Starting phenix.real_space_refine on Thu Feb 15 13:03:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxw_30008/02_2024/6lxw_30008.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxw_30008/02_2024/6lxw_30008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxw_30008/02_2024/6lxw_30008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxw_30008/02_2024/6lxw_30008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxw_30008/02_2024/6lxw_30008.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxw_30008/02_2024/6lxw_30008.pdb" } resolution = 3.27 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 7740 2.51 5 N 2118 2.21 5 O 2374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D GLU 363": "OE1" <-> "OE2" Residue "D ASP 378": "OD1" <-> "OD2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 468": "OD1" <-> "OD2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "P GLU 8": "OE1" <-> "OE2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "P ASP 125": "OD1" <-> "OD2" Residue "P GLU 223": "OE1" <-> "OE2" Residue "P GLU 244": "OE1" <-> "OE2" Residue "P PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 370": "OE1" <-> "OE2" Residue "P ASP 382": "OD1" <-> "OD2" Residue "P ASP 428": "OD1" <-> "OD2" Residue "P GLU 441": "OE1" <-> "OE2" Residue "P GLU 474": "OE1" <-> "OE2" Residue "P ASP 503": "OD1" <-> "OD2" Residue "P GLU 521": "OE1" <-> "OE2" Residue "S GLU 185": "OE1" <-> "OE2" Residue "S GLU 212": "OE1" <-> "OE2" Residue "S GLU 215": "OE1" <-> "OE2" Residue "S GLU 252": "OE1" <-> "OE2" Residue "S GLU 254": "OE1" <-> "OE2" 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: 12299 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1707 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 16, 'TRANS': 208} Chain breaks: 1 Chain: "B" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1660 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 16, 'TRANS': 201} Chain breaks: 1 Chain: "C" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 17, 'TRANS': 203} Chain: "D" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1740 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 17, 'TRANS': 211} Chain: "J" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1016 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 Chain: "P" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3988 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 489} Chain breaks: 4 Chain: "S" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 506 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain breaks: 1 Time building chain proxies: 6.89, per 1000 atoms: 0.56 Number of scatterers: 12299 At special positions: 0 Unit cell: (139.932, 102.672, 160.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 2374 8.00 N 2118 7.00 C 7740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.01 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS J 68 " distance=2.02 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 323 " distance=2.04 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 311 " - pdb=" SG CYS P 468 " distance=2.05 Simple disulfide: pdb=" SG CYS D 369 " - pdb=" SG CYS D 432 " distance=2.02 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS J 14 " distance=2.02 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.02 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 38 " - pdb=" SG CYS P 46 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 202 " distance=2.03 Simple disulfide: pdb=" SG CYS P 239 " - pdb=" SG CYS P 307 " distance=2.03 Simple disulfide: pdb=" SG CYS P 253 " - pdb=" SG CYS P 261 " distance=2.04 Simple disulfide: pdb=" SG CYS P 353 " - pdb=" SG CYS P 423 " distance=2.03 Simple disulfide: pdb=" SG CYS P 367 " - pdb=" SG CYS P 377 " distance=2.03 Simple disulfide: pdb=" SG CYS P 464 " - pdb=" SG CYS P 526 " distance=2.06 Simple disulfide: pdb=" SG CYS P 478 " - pdb=" SG CYS P 485 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 3.2 seconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 37 sheets defined 8.6% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.544A pdb=" N LEU A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 421 through 427 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.706A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.564A pdb=" N LEU C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.791A pdb=" N ASN C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 311 through 316 removed outlier: 4.565A pdb=" N TRP D 315 " --> pdb=" O CYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.646A pdb=" N LEU