Starting phenix.real_space_refine on Wed Sep 25 01:43:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/09_2024/6wpw_21866_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/09_2024/6wpw_21866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/09_2024/6wpw_21866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/09_2024/6wpw_21866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/09_2024/6wpw_21866_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/09_2024/6wpw_21866_neut.cif" } resolution = 3.1 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= 0.005 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 56 5.16 5 C 5881 2.51 5 N 1627 2.21 5 O 1698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9262 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1835 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2601 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 449 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 244 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3162 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 14, 'TRANS': 383} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 5.39, per 1000 atoms: 0.58 Number of scatterers: 9262 At special positions: 0 Unit cell: (167.48, 108.12, 98.58, 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 56 16.00 O 1698 8.00 N 1627 7.00 C 5881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.02 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.04 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " 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: 2.08 Conformation dependent library (CDL) restraints added in 1.0 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 40.7% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'C' and resid 11 through 39 removed outlier: 3.554A pdb=" N LYS C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 25 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 264 through 278 removed outlier: 3.876A pdb=" N GLU C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.854A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.531A pdb=" N GLU C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 4.215A pdb=" N ALA C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 353 removed outlier: 4.187A pdb=" N ILE C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 353 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 removed outlier: 3.852A pdb=" N ARG C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 381 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.552A pdb=" N GLU D 12 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 20 " --> pdb=" O ASN D 16 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA D 21 " --> pdb=" O GLN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.536A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 24 removed outlier: 3.665A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.613A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.748A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'R' and resid 27 through 48 removed outlier: 3.503A pdb=" N PHE R 31 " --> pdb=" O GLN R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 166 removed outlier: 3.686A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL R 143 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 removed outlier: 3.842A pdb=" N HIS R 170 " --> pdb=" O SER R 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 172 through 197 removed outlier: 3.501A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 202 removed outlier: 3.552A pdb=" N ARG R 201 " --> pdb=" O LEU R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 212 Processing helix chain 'R' and resid 221 through 252 removed outlier: 3.544A pdb=" N VAL R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA R 227 " --> pdb=" O GLY R 223 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU R 249 " --> pdb=" O GLU R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 273 removed outlier: 3.683A pdb=" N GLY R 269 " --> pdb=" O SER R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 287 removed outlier: 3.632A pdb=" N VAL R 280 " --> pdb=" O MET R 276 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 4.027A pdb=" N VAL R 