Starting phenix.real_space_refine on Wed Feb 14 08:04:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/02_2024/7cqi_30441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/02_2024/7cqi_30441.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/02_2024/7cqi_30441_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/02_2024/7cqi_30441_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/02_2024/7cqi_30441_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/02_2024/7cqi_30441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/02_2024/7cqi_30441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/02_2024/7cqi_30441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqi_30441/02_2024/7cqi_30441_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 51 5.16 5 C 5719 2.51 5 N 1486 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S ASP 76": "OD1" <-> "OD2" Residue "S PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 116": "NH1" <-> "NH2" Residue "S ARG 151": "NH1" <-> "NH2" Residue "S TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 189": "NH1" <-> "NH2" Residue "S ARG 203": "NH1" <-> "NH2" Residue "S ARG 236": "NH1" <-> "NH2" Residue "S ARG 239": "NH1" <-> "NH2" Residue "S TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 270": "NH1" <-> "NH2" Residue "S ARG 287": "NH1" <-> "NH2" Residue "S ARG 329": "NH1" <-> "NH2" Residue "S PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 405": "NH1" <-> "NH2" Residue "S ARG 459": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 106": "OE1" <-> "OE2" Residue "T ARG 129": "NH1" <-> "NH2" Residue "T ARG 151": "NH1" <-> "NH2" Residue "T TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 207": "NH1" <-> "NH2" Residue "T ARG 278": "NH1" <-> "NH2" Residue "T TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 326": "NH1" <-> "NH2" Residue "T TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 447": "NH1" <-> "NH2" Residue "T ARG 450": "NH1" <-> "NH2" Residue "T ARG 489": "NH1" <-> "NH2" Residue "T ARG 507": "NH1" <-> "NH2" Residue "T ARG 509": "NH1" <-> "NH2" Residue "T TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8881 Number of models: 1 Model: "" Number of chains: 6 Chain: "S" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3268 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 399} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3926 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 479} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1028 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 182 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "T" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'GE0': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 4.93, per 1000 atoms: 0.56 Number of scatterers: 8881 At special positions: 0 Unit cell: (91.8, 85.32, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 4 15.00 O 1621 8.00 N 1486 7.00 C 5719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.8 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 36.6% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'S' and resid 55 through 63 removed outlier: 3.518A pdb=" N GLU S 59 " --> pdb=" O LYS S 55 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU S 62 " --> pdb=" O GLU S 58 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU S 63 " --> pdb=" O GLU S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 80 No H-bonds generated for 'chain 'S' and resid 78 through 80' Processing helix chain 'S' and resid 115 through 120 Processing helix chain 'S' and resid 145 through 155 removed outlier: 3.725A pdb=" N ARG S 151 " --> pdb=" O ASP S 147 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA S 153 " --> pdb=" O GLU S 149 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS S 154 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 172 No H-bonds generated for 'chain 'S' and resid 169 through 172' Processing helix chain 'S' and resid 193 through 201 removed outlier: 3.554A pdb=" N ALA S 201 " --> pdb=" O LYS S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 229 removed outlier: 3.875A pdb=" N GLU S 223 " --> pdb=" O ARG S 219 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN S 224 " --> pdb=" O LEU S 220 " (cutoff:3.500A) Processing helix chain 'S' and resid 258 through 261 No H-bonds generated for 'chain 'S' and resid 258 through 261' Processing helix chain 'S' and resid 290 through 293 No H-bonds generated for 'chain 'S' and resid 290 through 293' Processing helix chain 'S' and resid 297 through 299 No H-bonds generated for 'chain 'S' and resid 297 through 299' Processing helix chain 'S' and resid 325 through 331 removed outlier: 4.016A pdb=" N GLN S 328 " --> pdb=" O ILE S 325 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG S 329 " --> pdb=" O ASP S 326 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU S 330 " --> pdb=" O HIS S 327 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER S 331 " --> pdb=" O GLN S 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 325 through 331' Processing helix chain 'S' and resid 333 through 336 No H-bonds generated for 'chain 'S' and resid 333 through 336' Processing helix chain 'S' and resid 347 through 358 removed outlier: 3.546A pdb=" N