D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 427 removed outlier: 3.708A pdb=" N GLY D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 67 removed outlier: 3.607A pdb=" N LEU J 67 " --> pdb=" O LEU J 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 170 removed outlier: 3.946A pdb=" N THR P 170 " --> pdb=" O PRO P 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 167 through 170' Processing helix chain 'P' and resid 193 through 197 removed outlier: 3.825A pdb=" N ASP P 196 " --> pdb=" O ARG P 193 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA P 197 " --> pdb=" O LEU P 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 193 through 197' Processing helix chain 'P' and resid 467 through 471 Processing helix chain 'S' and resid 184 through 195 removed outlier: 3.533A pdb=" N LYS S 189 " --> pdb=" O GLU S 185 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS S 191 " --> pdb=" O LYS S 187 " (cutoff:3.500A) Processing helix chain 'S' and resid 209 through 220 Processing helix chain 'S' and resid 255 through 268 removed outlier: 3.580A pdb=" N GLU S 259 " --> pdb=" O ALA S 255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 249 removed outlier: 3.694A pdb=" N VAL A 304 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281 removed outlier: 6.299A pdb=" N TYR A 327 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR A 332 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 297 removed outlier: 3.608A pdb=" N GLY A 300 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 5.375A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 352 removed outlier: 5.375A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA7, first strand: chain 'A' and resid 461 through 463 removed outlier: 3.687A pdb=" N PHE J 60 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 245 through 249 removed outlier: 5.532A pdb=" N TYR B 302 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 281 Processing sheet with id=AB1, first strand: chain 'B' and resid 349 through 352 Processing sheet with id=AB2, first strand: chain 'B' and resid 349 through 352 Processing sheet with id=AB3, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'C' and resid 247 through 249 removed outlier: 3.911A pdb=" N THR C 265 " --> pdb=" O HIS C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AB6, first strand: chain 'C' and resid 348 through 352 Processing sheet with id=AB7, first strand: chain 'C' and resid 348 through 352 removed outlier: 4.671A pdb=" N THR C 410 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AB9, first strand: chain 'C' and resid 461 through 463 removed outlier: 6.980A pdb=" N SER C 461 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N MET D 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL C 463 " --> pdb=" O MET D 464 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN D 459 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG J 20 " --> pdb=" O GLU J 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 245 through 248 removed outlier: 4.144A pdb=" N GLY D 270 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR D 302 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 278 through 281 Processing sheet with id=AC3, first strand: chain 'D' and resid 348 through 352 removed outlier: 5.312A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 348 through 352 removed outlier: 5.312A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR D 410 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'J' and resid 74 through 78 Processing sheet with id=AC7, first strand: chain 'J' and resid 110 through 115 Processing sheet with id=AC8, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.601A pdb=" N VAL P 10 " --> pdb=" O GLU P 108 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER P 110 " --> pdb=" O VAL P 10 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER P 12 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG P 89 " --> pdb=" O GLN P 40 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS P 35 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER P 51 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP P 37 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 17 through 23 Processing sheet with id=AD1, first strand: chain 'P' and resid 121 through 125 removed outlier: 6.634A pdb=" N TYR P 122 " --> pdb=" O GLN P 218 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU P 220 " --> pdb=" O TYR P 122 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL P 124 " --> pdb=" O LEU P 220 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLN P 