285 " --> pdb=" O PRO R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 330 removed outlier: 3.569A pdb=" N ARG R 308 " --> pdb=" O TRP R 304 " (cutoff:3.500A) Proline residue: R 310 - end of helix removed outlier: 3.768A pdb=" N ALA R 314 " --> pdb=" O PRO R 310 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 317 " --> pdb=" O LEU R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 335 removed outlier: 4.115A pdb=" N ALA R 335 " --> pdb=" O ALA R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 353 removed outlier: 3.596A pdb=" N LEU R 352 " --> pdb=" O ALA R 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 360 through 366 removed outlier: 3.584A pdb=" N PHE R 365 " --> pdb=" O GLU R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 389 removed outlier: 3.621A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU R 386 " --> pdb=" O LEU R 382 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU R 388 " --> pdb=" O PHE R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 removed outlier: 3.648A pdb=" N ALA R 397 " --> pdb=" O GLY R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 423 removed outlier: 3.502A pdb=" N HIS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG R 419 " --> pdb=" O TRP R 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 40 through 42 removed outlier: 3.955A pdb=" N PHE C 212 " --> pdb=" O PHE C 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.534A pdb=" N VAL C 247 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 244 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE C 290 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE C 246 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASN C 292 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 248 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.720A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY D 330 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.520A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 70 " --> pdb=" O TRP D 82 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.912A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.075A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 7.105A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 233 through 234 removed outlier: 3.530A pdb=" N CYS D 250 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.640A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.957A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.105A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 77 through 80 removed outlier: 3.516A pdb=" N LYS R 98 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 79 " --> pdb=" O VAL R 96 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1098 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: 2.70 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2946 1.34 - 1.46: 2279 1.46 - 1.58: 4170 1.58 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 9471 Sorted by residual: bond pdb=" N VAL D 276 " pdb=" CA VAL D 276 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.14e+01 bond pdb=" N ILE D 273 " pdb=" CA ILE D 273 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.86e+00 bond pdb=" N VAL D 315 " pdb=" CA VAL D 315 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.79e+00 bond pdb=" N TYR D 289 " pdb=" CA TYR D 289 " ideal model delta sigma weight residual 1.453 1.491 -0.037 1.22e-02 6.72e+03 9.40e+00 bond pdb=" N VAL R 363 " pdb=" CA VAL R 363 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.26e-02 6.30e+03 8.73e+00 ... (remaining 9466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 12582 2.82 - 5.64: 226 5.64 - 8.46: 24 8.46 - 11.28: 6 11.28 - 14.10: 2 Bond angle restraints: 12840 Sorted by residual: angle pdb=" N PRO R 53 " pdb=" CA PRO R 53 " pdb=" C PRO R 53 " ideal model delta sigma weight residual 112.47 126.57 -14.10 2.06e+00 2.36e-01 4.68e+01 angle pdb=" N LEU R 242 " pdb=" CA LEU R 242 " pdb=" C LEU R 242 " ideal model delta sigma weight residual 111.69 104.42 7.27 1.23e+00 6.61e-01 3.50e+01 angle pdb=" C VAL R 57 " pdb=" N CYS R 58 " pdb=" CA CYS R 58 " ideal model delta sigma weight residual 122.09 112.83 9.26 1.79e+00 3.12e-01 2.67e+01 angle pdb=" C GLY C 353 " pdb=" N ASP