GLU S 351 " --> pdb=" O ALA S 347 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU S 357 " --> pdb=" O LEU S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 364 through 367 No H-bonds generated for 'chain 'S' and resid 364 through 367' Processing helix chain 'S' and resid 369 through 375 removed outlier: 3.991A pdb=" N ILE S 373 " --> pdb=" O LYS S 369 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS S 374 " --> pdb=" O CYS S 370 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS S 375 " --> pdb=" O GLY S 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 369 through 375' Processing helix chain 'S' and resid 406 through 421 removed outlier: 3.559A pdb=" N LEU S 412 " --> pdb=" O ASP S 408 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU S 414 " --> pdb=" O ARG S 410 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE S 415 " --> pdb=" O LEU S 411 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET S 420 " --> pdb=" O VAL S 416 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN S 421 " --> pdb=" O ASP S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 454 through 468 Processing helix chain 'T' and resid 70 through 90 removed outlier: 4.198A pdb=" N TYR T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL T 80 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 133 No H-bonds generated for 'chain 'T' and resid 131 through 133' Processing helix chain 'T' and resid 178 through 180 No H-bonds generated for 'chain 'T' and resid 178 through 180' Processing helix chain 'T' and resid 195 through 198 No H-bonds generated for 'chain 'T' and resid 195 through 198' Processing helix chain 'T' and resid 215 through 227 removed outlier: 3.574A pdb=" N GLU T 220 " --> pdb=" O HIS T 216 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU T 222 " --> pdb=" O GLU T 218 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA T 224 " --> pdb=" O GLU T 220 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG T 225 " --> pdb=" O GLU T 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 242 through 249 Proline residue: T 247 - end of helix Processing helix chain 'T' and resid 264 through 271 Processing helix chain 'T' and resid 285 through 297 removed outlier: 4.056A pdb=" N ALA T 295 " --> pdb=" O LEU T 291 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE T 296 " --> pdb=" O LEU T 292 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL T 297 " --> pdb=" O LYS T 293 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 337 removed outlier: 3.595A pdb=" N LEU T 333 " --> pdb=" O GLU T 329 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS T 336 " --> pdb=" O ALA T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 359 through 363 removed outlier: 3.655A pdb=" N PHE T 363 " --> pdb=" O VAL T 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 359 through 363' Processing helix chain 'T' and resid 392 through 401 removed outlier: 4.456A pdb=" N TYR T 397 " --> pdb=" O GLU T 393 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR T 400 " --> pdb=" O ASP T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 403 through 407 Processing helix chain 'T' and resid 413 through 423 removed outlier: 3.636A pdb=" N GLN T 418 " --> pdb=" O PRO T 414 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE T 420 " --> pdb=" O VAL T 416 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR T 421 " --> pdb=" O GLU T 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 438 through 454 removed outlier: 3.682A pdb=" N ARG T 447 " --> pdb=" O ALA T 443 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 488 removed outlier: 4.232A pdb=" N GLY T 480 " --> pdb=" O PRO T 476 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY T 483 " --> pdb=" O ILE T 479 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG T 484 " --> pdb=" O GLY T 480 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET T 486 " --> pdb=" O PHE T 482 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU T 487 " --> pdb=" O GLY T 483 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS T 488 " --> pdb=" O ARG T 484 " (cutoff:3.500A) Processing helix chain 'T' and resid 518 through 534 removed outlier: 3.544A pdb=" N GLU T 527 " --> pdb=" O THR T 523 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU T 530 " --> pdb=" O LYS T 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 36 removed outlier: 3.642A pdb=" N TRP A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 65 removed outlier: 3.595A pdb=" N TRP A 49 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 55 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 56 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN A 57 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 60 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 61 " --> pdb=" O MET A 58 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU A 64 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS A 65 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 101 through 115 Proline residue: A 106 - end of helix removed outlier: 3.590A pdb=" N TYR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 127 No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 129 through 138 removed outlier: 