199 " --> pdb=" O GLN P 150 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN P 150 " --> pdb=" O GLN P 199 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU P 147 " --> pdb=" O VAL P 158 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL P 158 " --> pdb=" O LEU P 147 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR P 164 " --> pdb=" O ASP P 160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 130 through 133 Processing sheet with id=AD3, first strand: chain 'P' and resid 225 through 230 removed outlier: 6.218A pdb=" N GLU P 225 " --> pdb=" O GLN P 325 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE P 327 " --> pdb=" O GLU P 225 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL P 227 " --> pdb=" O PHE P 327 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASN P 329 " --> pdb=" O VAL P 227 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU P 229 " --> pdb=" O ASN P 329 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG P 304 " --> pdb=" O GLN P 255 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS P 250 " --> pdb=" O ASN P 266 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN P 266 " --> pdb=" O LYS P 250 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU P 252 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP P 262 " --> pdb=" O ARG P 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 234 through 239 removed outlier: 3.967A pdb=" N PHE P 290 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 340 through 344 Processing sheet with id=AD6, first strand: chain 'P' and resid 348 through 354 Processing sheet with id=AD7, first strand: chain 'P' and resid 365 through 367 removed outlier: 6.961A pdb=" N TRP P 366 " --> pdb=" O LEU P 380 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP P 386 " --> pdb=" O ASP P 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 460 through 465 removed outlier: 3.847A pdb=" N LEU P 508 " --> pdb=" O ASP P 503 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 474 through 475 Processing sheet with id=AE1, first strand: chain 'P' and resid 478 through 479 removed outlier: 4.023A pdb=" N GLY P 522 " --> pdb=" O VAL P 542 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL P 542 " --> pdb=" O GLY P 522 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3486 1.33 - 1.46: 3072 1.46 - 1.58: 5931 1.58 - 1.71: 1 1.71 - 1.84: 75 Bond restraints: 12565 Sorted by residual: bond pdb=" C GLN C 402 " pdb=" N GLU C 403 " ideal model delta sigma weight residual 1.331 1.202 0.129 2.07e-02 2.33e+03 3.85e+01 bond pdb=" C ARG P 278 " pdb=" N ILE P 279 " ideal model delta sigma weight residual 1.329 1.262 0.067 1.63e-02 3.76e+03 1.70e+01 bond pdb=" CB VAL P 265 " pdb=" CG2 VAL P 265 " ideal model delta sigma weight residual 1.521 1.395 0.126 3.30e-02 9.18e+02 1.46e+01 bond pdb=" CB CYS P 367 " pdb=" SG CYS P 367 " ideal model delta sigma weight residual 1.808 1.710 0.098 3.30e-02 9.18e+02 8.80e+00 bond pdb=" CB VAL A 379 " pdb=" CG1 VAL A 379 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.76e+00 ... (remaining 12560 not shown) Histogram of bond angle deviations from ideal: 97.47 - 104.99: 299 104.99 - 112.51: 6503 112.51 - 120.02: 4668 120.02 - 127.54: 5459 127.54 - 135.06: 167 Bond angle restraints: 17096 Sorted by residual: angle pdb=" C ALA C 312 " pdb=" N GLU C 313 " pdb=" CA GLU C 313 " ideal model delta sigma weight residual 120.06 125.95 -5.89 1.19e+00 7.06e-01 2.45e+01 angle pdb=" N ASN P 426 " pdb=" CA ASN P 426 " pdb=" C ASN P 426 " ideal model delta sigma weight residual 111.30 104.36 6.94 1.43e+00 4.89e-01 2.36e+01 angle pdb=" C SER J 88 " pdb=" N ASN J 89 " pdb=" CA ASN J 89 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" CA ASP J 131 " pdb=" CB ASP J 131 " pdb=" CG ASP J 131 " ideal model delta sigma weight residual 112.60 117.11 -4.51 1.00e+00 1.00e+00 2.04e+01 angle pdb=" C ALA P 42 " pdb=" N ARG P 43 " pdb=" CA ARG P 43 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 ... (remaining 17091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6630 17.74 - 35.49: 847 35.49 - 53.23: 140 53.23 - 70.97: 20 70.97 - 88.71: 10 Dihedral angle restraints: 7647 sinusoidal: 3053 harmonic: 4594 Sorted by residual: dihedral pdb=" CA ASP A 273 " pdb=" C ASP A 273 " pdb=" N ALA A 274 " pdb=" CA ALA A 274 " ideal model delta harmonic sigma weight residual 180.00 145.12 34.88 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CB CYS P 478 " pdb=" SG CYS P 478 " pdb=" SG CYS P 485 " pdb=" CB CYS P 485 " ideal model delta sinusoidal sigma weight residual 93.00 37.94 55.06 