C 354 " pdb=" CA ASP C 354 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.52e+01 angle pdb=" N PRO R 53 " pdb=" CA PRO R 53 " pdb=" CB PRO R 53 " ideal model delta sigma weight residual 103.25 98.01 5.24 1.05e+00 9.07e-01 2.49e+01 ... (remaining 12835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 5235 14.82 - 29.65: 292 29.65 - 44.47: 58 44.47 - 59.29: 8 59.29 - 74.12: 4 Dihedral angle restraints: 5597 sinusoidal: 2190 harmonic: 3407 Sorted by residual: dihedral pdb=" CA ASN R 59 " pdb=" C ASN R 59 " pdb=" N ARG R 60 " pdb=" CA ARG R 60 " ideal model delta harmonic sigma weight residual 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA CYS R 58 " pdb=" C CYS R 58 " pdb=" N ASN R 59 " pdb=" CA ASN R 59 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+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 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 998 0.054 - 0.108: 310 0.108 - 0.163: 92 0.163 - 0.217: 15 0.217 - 0.271: 5 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ILE D 273 " pdb=" N ILE D 273 " pdb=" C ILE D 273 " pdb=" CB ILE D 273 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA PRO R 53 " pdb=" N PRO R 53 " pdb=" C PRO R 53 " pdb=" CB PRO R 53 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA LEU R 242 " pdb=" N LEU R 242 " pdb=" C LEU R 242 " pdb=" CB LEU R 242 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1417 not shown) Planarity restraints: 1644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 59 " -0.024 2.00e-02 2.50e+03 1.99e-02 7.95e+00 pdb=" CG TYR D 59 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR D 59 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 59 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 59 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 59 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 59 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 316 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.21e+00 pdb=" C LEU R 316 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU R 316 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE R 317 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 318 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ASN R 318 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN R 318 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE R 319 " -0.016 2.00e-02 2.50e+03 ... (remaining 1641 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 13 2.37 - 3.00: 4432 3.00 - 3.63: 13402 3.63 - 4.27: 20910 4.27 - 4.90: 35167 Nonbonded interactions: 73924 Sorted by model distance: nonbonded pdb=" O ILE D 58 " pdb=" OG SER D 316 " model vdw 1.735 3.040 nonbonded pdb=" O GLY D 310 " pdb=" NZ LYS D 337 " model vdw 1.995 3.120 nonbonded pdb=" OG SER D 245 " pdb=" OD1 ASP D 247 " model vdw 2.204 3.040 nonbonded pdb=" O ASN D 313 " pdb=" OG SER D 331 " model vdw 2.226 3.040 nonbonded pdb=" OG SER D 161 " pdb=" OD1 ASP D 163 " model vdw 2.269 3.040 ... (remaining 73919 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.960 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 0.061 9471 Z= 0.434 Angle : 0.950 14.099 12840 Z= 0.553 Chirality : 0.059 0.271 1420 Planarity : 0.007 0.065 1644 Dihedral : 10.181 74.117 3377 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: -4.62 (0.20), residues: 1158 helix: -3.85 (0.14), residues: 441 sheet: -2.37 (0.32), residues: 228 loop : -2.40 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 339 HIS 0.016 0.002 HIS C 220 PHE 0.037 0.003 PHE C 238 TYR 0.048 0.003 TYR D 59 ARG 0.008 0.001 ARG D 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: C 13 ARG cc_start: 0.7386 (mtm180) cc_final: 0.6370 (mtt-85) REVERT: C 265 ARG cc_start: 0.7765 (mmt90) cc_final: 0.7233 (ptp-170) REVERT: C 293 LYS cc_start: 0.8323 (ptpt) cc_final: 0.8015 (pttt) REVERT: D 78 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8339 (mtpp) REVERT: G 17 GLU cc_start: 0.8605 (tp30) cc_final: 0.8229 (mm-30) REVERT: G 20 LYS cc_start: 0.8492 (mtmt) cc_final: 0.7750 (mtmt) REVERT: G 29 LYS cc_start: 0.8207 (mttm) cc_final: 0.7899 (mtpt) REVERT: G 32 LYS cc_start: 0.8223 (mttm) cc_final: 0.7789 (tmmt) REVERT: N 3 GLN cc_start: 0.8765 (tt0) cc_final: 0.8483 (tt0) REVERT: N 18 LEU