62 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 340 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117914 restraints weight = 12406.469| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.20 r_work: 0.3445 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8511 Z= 0.142 Angle : 0.529 9.029 11585 Z= 0.268 Chirality : 0.041 0.166 1333 Planarity : 0.004 0.039 1472 Dihedral : 4.140 29.575 1193 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.96 % Allowed : 26.12 % Favored : 70.92 % 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: 0.02 (0.26), residues: 1085 helix: 1.33 (0.29), residues: 350 sheet: 0.80 (0.31), residues: 273 loop : -1.57 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 221 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE B 241 TYR 0.019 0.001 TYR S 235 ARG 0.010 0.001 ARG R 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.20 seconds wall clock time: 42 minutes 37.73 seconds (2557.73 seconds total)