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CB CYS P 367 " pdb=" SG CYS P 367 " pdb=" SG CYS P 377 " pdb=" CB CYS P 377 " ideal model delta sinusoidal sigma weight residual 93.00 144.86 -51.86 1 1.00e+01 1.00e-02 3.67e+01 ... (remaining 7644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1562 0.083 - 0.165: 344 0.165 - 0.248: 42 0.248 - 0.331: 13 0.331 - 0.413: 1 Chirality restraints: 1962 Sorted by residual: chirality pdb=" CB VAL P 265 " pdb=" CA VAL P 265 " pdb=" CG1 VAL P 265 " pdb=" CG2 VAL P 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB VAL J 76 " pdb=" CA VAL J 76 " pdb=" CG1 VAL J 76 " pdb=" CG2 VAL J 76 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ASP J 131 " pdb=" N ASP J 131 " pdb=" C ASP J 131 " pdb=" CB ASP J 131 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 1959 not shown) Planarity restraints: 2195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG P 43 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C ARG P 43 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG P 43 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY P 44 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG J 35 " 0.015 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ARG J 35 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG J 35 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN J 36 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 313 " -0.047 5.00e-02 4.00e+02 6.98e-02 7.81e+00 pdb=" N PRO D 314 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 314 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 314 " -0.040 5.00e-02 4.00e+02 ... (remaining 2192 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2554 2.77 - 3.30: 10058 3.30 - 3.84: 19264 3.84 - 4.37: 22109 4.37 - 4.90: 40596 Nonbonded interactions: 94581 Sorted by model distance: nonbonded pdb=" O SER P 52 " pdb=" OG SER P 52 " model vdw 2.241 2.440 nonbonded pdb=" O GLU P 400 " pdb=" OG1 THR P 407 " model vdw 2.248 2.440 nonbonded pdb=" OG SER A 431 " pdb=" OG1 THR A 447 " model vdw 2.266 2.440 nonbonded pdb=" O THR S 208 " pdb=" OG1 THR S 208 " model vdw 2.277 2.440 nonbonded pdb=" O GLU S 259 " pdb=" OG1 THR S 263 " model vdw 2.283 2.440 ... (remaining 94576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 244 through 452 or resid 462)) selection = (chain 'B' and (resid 244 through 452 or resid 462)) selection = (chain 'C' and (resid 244 through 452 or resid 458)) selection = (chain 'D' and (resid 244 through 452 or resid 462)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.230 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.710 Find NCS groups from input model: 0.670 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.015 0.129 12565 Z= 0.942 Angle : 1.265 14.423 17096 Z= 0.661 Chirality : 0.070 0.413 1962 Planarity : 0.009 0.070 2195 Dihedral : 15.581 88.714 4610 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.16 % Favored : 86.71 % Rotamer: Outliers : 1.82 % Allowed : 16.15 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.18), residues: 1565 helix: -4.71 (0.19), residues: 122 sheet: -1.88 (0.20), residues: 615 loop : -3.28 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP P 477 HIS 0.011 0.003 HIS P 465 PHE 0.036 0.004 PHE D 374 TYR 0.037 0.005 TYR D 327 ARG 0.018 0.001 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: B 378 ASP cc_start: 0.8011 (m-30) cc_final: 0.7773 (m-30) REVERT: B 392 ARG cc_start: 0.8152 (ptp-170) cc_final: 0.7716 (tpt90) REVERT: C 357 GLU cc_start: 0.7445 (mp0) cc_final: 0.6939 (mp0) REVERT: D 428 ASP cc_start: 0.8150 (m-30) cc_final: 0.7897 (m-30) REVERT: J 5 ILE cc_start: 0.8237 (pt) cc_final: 0.8025 (pt) REVERT: J 20 ARG cc_start: 0.7442 (ttp-170) cc_final: 0.7235 (ptm160) REVERT: J 70 LYS cc_start: 0.8137 (mttp) cc_final: 0.7636 (mmtm) REVERT: P 416 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.7069 (mpp-170) outliers start: 25 outliers final: 17 residues processed: 201 average time/residue: 0.3305 time to fit residues: 87.6156 Evaluate side-chains 160 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN B 459 ASN D 249 HIS D 317 HIS D 402 GLN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN P 30 ASN P 32 HIS P 356 ASN P 481 ASN P 530 GLN S 193 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12565 Z= 0.218 Angle : 0.667 10.542 17096 Z= 0.336 Chirality : 0.043 0.176 1962 Planarity : 0.006 0.058 2195 Dihedral : 6.615 36.568 1729 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.49 % Allowed : 19.56 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.48 (0.19), residues: 1565 helix: -3.65 (0.31), residues: 118 sheet: -1.44 (0.20), residues: 620 loop : -2.85 (0.19), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 477 HIS 0.005 0.001 HIS P 465 PHE 0.013 0.001 PHE P 406 TYR 0.015 0.001 TYR A 472 ARG 0.003 0.000 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 175 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 245 ARG cc_start: 0.7238 (mmm-85) cc_final: 0.6989 (mmm160) REVERT: B 265 THR cc_start: 0.7194 (OUTLIER) cc_final: 0.6866 (p) REVERT: B 392 ARG cc_start: 0.7897 (ptp-170) cc_final: 0.7528 (tpt170) REVERT: B 459 ASN cc_start: 0.7666 (t0) cc_final: 0.7431 (t0) REVERT: C 357 GLU cc_start: 0.7427 (mp0) cc_final: 0.7153 (tt0) REVERT: C 422 GLU cc_start: 0.7541 (pp20) cc_final: 0.6802 (pm20) REVERT: D 428 ASP cc_start: 0.8085 (m-30) cc_final: 0.7849 (m-30) REVERT: J 20 ARG cc_start: 0.7396 (ttp-170) cc_final: 0.7161 (ptm160) REVERT: J 29 ASN cc_start: 0.7388 (p0) cc_final: 0.7182 (p0) REVERT: J 38 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7946 (tmm-80) REVERT: J 49 ILE cc_start: 0.8672 (tp) cc_final: 0.8086 (pt) REVERT: J 70 LYS cc_start: 0.8122 (mttp) cc_final: 0.7476 (mmtm) REVERT: J 131 ASP cc_start: 0.8393 (p0) cc_final: 0.8091 (p0) REVERT: P 416 ARG cc_start: 0.7289 (mtm-85) cc_final: 0.7027 (mpp-170) REVERT: P 536 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6812 (tm-30) REVERT: S 266 LYS cc_start: 0.8173 (tppt) cc_final: 0.7970 (tppt) outliers start: 48 outliers final: 33 residues processed: 212 average time/residue: 0.3152 time to fit residues: 89.7619 Evaluate side-chains 182 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 433 THR Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 205 THR Chi-restraints excluded: chain S residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 0.0770 chunk 113 optimal weight: 3.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN D 249 HIS ** D 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN P 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12565 Z= 0.285 Angle : 0.660 10.077 17096 Z= 0.330 Chirality : 0.043 0.179 1962 Planarity : 0.005 0.060 2195 Dihedral : 6.290 37.485 1725 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 5.31 % Allowed : 20.65 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -3.07 (0.20), residues: 1565 helix: -2.91 (0.37), residues: 119 sheet: -1.23 (0.20), residues: 628 loop : -2.60 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 366 HIS 0.005 0.001 HIS P 465 PHE 0.022 0.001 PHE D 279 TYR 0.015 0.002 TYR D 327 ARG 0.004 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 156 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8052 (mp) REVERT: B 265 THR cc_start: 0.7148 (OUTLIER) cc_final: 0.6844 (p) REVERT: B 392 ARG cc_start: 0.7952 (ptp-170) cc_final: 0.7514 (tpt90) REVERT: C 357 GLU cc_start: 0.7494 (mp0) cc_final: 0.7195 (tt0) REVERT: C 422 GLU cc_start: 0.7598 (pp20) cc_final: 0.6837 (pm20) REVERT: C 443 PHE cc_start: 0.7589 (m-80) cc_final: 0.7340 (m-80) REVERT: J 20 ARG cc_start: 0.7372 (ttp-170) cc_final: 0.7144 (ptm160) REVERT: J 29 ASN cc_start: 0.7387 (p0) cc_final: 0.7158 (p0) REVERT: J 38 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7964 (ttp-170) REVERT: J 44 ASN cc_start: 0.8103 (t0) cc_final: 0.7805 (t0) REVERT: J 49 ILE cc_start: 0.8696 (tp) cc_final: 0.8032 (pt) REVERT: J 70 LYS cc_start: 0.8149 (mttp) cc_final: 0.7494 (mmtm) REVERT: J 131 ASP cc_start: 0.8526 (p0) cc_final: 0.8225 (p0) REVERT: P 416 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.7055 (mpp-170) REVERT: P 536 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6724 (tm-30) outliers start: 73 outliers final: 50 residues processed: 216 average time/residue: 0.2992 time to fit residues: 87.4426 Evaluate side-chains 201 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 147 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN D 249 HIS ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN P 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12565 Z= 0.276 Angle : 0.644 9.528 17096 Z= 0.321 Chirality : 0.043 0.177 1962 Planarity : 0.005 0.060 2195 Dihedral : 6.126 40.891 1725 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 6.55 % Allowed : 21.53 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.20), residues: 1565 helix: -2.42 (0.40), residues: 119 sheet: -0.96 (0.21), residues: 621 loop : -2.40 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 477 HIS 0.005 0.001 HIS P 465 PHE 0.017 0.001 PHE D 279 TYR 0.014 0.002 TYR D 327 ARG 0.008 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 156 