4.099A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'E' and resid 12 through 22 removed outlier: 3.805A pdb=" N TYR E 17 " --> pdb=" O SER E 14 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN E 19 " --> pdb=" O PHE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 51 removed outlier: 3.591A pdb=" N VAL E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 39 removed outlier: 4.100A pdb=" N ILE C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'S' and resid 92 through 94 Processing sheet with id= B, first strand: chain 'S' and resid 160 through 164 Processing sheet with id= C, first strand: chain 'S' and resid 206 through 208 removed outlier: 6.094A pdb=" N VAL S 185 " --> pdb=" O LYS S 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 383 through 385 Processing sheet with id= E, first strand: chain 'T' and resid 231 through 234 removed outlier: 3.736A pdb=" N GLY T 390 " --> pdb=" O ALA T 231 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY T 375 " --> pdb=" O TYR T 387 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU T 255 " --> pdb=" O LEU T 311 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU T 313 " --> pdb=" O LEU T 255 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU T 257 " --> pdb=" O LEU T 313 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR T 276 " --> pdb=" O ILE T 256 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER T 258 " --> pdb=" O THR T 276 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG T 278 " --> pdb=" O SER T 258 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 494 through 496 removed outlier: 3.953A pdb=" N VAL T 494 " --> pdb=" O ARG T 509 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG T 507 " --> pdb=" O VAL T 496 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 546 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: 2.06 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1649 1.32 - 1.45: 2352 1.45 - 1.58: 4978 1.58 - 1.70: 12 1.70 - 1.83: 84 Bond restraints: 9075 Sorted by residual: bond pdb=" C1' GE0 T 602 " pdb=" C2' GE0 T 602 " ideal model delta sigma weight residual 1.300 1.500 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C4' GE0 T 602 " pdb=" O4' GE0 T 602 " ideal model delta sigma weight residual 1.268 1.448 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C1' GE0 T 602 " pdb=" O4' GE0 T 602 " ideal model delta sigma weight residual 1.619 1.442 0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" CAE GE0 T 602 " pdb=" NAD GE0 T 602 " ideal model delta sigma weight residual 1.496 1.338 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" C6 GE0 T 602 " pdb=" N6 GE0 T 602 " ideal model delta sigma weight residual 1.459 1.324 0.135 2.00e-02 2.50e+03 4.54e+01 ... (remaining 9070 not shown) Histogram of bond angle deviations from ideal: 95.91 - 103.57: 144 103.57 - 111.22: 3434 111.22 - 118.87: 3767 118.87 - 126.52: 4824 126.52 - 134.17: 120 Bond angle restraints: 12289 Sorted by residual: angle pdb=" N VAL S 144 " pdb=" CA VAL S 144 " pdb=" C VAL S 144 " ideal model delta sigma weight residual 113.42 97.86 15.56 1.17e+00 7.31e-01 1.77e+02 angle pdb=" N LEU T 69 " pdb=" CA LEU T 69 " pdb=" C LEU T 69 " ideal model delta sigma weight residual 113.55 100.90 12.65 1.26e+00 6.30e-01 1.01e+02 angle pdb=" C HIS S 77 " pdb=" N PRO S 78 " pdb=" CA PRO S 78 " ideal model delta sigma weight residual 119.24 128.77 -9.53 1.04e+00 9.25e-01 8.40e+01 angle pdb=" C GLN T 300 " pdb=" N PRO T 301 " pdb=" CA PRO T 301 " ideal model delta sigma weight residual 119.84 130.56 -10.72 1.25e+00 6.40e-01 7.36e+01 angle pdb=" N TYR T 199 " pdb=" CA TYR T 199 " pdb=" C TYR T 199 " ideal model delta sigma weight residual 111.36 120.39 -9.03 1.09e+00 8.42e-01 6.87e+01 ... (remaining 12284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4754 17.20 - 34.39: 392 34.39 - 51.59: 209 51.59 - 68.79: 56 68.79 - 85.98: 6 Dihedral angle restraints: 5417 sinusoidal: 2184 harmonic: 3233 Sorted by residual: dihedral pdb=" CA LEU A 38 " pdb=" C LEU A 38 " pdb=" N SER A 39 " pdb=" CA SER A 39 " ideal model delta harmonic sigma weight residual -180.00 -138.52 -41.48 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA LEU A 142 " pdb=" C LEU A 142 " pdb=" N HIS A 143 " pdb=" CA HIS A 143 " ideal model delta harmonic sigma weight residual -180.00 -139.84 -40.16 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" C PHE S 394 " pdb=" N PHE S 394 " pdb=" CA PHE S 394 " pdb=" CB PHE S 394 " ideal model delta harmonic sigma weight residual -122.60 -139.75 17.15 0 2.50e+00 1.60e-01 4.70e+01 ... (remaining 5414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 1238 0.138 - 0.277: 118 0.277 - 0.415: 16 0.415 - 0.553: 2 0.553 - 0.692: 1 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA PHE S 394 " pdb=" N PHE S 394 " pdb=" C PHE S 394 " pdb=" CB PHE S 394 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ASN T 120 " pdb=" N ASN T 120 " pdb=" C ASN T 120 " pdb=" CB ASN T 120 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA TYR T 235 " pdb=" N TYR T 235 " pdb=" C TYR T 235 " pdb=" CB TYR T 235 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1372 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG T 305 " 0.047 