cc_start: 0.8231 (mt) cc_final: 0.7988 (mt) REVERT: N 76 LYS cc_start: 0.9063 (mttp) cc_final: 0.8844 (mttt) REVERT: N 117 TYR cc_start: 0.8893 (m-80) cc_final: 0.8566 (m-80) REVERT: R 230 PHE cc_start: 0.7872 (t80) cc_final: 0.7595 (t80) REVERT: R 252 LEU cc_start: 0.8494 (mp) cc_final: 0.8254 (mp) REVERT: R 412 ARG cc_start: 0.7373 (ttp-110) cc_final: 0.6776 (mmp80) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2795 time to fit residues: 72.8216 Evaluate side-chains 149 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN C 357 HIS C 387 HIS D 88 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 HIS D 311 HIS N 82 GLN P 1 HIS R 170 HIS R 177 HIS R 238 ASN R 250 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9471 Z= 0.161 Angle : 0.574 6.590 12840 Z= 0.306 Chirality : 0.042 0.166 1420 Planarity : 0.004 0.041 1644 Dihedral : 5.374 39.346 1279 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.32 % Allowed : 7.63 % Favored : 91.05 % 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: -2.70 (0.23), residues: 1158 helix: -1.59 (0.21), residues: 437 sheet: -1.92 (0.32), residues: 233 loop : -1.71 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 25 HIS 0.006 0.001 HIS D 311 PHE 0.020 0.001 PHE R 230 TYR 0.023 0.001 TYR R 145 ARG 0.005 0.000 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.7495 (mtm180) cc_final: 0.6329 (mtt-85) REVERT: C 20 ARG cc_start: 0.8303 (ttp-170) cc_final: 0.7556 (ttp80) REVERT: C 29 GLN cc_start: 0.7785 (tp40) cc_final: 0.7437 (tp-100) REVERT: C 265 ARG cc_start: 0.7464 (mmt90) cc_final: 0.6889 (ptp-170) REVERT: C 293 LYS cc_start: 0.8062 (ptpt) cc_final: 0.7752 (ptpt) REVERT: C 378 ASP cc_start: 0.7982 (m-30) cc_final: 0.7759 (m-30) REVERT: G 20 LYS cc_start: 0.8339 (mtmt) cc_final: 0.8030 (mtmt) REVERT: G 32 LYS cc_start: 0.8184 (mttm) cc_final: 0.7706 (tmmt) REVERT: N 34 MET cc_start: 0.8869 (mmm) cc_final: 0.8574 (mmm) REVERT: N 53 GLN cc_start: 0.8552 (mp10) cc_final: 0.8180 (mp10) REVERT: R 95 PHE cc_start: 0.7645 (m-80) cc_final: 0.6553 (m-10) REVERT: R 346 ARG cc_start: 0.6927 (tpp-160) cc_final: 0.6681 (tpp-160) REVERT: R 412 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.6804 (mmp80) outliers start: 13 outliers final: 4 residues processed: 197 average time/residue: 0.2857 time to fit residues: 73.6524 Evaluate side-chains 169 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 165 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 403 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN R 238 ASN R 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9471 Z= 0.195 Angle : 0.546 6.264 12840 Z= 0.287 Chirality : 0.042 0.168 1420 Planarity : 0.004 0.034 1644 Dihedral : 4.888 32.365 1279 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.03 % Allowed : 8.85 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.24), residues: 1158 helix: -0.15 (0.24), residues: 440 sheet: -1.59 (0.33), residues: 221 loop : -1.51 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 339 HIS 0.006 0.001 HIS C 357 PHE 0.014 0.001 PHE C 212 TYR 0.022 0.002 TYR R 145 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 1.373 Fit side-chains REVERT: C 13 ARG cc_start: 0.7499 (mtm180) cc_final: 0.6337 (mtt-85) REVERT: C 20 ARG cc_start: 0.8275 (ttp-170) cc_final: 0.7583 (ttp80) REVERT: C 29 GLN cc_start: 0.7797 (tp40) cc_final: 0.7453 (tp-100) REVERT: C 265 ARG cc_start: 0.7473 (mmt90) cc_final: 0.6941 (ptp-170) REVERT: C 378 ASP cc_start: 0.8005 (m-30) cc_final: 0.7772 (m-30) REVERT: D 19 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.7033 (ttp-110) REVERT: D 268 ASN cc_start: 0.8230 (t0) cc_final: 0.8025 (t0) REVERT: G 20 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7850 (mtmt) REVERT: G 32 LYS cc_start: 0.8160 (mttm) cc_final: 0.7757 (tmmt) REVERT: N 3 GLN cc_start: 0.8441 (tt0) cc_final: 0.8179 (tt0) REVERT: R 34 GLU cc_start: 0.8381 (tt0) cc_final: 0.8129 (tt0) REVERT: R 412 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.6583 (mmp80) outliers start: 20 outliers final: 11 residues processed: 180 average time/residue: 0.2547 time to fit residues: 61.0298 Evaluate side-chains 169 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain R residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9471 