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 265 THR cc_start: 0.7204 (OUTLIER) cc_final: 0.6891 (p) REVERT: B 392 ARG cc_start: 0.7920 (ptp-170) cc_final: 0.7419 (tpt90) REVERT: C 357 GLU cc_start: 0.7473 (mp0) cc_final: 0.7165 (tt0) REVERT: C 422 GLU cc_start: 0.7618 (pp20) cc_final: 0.6837 (pm20) REVERT: C 443 PHE cc_start: 0.7626 (m-80) cc_final: 0.7380 (m-80) REVERT: J 29 ASN cc_start: 0.7352 (p0) cc_final: 0.7144 (p0) REVERT: J 38 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8000 (ttp-170) REVERT: J 44 ASN cc_start: 0.8131 (t0) cc_final: 0.7806 (t0) REVERT: J 49 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8026 (pt) REVERT: J 70 LYS cc_start: 0.8107 (mttp) cc_final: 0.7540 (mmtm) REVERT: J 131 ASP cc_start: 0.8649 (p0) cc_final: 0.8318 (p0) REVERT: P 416 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.7055 (mpp-170) REVERT: P 536 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6750 (tm-30) outliers start: 90 outliers final: 62 residues processed: 222 average time/residue: 0.2730 time to fit residues: 83.8427 Evaluate side-chains 209 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 142 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 263 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN D 249 HIS ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 12565 Z= 0.456 Angle : 0.739 10.233 17096 Z= 0.369 Chirality : 0.047 0.199 1962 Planarity : 0.006 0.062 2195 Dihedral : 6.587 42.256 1725 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 6.84 % Allowed : 22.84 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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 (0.20), residues: 1565 helix: -2.31 (0.41), residues: 120 sheet: -1.00 (0.21), residues: 612 loop : -2.47 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 477 HIS 0.007 0.001 HIS P 465 PHE 0.034 0.002 PHE B 279 TYR 0.017 0.002 TYR P 164 ARG 0.005 0.001 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 146 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 265 THR cc_start: 0.7157 (OUTLIER) cc_final: 0.6859 (p) REVERT: B 392 ARG cc_start: 0.8042 (ptp-170) cc_final: 0.7609 (tpt90) REVERT: C 357 GLU cc_start: 0.7561 (mp0) cc_final: 0.7226 (tt0) REVERT: C 422 GLU cc_start: 0.7619 (pp20) cc_final: 0.6808 (pm20) REVERT: C 443 PHE cc_start: 0.7638 (m-80) cc_final: 0.7421 (m-80) REVERT: J 38 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8148 (ttp-170) REVERT: J 44 ASN cc_start: 0.8213 (t0) cc_final: 0.7936 (t0) REVERT: J 49 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8067 (pt) REVERT: J 70 LYS cc_start: 0.8243 (mttp) cc_final: 0.7584 (mmtm) REVERT: J 131 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8243 (p0) REVERT: P 416 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.7045 (mpp-170) REVERT: P 536 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6669 (tm-30) outliers start: 94 outliers final: 69 residues processed: 218 average time/residue: 0.2825 time to fit residues: 85.0451 Evaluate side-chains 215 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 140 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 382 ASP Chi-restraints excluded: chain P residue 426 ASN Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 0.0010 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.5266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12565 Z= 0.186 Angle : 0.609 9.254 17096 Z= 0.302 Chirality : 0.042 0.197 1962 Planarity : 0.005 0.059 2195 Dihedral : 5.806 43.988 1725 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.95 % Allowed : 24.87 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.36 (0.21), residues: 1565 helix: -1.74 (0.44), residues: 119 sheet: -0.81 (0.21), residues: 634 loop : -2.18 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP P 366 HIS 0.004 0.001 HIS P 465 PHE 0.016 0.001 PHE D 279 TYR 0.012 0.001 TYR A 472 ARG 0.005 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 157 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8024 (mp) REVERT: B 265 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6867 (p) REVERT: B 392 ARG cc_start: 0.7837 (ptp-170) cc_final: 0.7419 (tpt170) REVERT: C 357 GLU cc_start: 0.7427 (mp0) cc_final: 0.7115 (tt0) REVERT: C 422 GLU cc_start: 0.7580 (pp20) cc_final: 0.6780 (pm20) REVERT: C 443 PHE cc_start: 0.7599 (m-80) cc_final: 0.7356 (m-80) REVERT: J 38 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7979 (tmm-80) REVERT: J 44 ASN cc_start: 0.8088 (t0) cc_final: 0.7819 (t0) REVERT: J 49 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.7989 (pt) REVERT: J 70 LYS cc_start: 0.8114 (mttp) cc_final: 0.7445 (mmtm) REVERT: P 416 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.7037 (mpp-170) REVERT: P 536 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6962 (tm-30) outliers start: 68 outliers final: 49 residues processed: 212 average time/residue: 0.3044 time to fit residues: 87.9920 Evaluate side-chains 200 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 146 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 overall best weight: 1.