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO T 306 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO T 306 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO T 306 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 45 " 0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO A 46 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 46 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 46 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE S 61 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C ILE S 61 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE S 61 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU S 62 " -0.016 2.00e-02 2.50e+03 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 1.00 - 1.78: 8 1.78 - 2.56: 85 2.56 - 3.34: 10255 3.34 - 4.12: 20021 4.12 - 4.90: 38230 Warning: very small nonbonded interaction distances. Nonbonded interactions: 68599 Sorted by model distance: nonbonded pdb=" OD1 ASP T 344 " pdb=" CE MET T 374 " model vdw 0.997 3.460 nonbonded pdb=" OD2 ASP S 188 " pdb=" OH TYR S 248 " model vdw 1.295 2.440 nonbonded pdb=" CG1 VAL T 195 " pdb=" OE1 GLU T 417 " model vdw 1.387 3.460 nonbonded pdb=" OE1 GLU T 119 " pdb=" O PHE A 72 " model vdw 1.491 3.040 nonbonded pdb=" O LYS T 194 " pdb=" OE2 GLU T 197 " model vdw 1.636 3.040 ... (remaining 68594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 4.060 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 26.620 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.012 0.200 9075 Z= 0.825 Angle : 1.506 17.689 12289 Z= 0.882 Chirality : 0.090 0.692 1375 Planarity : 0.008 0.072 1550 Dihedral : 16.965 85.983 3347 Min Nonbonded Distance : 0.997 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.68 % Favored : 88.60 % Rotamer: Outliers : 13.06 % Allowed : 9.98 % Favored : 76.96 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -5.50 (0.19), residues: 1105 helix: -4.40 (0.13), residues: 474 sheet: -2.54 (0.52), residues: 92 loop : -3.07 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP T 134 HIS 0.029 0.003 HIS C 24 PHE 0.036 0.004 PHE T 377 TYR 0.039 0.003 TYR S 166 ARG 0.007 0.001 ARG T 543 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 179 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 249 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7779 (ttm) REVERT: S 266 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8391 (ttpt) REVERT: S 391 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8351 (p) REVERT: S 395 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7216 (p-80) REVERT: S 459 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7646 (ttp80) REVERT: T 82 THR cc_start: 0.8570 (m) cc_final: 0.8166 (p) REVERT: T 88 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7863 (mmm-85) REVERT: T 106 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6200 (mt-10) REVERT: T 119 GLU cc_start: 0.5222 (OUTLIER) cc_final: 0.4954 (mm-30) REVERT: T 262 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8827 (m110) REVERT: T 278 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8487 (mtt-85) REVERT: T 304 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7827 (mmm-85) REVERT: T 369 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7642 (t0) REVERT: T 418 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.7938 (tm130) REVERT: T 423 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8722 (ttp) REVERT: T 427 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7501 (mpt) REVERT: A 17 MET cc_start: 0.5378 (pp-130) cc_final: 0.3133 (mmm) REVERT: A 73 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.5044 (pp20) outliers start: 123 outliers final: 65 residues processed: 275 average time/residue: 0.2551 time to fit residues: 90.9314 Evaluate side-chains 186 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 106 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 197 LYS Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 240 ARG Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 249 MET Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 266 LYS Chi-restraints excluded: chain S residue 325 ILE Chi-restraints excluded: chain S residue 326 ASP Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 391 SER Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 405 ARG Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 459 ARG Chi-restraints excluded: chain S residue 467 VAL Chi-restraints excluded: chain S residue 472 LEU Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 68 MET Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 TYR Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 106 GLU Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 145 ARG Chi-restraints excluded: chain T residue 165 ASN Chi-restraints excluded: chain T residue 166 ILE Chi-restraints excluded: chain T residue 173 MET Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 196 LEU Chi-restraints excluded: chain T residue 209 GLU Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 262 ASN Chi-restraints excluded: chain T residue 277 ILE Chi-restraints excluded: chain T residue 278 ARG Chi-restraints excluded: chain T residue 285 MET Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 345 