Z= 0.143 Angle : 0.490 5.731 12840 Z= 0.260 Chirality : 0.041 0.174 1420 Planarity : 0.003 0.033 1644 Dihedral : 4.543 25.477 1279 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.83 % Allowed : 11.70 % Favored : 86.47 % 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: -0.96 (0.25), residues: 1158 helix: 0.61 (0.25), residues: 444 sheet: -1.42 (0.33), residues: 230 loop : -1.33 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 339 HIS 0.004 0.001 HIS C 357 PHE 0.013 0.001 PHE C 212 TYR 0.020 0.001 TYR R 145 ARG 0.002 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.076 Fit side-chains REVERT: C 13 ARG cc_start: 0.7464 (mtm180) cc_final: 0.6280 (mtt-85) REVERT: C 20 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7567 (ttp80) REVERT: C 29 GLN cc_start: 0.7791 (tp40) cc_final: 0.7466 (tp-100) REVERT: C 265 ARG cc_start: 0.7460 (mmt90) cc_final: 0.6951 (ptp-170) REVERT: C 378 ASP cc_start: 0.7970 (m-30) cc_final: 0.7763 (m-30) REVERT: D 19 ARG cc_start: 0.7516 (ttp-110) cc_final: 0.7053 (ttp-110) REVERT: D 191 SER cc_start: 0.9129 (t) cc_final: 0.8796 (t) REVERT: D 268 ASN cc_start: 0.8312 (t0) cc_final: 0.7989 (t0) REVERT: G 20 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7786 (mtmt) REVERT: G 32 LYS cc_start: 0.8121 (mttm) cc_final: 0.7741 (tmmt) REVERT: N 3 GLN cc_start: 0.8357 (tt0) cc_final: 0.8104 (tt0) REVERT: N 53 GLN cc_start: 0.8537 (mp10) cc_final: 0.8148 (mp10) REVERT: N 67 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7992 (ttp-110) REVERT: R 412 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.6657 (mmp80) REVERT: R 413 ARG cc_start: 0.7811 (mtp-110) cc_final: 0.7537 (ttp80) outliers start: 18 outliers final: 13 residues processed: 183 average time/residue: 0.2625 time to fit residues: 63.2765 Evaluate side-chains 172 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 403 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9471 Z= 0.144 Angle : 0.487 5.623 12840 Z= 0.257 Chirality : 0.041 0.178 1420 Planarity : 0.003 0.033 1644 Dihedral : 4.374 21.312 1279 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.14 % Allowed : 12.41 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.26), residues: 1158 helix: 1.10 (0.25), residues: 444 sheet: -1.19 (0.34), residues: 228 loop : -1.23 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 339 HIS 0.004 0.001 HIS C 357 PHE 0.019 0.001 PHE R 230 TYR 0.020 0.001 TYR R 145 ARG 0.002 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.006 Fit side-chains REVERT: C 13 ARG cc_start: 0.7473 (mtm180) cc_final: 0.6239 (mtt-85) REVERT: C 20 ARG cc_start: 0.8173 (ttp-170) cc_final: 0.7561 (ttp80) REVERT: C 29 GLN cc_start: 0.7793 (tp40) cc_final: 0.7470 (tp-100) REVERT: C 265 ARG cc_start: 0.7476 (mmt90) cc_final: 0.6967 (ptp-170) REVERT: C 378 ASP cc_start: 0.7949 (m-30) cc_final: 0.7737 (m-30) REVERT: D 191 SER cc_start: 0.9099 (t) cc_final: 0.8778 (t) REVERT: D 268 ASN cc_start: 0.8363 (t0) cc_final: 0.8063 (t0) REVERT: G 20 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7741 (mtmt) REVERT: G 29 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7873 (mttp) REVERT: G 32 LYS cc_start: 0.8116 (mttm) cc_final: 0.7743 (tmmt) REVERT: N 3 GLN cc_start: 0.8309 (tt0) cc_final: 0.8055 (tt0) REVERT: N 76 LYS cc_start: 0.8835 (mttp) cc_final: 0.8602 (mttp) REVERT: R 412 ARG cc_start: 0.7417 (ttp-110) cc_final: 0.6731 (mmp80) outliers start: 21 outliers final: 14 residues processed: 178 average time/residue: 0.2512 time to fit residues: 59.9736 Evaluate side-chains 174 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 343 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9471 Z= 0.162 Angle : 0.485 5.533 12840 Z= 0.257 Chirality : 0.041 0.191 1420 Planarity : 0.003 0.033 1644 Dihedral : 4.337 19.712 1279 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.14 % Allowed : 12.72 % Favored : 85.15 % 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: -0.29 (0.26), residues: 1158 helix: 1.38 (0.25), residues: 445 sheet: -1.14 (0.34), residues: 230 loop : -1.16 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 241 HIS 0.004 0.001 HIS C 357 PHE 0.020 0.001 PHE R 230 TYR 0.020 0.001 TYR R 145 ARG 0.003 0.000 