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN C 350 HIS D 249 HIS D 362 ASN P 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12565 Z= 0.287 Angle : 0.646 9.397 17096 Z= 0.320 Chirality : 0.044 0.217 1962 Planarity : 0.005 0.059 2195 Dihedral : 5.964 42.217 1725 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.60 % Allowed : 25.38 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -2.29 (0.21), residues: 1565 helix: -1.58 (0.45), residues: 119 sheet: -0.78 (0.21), residues: 635 loop : -2.15 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 366 HIS 0.005 0.001 HIS P 465 PHE 0.014 0.001 PHE D 279 TYR 0.013 0.002 TYR D 327 ARG 0.008 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 145 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8030 (mp) REVERT: B 265 THR cc_start: 0.7170 (OUTLIER) cc_final: 0.6879 (p) REVERT: B 392 ARG cc_start: 0.7903 (ptp-170) cc_final: 0.7417 (tpt90) REVERT: C 357 GLU cc_start: 0.7497 (mp0) cc_final: 0.7245 (tt0) REVERT: C 422 GLU cc_start: 0.7590 (pp20) cc_final: 0.6814 (pm20) REVERT: J 38 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8090 (ttp-170) REVERT: J 44 ASN cc_start: 0.8156 (t0) cc_final: 0.7874 (t0) REVERT: J 49 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8001 (pt) REVERT: J 70 LYS cc_start: 0.8182 (mttp) cc_final: 0.7529 (mmtm) REVERT: P 416 ARG cc_start: 0.7272 (mtm-85) cc_final: 0.7014 (mpp-170) REVERT: P 536 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6827 (tm-30) outliers start: 77 outliers final: 61 residues processed: 205 average time/residue: 0.2943 time to fit residues: 81.9916 Evaluate side-chains 208 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 142 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 382 ASP Chi-restraints excluded: chain P residue 426 ASN Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 0.0770 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 118 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12565 Z= 0.246 Angle : 0.625 9.225 17096 Z= 0.310 Chirality : 0.043 0.199 1962 Planarity : 0.005 0.058 2195 Dihedral : 5.837 43.953 1725 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 5.60 % Allowed : 25.82 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.14 (0.21), residues: 1565 helix: -1.34 (0.46), residues: 119 sheet: -0.69 (0.21), residues: 631 loop : -2.06 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 366 HIS 0.005 0.001 HIS P 465 PHE 0.015 0.001 PHE D 279 TYR 0.012 0.001 TYR D 327 ARG 0.006 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 147 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8008 (mp) REVERT: B 265 THR cc_start: 0.7182 (OUTLIER) cc_final: 0.6890 (p) REVERT: B 392 ARG cc_start: 0.7871 (ptp-170) cc_final: 0.7390 (tpt90) REVERT: C 357 GLU cc_start: 0.7478 (mp0) cc_final: 0.7227 (tt0) REVERT: C 422 GLU cc_start: 0.7580 (pp20) cc_final: 0.6817 (pm20) REVERT: D 433 MET cc_start: 0.7287 (ttt) cc_final: 0.7073 (ttt) REVERT: J 38 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8132 (ttp-170) REVERT: J 44 ASN cc_start: 0.8128 (t0) cc_final: 0.7850 (t0) REVERT: J 49 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.7998 (pt) REVERT: J 70 LYS cc_start: 0.8162 (mttp) cc_final: 0.7516 (mmtm) REVERT: P 416 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.7008 (mpp-170) REVERT: P 536 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6953 (tm-30) outliers start: 77 outliers final: 65 residues processed: 208 average time/residue: 0.3005 time to fit residues: 85.0873 Evaluate side-chains 215 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 145 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 382 ASP Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12565 Z= 0.274 Angle : 0.639 9.312 17096 Z= 0.317 Chirality : 0.044 0.205 1962 Planarity : 0.005 0.057 2195 Dihedral : 5.901 45.768 1725 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 6.04 % Allowed : 25.60 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -2.13 (0.21), residues: 1565 helix: -1.26 (0.45), residues: 125 sheet: -0.70 (0.21), residues: 633 loop : -2.04 