GLU Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 379 LYS Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 418 GLN Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 423 MET Chi-restraints excluded: chain T residue 426 ILE Chi-restraints excluded: chain T residue 427 MET Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 475 MET Chi-restraints excluded: chain T residue 494 VAL Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 506 SER Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 542 HIS Chi-restraints excluded: chain A residue 73 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 83 ASN S 114 ASN S 211 HIS S 224 GLN S 327 HIS ** S 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 120 ASN T 262 ASN T 263 HIS T 284 ASN T 418 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN E 38 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9075 Z= 0.254 Angle : 0.719 11.408 12289 Z= 0.365 Chirality : 0.048 0.233 1375 Planarity : 0.006 0.058 1550 Dihedral : 13.832 91.566 1441 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 6.90 % Allowed : 14.44 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.21), residues: 1105 helix: -2.97 (0.19), residues: 456 sheet: -2.11 (0.52), residues: 101 loop : -2.75 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 94 HIS 0.006 0.001 HIS C 24 PHE 0.017 0.002 PHE A 101 TYR 0.021 0.002 TYR T 342 ARG 0.008 0.001 ARG S 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 114 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: S 60 LEU cc_start: 0.8444 (tt) cc_final: 0.8158 (mp) REVERT: S 236 ARG cc_start: 0.7234 (ttm110) cc_final: 0.6936 (ttp-110) REVERT: T 88 ARG cc_start: 0.8199 (tpp80) cc_final: 0.7774 (mmm-85) REVERT: T 106 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.6010 (mt-10) REVERT: T 119 GLU cc_start: 0.4953 (OUTLIER) cc_final: 0.4592 (tp30) REVERT: T 304 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7950 (mmm-85) REVERT: T 327 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8793 (tp) REVERT: T 418 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: T 441 GLN cc_start: 0.8307 (tp40) cc_final: 0.8098 (tp40) REVERT: T 475 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7334 (mpt) REVERT: A 17 MET cc_start: 0.5678 (pp-130) cc_final: 0.3366 (mtp) REVERT: C 24 HIS cc_start: 0.5621 (OUTLIER) cc_final: 0.5353 (t-170) outliers start: 65 outliers final: 32 residues processed: 167 average time/residue: 0.2277 time to fit residues: 51.8152 Evaluate side-chains 136 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 98 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 326 ASP Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 98 LYS Chi-restraints excluded: chain T residue 106 GLU Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 209 GLU Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 393 GLU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 418 GLN Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 426 ILE Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 475 MET Chi-restraints excluded: chain T residue 501 THR Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 0.0060 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 107 ASN S 327 HIS A 18 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9075 Z= 0.163 Angle : 0.601 8.318 12289 Z= 0.306 Chirality : 0.044 0.175 1375 Planarity : 0.004 0.052 1550 Dihedral : 11.042 88.385 1316 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 4.46 % Allowed : 16.67 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.23), residues: 1105 helix: -2.03 (0.22), residues: 462 sheet: -2.01 (0.54), residues: 101 loop : -2.43 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 94 HIS 0.004 0.001 HIS C 24 PHE 0.014 0.001 PHE A 101 TYR 0.016 0.001 TYR E 50 ARG 0.004 0.000 ARG S 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 113 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: S 60 LEU cc_start: 0.8480 (tt) cc_final: 0.8212 (mp) REVERT: S 183 ASP cc_start: 0.7411 (m-30) cc_final: 0.7092 (m-30) REVERT: S 326 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7399 (t0) REVERT: S 369 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8853 (mmtp) REVERT: S 395 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7531 (p-80) REVERT: S 408 ASP cc_start: 0.7914 (t0) cc_final: 0.7616 (m-30) REVERT: S 469 GLN cc_start: 0.7308 (mt0) cc_final: 0.7023 (mp10) REVERT: T 88 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7958 (mmm-85) REVERT: T 196 LEU cc_start: 0.9332 (tm) cc_final: 0.9131 (tp) REVERT: T 249 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8842 (mt) REVERT: T 304 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7988 (mmm-85) REVERT: T 441 GLN cc_start: 0.8262 (tp40) cc_final: 0.8061 (tp40) REVERT: T 475 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7297 (mpt) REVERT: A 17 MET cc_start: 0.5559 (pp-130) cc_final: 0.2911 (mtp) REVERT: C 24 HIS cc_start: 0.5425 (OUTLIER) cc_final: 0.5081 (t-170) outliers start: 42 outliers final: 23 residues processed: 147 average time/residue: 0.2127 time to fit residues: 43.5948 Evaluate side-chains 130 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 326 ASP Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 