ARG R 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 1.123 Fit side-chains REVERT: C 13 ARG cc_start: 0.7464 (mtm180) cc_final: 0.6239 (mtt-85) REVERT: C 20 ARG cc_start: 0.8161 (ttp-170) cc_final: 0.7557 (ttp80) REVERT: C 29 GLN cc_start: 0.7855 (tp40) cc_final: 0.7526 (tp-100) REVERT: C 221 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8018 (tpp) REVERT: C 265 ARG cc_start: 0.7484 (mmt90) cc_final: 0.7024 (ptp-170) REVERT: C 268 GLU cc_start: 0.8127 (tt0) cc_final: 0.7565 (mt-10) REVERT: D 191 SER cc_start: 0.9146 (t) cc_final: 0.8793 (t) REVERT: D 268 ASN cc_start: 0.8354 (t0) cc_final: 0.8038 (t0) REVERT: G 20 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7749 (mtmt) REVERT: G 32 LYS cc_start: 0.8036 (mttm) cc_final: 0.7633 (ttpt) REVERT: N 53 GLN cc_start: 0.8535 (mp10) cc_final: 0.8167 (mp10) REVERT: N 76 LYS cc_start: 0.8892 (mttp) cc_final: 0.8649 (mttp) REVERT: R 230 PHE cc_start: 0.7781 (t80) cc_final: 0.7577 (t80) REVERT: R 412 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.6748 (mmp80) outliers start: 21 outliers final: 16 residues processed: 167 average time/residue: 0.2454 time to fit residues: 54.9069 Evaluate side-chains 172 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain R residue 403 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9471 Z= 0.354 Angle : 0.593 5.645 12840 Z= 0.312 Chirality : 0.044 0.180 1420 Planarity : 0.004 0.035 1644 Dihedral : 4.847 24.726 1279 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.34 % Allowed : 12.41 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1158 helix: 1.29 (0.25), residues: 447 sheet: -1.29 (0.33), residues: 231 loop : -1.32 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 339 HIS 0.007 0.001 HIS C 357 PHE 0.018 0.002 PHE R 230 TYR 0.021 0.002 TYR R 145 ARG 0.004 0.001 ARG R 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: C 13 ARG cc_start: 0.7396 (mtm180) cc_final: 0.6100 (mtt-85) REVERT: C 20 ARG cc_start: 0.8234 (ttp-170) cc_final: 0.7529 (ttp80) REVERT: C 265 ARG cc_start: 0.7573 (mmt90) cc_final: 0.7021 (ptp-170) REVERT: D 19 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.7006 (ttp-110) REVERT: D 268 ASN cc_start: 0.8306 (t0) cc_final: 0.8004 (t0) REVERT: G 32 LYS cc_start: 0.8139 (mttm) cc_final: 0.7765 (tmmt) REVERT: N 53 GLN cc_start: 0.8648 (mp10) cc_final: 0.8239 (mp10) REVERT: R 412 ARG cc_start: 0.7766 (ttp-110) cc_final: 0.6736 (mmp80) outliers start: 23 outliers final: 18 residues processed: 168 average time/residue: 0.2502 time to fit residues: 56.4085 Evaluate side-chains 170 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain R residue 403 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9471 Z= 0.163 Angle : 0.502 5.473 12840 Z= 0.267 Chirality : 0.041 0.184 1420 Planarity : 0.003 0.031 1644 Dihedral : 4.512 20.730 1279 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.24 % Allowed : 13.43 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1158 helix: 1.56 (0.26), residues: 444 sheet: -1.16 (0.33), residues: 229 loop : -1.19 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 234 HIS 0.004 0.001 HIS C 357 PHE 0.022 0.001 PHE R 230 TYR 0.019 0.001 TYR R 145 ARG 0.004 0.000 ARG R 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.085 Fit side-chains REVERT: C 13 ARG cc_start: 0.7445 (mtm180) cc_final: 0.5983 (mtt-85) REVERT: C 20 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7474 (ttp80) REVERT: C 221 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8030 (tpp) REVERT: C 265 ARG cc_start: 0.7474 (mmt90) cc_final: 0.7008 (ptp-170) REVERT: D 19 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.6999 (ttp-110) REVERT: D 268 ASN cc_start: 0.8335 (t0) cc_final: 0.8020 (t0) REVERT: G 20 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7711 (mtmt) REVERT: G 29 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7974 (mtpt) REVERT: G 32 LYS cc_start: 0.8090 (mttm) cc_final: 0.7680 (ttpt) REVERT: N 53 GLN cc_start: 0.8646 (mp10) cc_final: 0.8267 (mp10) REVERT: R 412 ARG cc_start: 0.7622 (ttp-110) cc_final: 0.6643 (mmp80) outliers start: 22 outliers final: 16 residues processed: 173 average time/residue: 0.2390 time to fit residues: 55.5499 Evaluate side-chains 167 