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 315 HIS 0.005 0.001 HIS P 465 PHE 0.015 0.001 PHE D 279 TYR 0.013 0.002 TYR D 327 ARG 0.007 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 147 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8011 (mp) REVERT: A 464 MET cc_start: 0.8245 (mmm) cc_final: 0.7897 (mmm) REVERT: B 265 THR cc_start: 0.7185 (OUTLIER) cc_final: 0.6892 (p) REVERT: B 392 ARG cc_start: 0.7885 (ptp-170) cc_final: 0.7409 (tpt90) REVERT: C 357 GLU cc_start: 0.7498 (mp0) cc_final: 0.7226 (tt0) REVERT: C 422 GLU cc_start: 0.7573 (pp20) cc_final: 0.6809 (pm20) REVERT: J 5 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7766 (pt) REVERT: J 38 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8209 (ttp-170) REVERT: J 44 ASN cc_start: 0.8145 (t0) cc_final: 0.7865 (t0) REVERT: J 49 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.7994 (pt) REVERT: J 70 LYS cc_start: 0.8190 (mttp) cc_final: 0.7523 (mmtm) REVERT: P 416 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.6992 (mpp-170) REVERT: P 536 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6824 (tm-30) outliers start: 83 outliers final: 69 residues processed: 212 average time/residue: 0.3012 time to fit residues: 86.6843 Evaluate side-chains 217 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 142 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 382 ASP Chi-restraints excluded: chain P residue 426 ASN Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 ASN P 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12565 Z= 0.238 Angle : 0.621 9.238 17096 Z= 0.307 Chirality : 0.043 0.216 1962 Planarity : 0.005 0.056 2195 Dihedral : 5.757 47.039 1725 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 5.82 % Allowed : 25.89 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.01 (0.21), residues: 1565 helix: -1.16 (0.45), residues: 125 sheet: -0.61 (0.21), residues: 631 loop : -1.97 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 315 HIS 0.005 0.001 HIS P 465 PHE 0.014 0.001 PHE D 279 TYR 0.013 0.001 TYR D 327 ARG 0.007 0.000 ARG A 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 153 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 464 MET cc_start: 0.8213 (mmm) cc_final: 0.7855 (mmm) REVERT: B 265 THR cc_start: 0.7165 (OUTLIER) cc_final: 0.6879 (p) REVERT: B 392 ARG cc_start: 0.7852 (ptp-170) cc_final: 0.7420 (tpt90) REVERT: C 357 GLU cc_start: 0.7478 (mp0) cc_final: 0.7233 (tt0) REVERT: C 422 GLU cc_start: 0.7563 (pp20) cc_final: 0.6796 (pm20) REVERT: D 433 MET cc_start: 0.7283 (ttt) cc_final: 0.7070 (ttt) REVERT: J 5 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7725 (pt) REVERT: J 38 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8138 (ttp-170) REVERT: J 44 ASN cc_start: 0.8117 (t0) cc_final: 0.7843 (t0) REVERT: J 49 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.7979 (pt) REVERT: J 70 LYS cc_start: 0.8178 (mttp) cc_final: 0.7506 (mmtm) REVERT: P 416 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.7007 (mpp-170) REVERT: P 536 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6926 (tm-30) outliers start: 80 outliers final: 69 residues processed: 214 average time/residue: 0.2940 time to fit residues: 85.5432 Evaluate side-chains 226 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 151 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 348 SER Chi-restraints excluded: chain P residue 351 VAL Chi-restraints excluded: chain P residue 382 ASP Chi-restraints excluded: chain P residue 435 VAL Chi-restraints excluded: chain P residue 536 GLU Chi-restraints excluded: chain S residue 256 THR Chi-restraints excluded: chain S residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.195998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.160866 restraints weight = 14360.658| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.12 r_work: 0.3726 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12565 Z= 0.197 Angle : 0.609 10.936 17096 Z= 0.301 Chirality : 0.042 0.194 1962 Planarity : 0.005 0.055 2195 Dihedral : 5.579 46.656 1725 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 5.02 % Allowed : 26.69 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: -1.89 (0.21), residues: 1565 helix: -0.97 (0.45), residues: 125 sheet: -0.54 (0.21), residues: 624 loop : -1.89 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 315 HIS 0.004 0.001 HIS P 465 PHE 0.014 0.001 PHE D 279 TYR 0.012 0.001 TYR D 327 ARG 0.007 0.000 ARG A 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.34 seconds wall clock time: 55 minutes 56.18 seconds (3356.18 seconds total)