257 LEU Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 393 GLU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 475 MET Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 0.0000 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 407 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9075 Z= 0.380 Angle : 0.716 9.627 12289 Z= 0.360 Chirality : 0.049 0.176 1375 Planarity : 0.005 0.050 1550 Dihedral : 10.755 86.783 1296 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.42 % Favored : 91.49 % Rotamer: Outliers : 5.52 % Allowed : 16.56 % Favored : 77.92 % 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: -3.26 (0.24), residues: 1105 helix: -1.76 (0.22), residues: 480 sheet: -2.05 (0.51), residues: 105 loop : -2.54 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP T 94 HIS 0.006 0.001 HIS C 24 PHE 0.022 0.002 PHE S 394 TYR 0.016 0.002 TYR E 50 ARG 0.004 0.001 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 101 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: S 60 LEU cc_start: 0.8568 (tt) cc_final: 0.8300 (mp) REVERT: S 321 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7837 (ttp80) REVERT: S 326 ASP cc_start: 0.8255 (t70) cc_final: 0.7476 (t0) REVERT: S 391 SER cc_start: 0.8548 (t) cc_final: 0.8125 (p) REVERT: S 395 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7349 (p-80) REVERT: S 408 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: S 410 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.7589 (mtp85) REVERT: T 88 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7996 (mmm-85) REVERT: T 441 GLN cc_start: 0.8418 (tp40) cc_final: 0.8203 (tp40) REVERT: A 17 MET cc_start: 0.5349 (pp-130) cc_final: 0.2841 (mtp) REVERT: C 24 HIS cc_start: 0.5518 (OUTLIER) cc_final: 0.5275 (t-170) outliers start: 52 outliers final: 32 residues processed: 145 average time/residue: 0.2368 time to fit residues: 46.7174 Evaluate side-chains 131 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 321 ARG Chi-restraints excluded: chain S residue 331 SER Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 393 GLU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 501 THR Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 79 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9075 Z= 0.203 Angle : 0.594 10.767 12289 Z= 0.301 Chirality : 0.045 0.176 1375 Planarity : 0.004 0.046 1550 Dihedral : 9.951 87.551 1284 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 4.25 % Allowed : 17.83 % Favored : 77.92 % 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: -2.88 (0.24), residues: 1105 helix: -1.41 (0.24), residues: 479 sheet: -1.91 (0.55), residues: 96 loop : -2.37 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 94 HIS 0.006 0.001 HIS C 24 PHE 0.017 0.001 PHE S 394 TYR 0.014 0.001 TYR T 539 ARG 0.003 0.000 ARG T 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 104 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: S 60 LEU cc_start: 0.8636 (tt) cc_final: 0.8353 (mp) REVERT: S 183 ASP cc_start: 0.7407 (m-30) cc_final: 0.7170 (m-30) REVERT: S 321 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7750 (ttp80) REVERT: S 326 ASP cc_start: 0.8217 (t70) cc_final: 0.7430 (t0) REVERT: S 395 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7474 (p-80) REVERT: S 408 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: S 410 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7538 (mtp-110) REVERT: S 469 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.7067 (mp10) REVERT: T 87 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7678 (tt) REVERT: T 88 ARG cc_start: 0.8301 (tpp80) cc_final: 0.8023 (mmm-85) REVERT: T 441 GLN cc_start: 0.8264 (tp40) cc_final: 0.8047 (tp40) REVERT: T 491 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8830 (mt) REVERT: A 17 MET cc_start: 0.5294 (pp-130) cc_final: 0.2834 (mtp) REVERT: C 24 HIS cc_start: 0.5447 (OUTLIER) cc_final: 0.5239 (t-170) outliers start: 40 outliers final: 25 residues processed: 137 average time/residue: 0.2286 time to fit residues: 43.2776 Evaluate side-chains 128 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 321 ARG Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain S residue 469 GLN Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 393 GLU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 542 HIS ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9075 Z= 0.301 Angle : 0.643 8.574 12289 Z= 0.324 Chirality : 0.047 0.177 1375 Planarity : 0.004 0.047 1550 Dihedral : 9.930 86.158 1284 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.87 % Favored : 92.04 % Rotamer: Outliers : 5.10 % Allowed : 17.83 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.24), residues: 1105 helix: -1.32 (0.24), residues: 479 sheet: -1.97 (0.58), residues: 81 loop : -2.28 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 94 HIS 0.007 0.001 HIS C 24 PHE 0.017 0.002 PHE S 394 TYR 0.015 0.002 TYR T 539 ARG 0.005 0.000 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 93 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: S 183 ASP cc_start: 0.7357 (m-30) cc_final: 0.7121 (m-30) REVERT: S 326 ASP cc_start: 0.8226 (t70) cc_final: 0.7447 (t0) REVERT: S 395 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7497 (p-80) REVERT: S 408 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: S 410 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7546 (mtp-110) REVERT: S 469 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7107 (mp10) REVERT: T 88 ARG cc_start: 0.8222 (tpp80) cc_final: 0.8001 (mmm-85) REVERT: T 441 GLN cc_start: 0.8325 (tp40) cc_final: 0.8100 (tp40) REVERT: A 17 MET cc_start: 0.5427 (pp-130) cc_final: 0.2965 (mtp) REVERT: C 24 HIS cc_start: 0.5782 (OUTLIER) cc_final: 0.5411 (t-170) outliers start: 48 outliers final: 32 residues processed: 134 average time/residue: 0.2171 time to fit residues: 40.4378 Evaluate side-chains 128 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 300 ILE Chi-restraints excluded: chain S residue 331 SER Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain S residue 469 GLN Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 393 GLU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 542 HIS Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 542 HIS ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9075 Z= 0.174 Angle : 0.585 8.609 12289 Z= 0.292 Chirality : 0.044 0.176 1375 Planarity : 0.004 0.047 1550 Dihedral : 9.548 87.754 1282 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 4.35 % Allowed : 19.11 % Favored : 76.54 % 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: -2.56 (0.25), residues: 1105 helix: -1.09 (0.24), residues: 478 sheet: -1.87 (0.58), residues: 82 loop : -2.22 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 94 HIS 0.008 0.001 HIS T 542 PHE 0.017 0.001 PHE S 394 TYR 0.013 0.001 TYR T 539 ARG 0.006 0.000 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 100 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: S 183 ASP cc_start: 0.7330 (m-30) cc_final: 0.7104 (m-30) REVERT: S 326 ASP cc_start: 0.8210 (t70) cc_final: 0.7436 (t0) REVERT: S 395 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.7626 (p-80) REVERT: S 408 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7794 (m-30) REVERT: S 410 ARG cc_start: 0.7690 (mtp-110) cc_final: 0.7445 (mtp-110) REVERT: S 469 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: T 88 ARG cc_start: 0.8227 (tpp80) cc_final: 0.7960 (mmm-85) REVERT: T 94 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.6997 (p90) REVERT: T 441 GLN cc_start: 0.8244 (tp40) cc_final: 0.8025 (tp40) REVERT: T 539 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.6763 (p90) REVERT: A 17 MET cc_start: 0.5342 (pp-130) cc_final: 0.2770 (mtm) REVERT: C 24 HIS cc_start: 0.5659 (OUTLIER) cc_final: 0.5411 (t-170) outliers start: 41 outliers final: 26 residues processed: 133 average time/residue: 0.2168 time to fit residues: 39.9210 Evaluate side-chains 124 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain S residue 469 GLN Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 393 GLU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 0.0070 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.0470 chunk 101 optimal weight: 0.0970 chunk 92 optimal weight: 6.9990 overall best weight: 1.0298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 107 ASN S 327 HIS S 395 HIS ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9075 Z= 0.194 Angle : 0.589 8.243 12289 Z= 0.300 Chirality : 0.045 0.207 1375 Planarity : 0.004 0.046 1550 Dihedral : 9.258 87.558 1282 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.85 % Rotamer: Outliers : 4.35 % Allowed : 20.38 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.25), residues: 1105 helix: -0.91 (0.24), residues: 478 sheet: -1.74 (0.58), residues: 81 loop : -2.17 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 94 HIS 0.007 0.001 HIS C 24 PHE 0.014 0.001 PHE T 280 TYR 0.013 0.001 TYR T 539 ARG 0.007 0.000 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 96 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: S 183 ASP cc_start: 0.7275 (m-30) cc_final: 0.7038 (m-30) REVERT: S 326 ASP cc_start: 0.8207 (t70) cc_final: 0.7438 (t0) REVERT: S 345 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9125 (mt) REVERT: S 395 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7033 (p90) REVERT: S 408 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: S 469 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6977 (mp10) REVERT: T 88 ARG cc_start: 0.8307 (tpp80) cc_final: 0.7973 (mmm-85) REVERT: T 94 TRP cc_start: 0.8149 (OUTLIER) cc_final: 0.7279 (p90) REVERT: T 441 GLN cc_start: 0.8245 (tp40) cc_final: 0.8027 (tp40) REVERT: T 539 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7732 (p90) REVERT: A 17 MET cc_start: 0.5121 (pp-130) cc_final: 0.2642 (mtm) REVERT: C 24 HIS cc_start: 0.5748 (OUTLIER) cc_final: 0.5462 (t-170) outliers start: 41 outliers final: 26 residues processed: 131 average time/residue: 0.2100 time to fit residues: 38.7699 Evaluate side-chains 129 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 96 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 331 SER Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 345 LEU Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain S residue 469 GLN Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 393 GLU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.4980 chunk 101 