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain R residue 403 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 0.0040 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9471 Z= 0.152 Angle : 0.497 6.556 12840 Z= 0.264 Chirality : 0.041 0.199 1420 Planarity : 0.003 0.031 1644 Dihedral : 4.350 18.424 1279 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.34 % Allowed : 13.84 % Favored : 83.83 % 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: -0.12 (0.26), residues: 1158 helix: 1.62 (0.25), residues: 447 sheet: -1.01 (0.33), residues: 236 loop : -1.20 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 241 HIS 0.008 0.001 HIS C 220 PHE 0.013 0.001 PHE C 212 TYR 0.018 0.001 TYR R 145 ARG 0.003 0.000 ARG R 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.092 Fit side-chains REVERT: C 13 ARG cc_start: 0.7305 (mtm180) cc_final: 0.6118 (mtt-85) REVERT: C 221 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7996 (tpp) REVERT: C 265 ARG cc_start: 0.7467 (mmt90) cc_final: 0.6999 (ptp-170) REVERT: D 268 ASN cc_start: 0.8361 (t0) cc_final: 0.8050 (t0) REVERT: G 20 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7735 (mtmt) REVERT: G 32 LYS cc_start: 0.8077 (mttm) cc_final: 0.7673 (ttpt) REVERT: N 53 GLN cc_start: 0.8639 (mp10) cc_final: 0.8252 (mp10) REVERT: N 123 GLN cc_start: 0.8568 (tp40) cc_final: 0.8185 (tp-100) REVERT: R 412 ARG cc_start: 0.7600 (ttp-110) cc_final: 0.6595 (mmp80) outliers start: 23 outliers final: 17 residues processed: 170 average time/residue: 0.2443 time to fit residues: 55.5605 Evaluate side-chains 166 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain R residue 403 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9471 Z= 0.172 Angle : 0.507 6.628 12840 Z= 0.267 Chirality : 0.041 0.204 1420 Planarity : 0.003 0.032 1644 Dihedral : 4.340 18.405 1279 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.24 % Allowed : 14.14 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1158 helix: 1.68 (0.25), residues: 447 sheet: -0.80 (0.34), residues: 234 loop : -1.20 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 241 HIS 0.006 0.001 HIS C 220 PHE 0.023 0.001 PHE R 230 TYR 0.019 0.001 TYR R 145 ARG 0.006 0.000 ARG R 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.194 Fit side-chains REVERT: C 13 ARG cc_start: 0.7270 (mtm180) cc_final: 0.6042 (mtt-85) REVERT: C 20 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7488 (ttp80) REVERT: C 221 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7618 (tpp) REVERT: C 265 ARG cc_start: 0.7479 (mmt90) cc_final: 0.7005 (ptp-170) REVERT: D 268 ASN cc_start: 0.8355 (t0) cc_final: 0.8082 (t0) REVERT: G 20 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7730 (mtmt) REVERT: G 32 LYS cc_start: 0.8083 (mttm) cc_final: 0.7730 (ttpt) REVERT: N 53 GLN cc_start: 0.8664 (mp10) cc_final: 0.8270 (mp10) REVERT: N 123 GLN cc_start: 0.8595 (tp40) cc_final: 0.8201 (tp-100) REVERT: R 95 PHE cc_start: 0.7668 (m-10) cc_final: 0.7360 (m-80) REVERT: R 412 ARG cc_start: 0.7619 (ttp-110) cc_final: 0.6599 (mmp80) outliers start: 22 outliers final: 20 residues processed: 161 average time/residue: 0.2417 time to fit residues: 52.2806 Evaluate side-chains 170 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain R residue 403 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 0.0470 chunk 65 optimal weight: 0.0870 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101942 restraints weight = 14421.214| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.75 r_work: 0.3107 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9471 Z= 0.138 Angle : 0.489 6.630 12840 Z= 0.260 Chirality : 0.041 0.206 1420 Planarity : 0.003 0.031 1644 Dihedral : 4.247 19.491 1279 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.14 % Allowed : 14.55 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1158 helix: 1.76 (0.25), residues: 447 sheet: -0.59 (0.35), residues: 222 loop : -1.27 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 241 HIS 0.003 0.001 HIS C 357 PHE 0.018 0.001 PHE C 222 TYR 0.018 0.001 TYR R 145 ARG 0.006 0.000 ARG R 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2360.55 seconds wall clock time: 46 minutes 42.89 seconds (2802.89 seconds total)