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 107 ASN S 327 HIS S 428 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9075 Z= 0.145 Angle : 0.560 8.478 12289 Z= 0.283 Chirality : 0.044 0.232 1375 Planarity : 0.004 0.045 1550 Dihedral : 8.855 88.578 1281 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.97 % Favored : 93.94 % Rotamer: Outliers : 3.93 % Allowed : 20.49 % Favored : 75.58 % 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: -2.08 (0.25), residues: 1105 helix: -0.66 (0.25), residues: 469 sheet: -1.58 (0.59), residues: 82 loop : -1.99 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 94 HIS 0.006 0.001 HIS C 24 PHE 0.012 0.001 PHE T 280 TYR 0.011 0.001 TYR T 342 ARG 0.006 0.000 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 105 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: S 80 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7992 (mm) REVERT: S 183 ASP cc_start: 0.7265 (m-30) cc_final: 0.6995 (m-30) REVERT: S 236 ARG cc_start: 0.7170 (ttm110) cc_final: 0.6830 (ttp-110) REVERT: S 326 ASP cc_start: 0.8194 (t70) cc_final: 0.7421 (t0) REVERT: S 345 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9077 (mt) REVERT: S 395 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7036 (p90) REVERT: S 408 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: S 469 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6972 (mp10) REVERT: T 88 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7931 (mmm-85) REVERT: T 94 TRP cc_start: 0.8076 (OUTLIER) cc_final: 0.7538 (p90) REVERT: T 441 GLN cc_start: 0.8184 (tp40) cc_final: 0.7972 (tp40) REVERT: T 539 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7733 (p90) REVERT: A 17 MET cc_start: 0.4806 (pp-130) cc_final: 0.2374 (mtm) REVERT: A 20 ARG cc_start: 0.3662 (tpp-160) cc_final: 0.3421 (tpp-160) outliers start: 37 outliers final: 20 residues processed: 137 average time/residue: 0.2036 time to fit residues: 39.1494 Evaluate side-chains 123 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 345 LEU Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain S residue 469 GLN Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 545 VAL Chi-restraints excluded: chain A residue 120 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 0.0170 chunk 109 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 327 HIS S 428 GLN T 245 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9075 Z= 0.161 Angle : 0.563 8.594 12289 Z= 0.284 Chirality : 0.044 0.191 1375 Planarity : 0.004 0.043 1550 Dihedral : 8.481 88.284 1273 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 3.08 % Allowed : 21.23 % Favored : 75.69 % 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: -2.03 (0.25), residues: 1105 helix: -0.60 (0.25), residues: 473 sheet: -1.41 (0.59), residues: 81 loop : -2.02 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 94 HIS 0.004 0.000 HIS T 542 PHE 0.023 0.001 PHE S 108 TYR 0.023 0.001 TYR A 119 ARG 0.008 0.000 ARG S 410 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 80 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7984 (mm) REVERT: S 183 ASP cc_start: 0.7260 (m-30) cc_final: 0.7011 (m-30) REVERT: S 236 ARG cc_start: 0.7104 (ttm110) cc_final: 0.6714 (ttp-110) REVERT: S 326 ASP cc_start: 0.8188 (t70) cc_final: 0.7425 (t0) REVERT: S 395 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7085 (p90) REVERT: S 407 GLN cc_start: 0.7950 (mm110) cc_final: 0.7702 (mt0) REVERT: S 408 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: S 469 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: T 88 ARG cc_start: 0.8190 (tpp80) cc_final: 0.7742 (mmm-85) REVERT: T 94 TRP cc_start: 0.8063 (OUTLIER) cc_final: 0.7655 (p90) REVERT: T 173 MET cc_start: 0.8326 (mtp) cc_final: 0.7816 (mmt) REVERT: T 441 GLN cc_start: 0.8200 (tp40) cc_final: 0.7973 (tp40) REVERT: T 539 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7745 (p90) REVERT: A 17 MET cc_start: 0.4807 (pp-130) cc_final: 0.2787 (ttm) REVERT: A 20 ARG cc_start: 0.3667 (tpp-160) cc_final: 0.3425 (tpp-160) outliers start: 29 outliers final: 21 residues processed: 125 average time/residue: 0.2238 time to fit residues: 39.0292 Evaluate side-chains 124 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain S residue 469 GLN Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 545 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109051 restraints weight = 12129.905| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.28 r_work: 0.3018 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9075 Z= 0.186 Angle : 0.576 8.396 12289 Z= 0.290 Chirality : 0.045 0.214 1375 Planarity : 0.004 0.048 1550 Dihedral : 8.505 87.511 1273 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 2.87 % Allowed : 21.55 % Favored : 75.58 % 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: -1.97 (0.25), residues: 1105 helix: -0.50 (0.25), residues: 475 sheet: -1.36 (0.58), residues: 81 loop : -2.05 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 94 HIS 0.004 0.000 HIS T 542 PHE 0.014 0.001 PHE T 280 TYR 0.020 0.001 TYR A 119 ARG 0.007 0.000 ARG T 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2233.02 seconds wall clock time: 41 minutes 31.72 seconds (2491.72 seconds total)