Starting phenix.real_space_refine on Fri Feb 16 15:52:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c81_16468/02_2024/8c81_16468_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c81_16468/02_2024/8c81_16468.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c81_16468/02_2024/8c81_16468_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c81_16468/02_2024/8c81_16468_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c81_16468/02_2024/8c81_16468_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c81_16468/02_2024/8c81_16468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c81_16468/02_2024/8c81_16468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c81_16468/02_2024/8c81_16468_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c81_16468/02_2024/8c81_16468_updated.pdb" } resolution = 3.3 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= 0.027 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 64 5.16 5 C 10122 2.51 5 N 2610 2.21 5 O 2912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 497": "OD1" <-> "OD2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 517": "OE1" <-> "OE2" Residue "C ASP 520": "OD1" <-> "OD2" Residue "C ASP 534": "OD1" <-> "OD2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E ASP 222": "OD1" <-> "OD2" Residue "E TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15709 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1502 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "B" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4228 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 26, 'TRANS': 512} Chain: "C" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4435 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 30, 'TRANS': 530} Chain: "D" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 586 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "E" Number of atoms: 4726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4726 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 21, 'TRANS': 563} Chain breaks: 3 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 159 Unusual residues: {'ERG': 1, 'Q7G': 1, 'Z8A': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ERG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 8.44, per 1000 atoms: 0.54 Number of scatterers: 15709 At special positions: 0 Unit cell: (146.916, 118.272, 123.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 1 15.00 O 2912 8.00 N 2610 7.00 C 10122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.62 Conformation dependent library (CDL) restraints added in 2.8 seconds 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3650 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 16 sheets defined 41.7% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 108 through 128 Processing helix chain 'A' and resid 147 through 154 removed outlier: 6.124A pdb=" N ASP A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASP A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'B' and resid 20 through 35 removed outlier: 3.819A pdb=" N PHE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN B 30 " --> pdb=" O TRP B 26 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 31 " --> pdb=" O TYR B 27 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 32 " --> pdb=" O TYR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 54 through 71 Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 113 through 119 removed outlier: 4.493A pdb=" N TRP B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG B 117 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.547A pdb=" N LEU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix No H-bonds generated for 'chain 'B' and resid 218 through 224' Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 261 through 278 Processing helix chain 'B' and resid 303 through 313 Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 343 through 346 No H-bonds generated for 'chain 'B' and resid 343 through 346' Processing helix chain 'B' and resid 369 through 378 removed outlier: 4.096A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 390 through 405 Processing helix chain 'B' and resid 408 through 424 removed outlier: 3.806A pdb=" N PHE B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 457 Processing helix chain 'B' and resid 462 through 475 Processing helix chain 'B' and resid 483 through 502 Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 535 through 553 Processing helix chain 'C' and resid 20 through 27 Processing helix chain 'C' and resid 58 through 85 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 115 through 121 removed outlier: 5.563A pdb=" N ASP C 120 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 225 through 235 removed outlier: 4.322A pdb=" N PHE C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASN C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 272 through 285 removed outlier: 3.511A pdb=" N VAL C 284 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 324 Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 379 through 388 removed outlier: 4.014A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 394 No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 400 through 414 Processing helix chain 'C' and resid 422 through 443 Processing helix chain 'C' and resid 463 through 475 Proline residue: C 467 - end of helix removed outlier: 3.612A pdb=" N SER C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 522 Processing helix chain 'C' and resid 529 through 531 No H-bonds generated for 'chain 'C' and resid 529 through 531' Processing helix chain 'C' and resid 542 through 548 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 26 through 45 removed outlier: 4.531A pdb=" N ILE D 31 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS D 45 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 70 removed outlier: 3.626A pdb=" N PHE D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 106 through 120 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.746A pdb=" N GLU E 163 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP E 164 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE E 168 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS E 170 " --> pdb=" O ASN E 167 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN E 171 " --> pdb=" O PHE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 178 removed outlier: 3.796A pdb=" N SER E 177 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 283 through 296 Processing helix chain 'E' and resid 308 through 325 Proline residue: E 313 - end of helix removed outlier: 3.647A pdb=" N GLU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 354 Processing helix chain 'E' and resid 398 through 418 removed outlier: 3.543A pdb=" N GLN E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS E 413 " --> pdb=" O TRP E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 431 through 452 Processing helix chain 'E' and resid 473 through 489 removed outlier: 3.598A pdb=" N SER E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 502 Processing helix chain 'E' and resid 522 through 537 removed outlier: 3.809A pdb=" N ILE E 527 " --> pdb=" O TYR E 523 " (cutoff:3.500A) Proline residue: E 528 - end of helix Processing helix chain 'E' and resid 563 through 574 Processing helix chain 'E' and resid 576 through 578 No H-bonds generated for 'chain 'E' and resid 576 through 578' Processing sheet with id= A, first strand: chain 'A' and resid 55 through 57 Processing sheet with id= B, first strand: chain 'B' and resid 135 through 137 Processing sheet with id= C, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.577A pdb=" N PHE B 364 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 316 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 231 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL B 289 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 233 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR B 252 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ALA B 234 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR B 254 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 434 through 436 Processing sheet with id= E, first strand: chain 'C' and resid 133 through 137 Processing sheet with id= F, first strand: chain 'C' and resid 139 through 142 removed outlier: 4.059A pdb=" N TYR C 147 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 218 through 222 removed outlier: 3.844A pdb=" N GLY C 373 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 359 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 242 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS C 300 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE C 244 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N GLU C 302 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N ASP C 246 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA C 263 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER C 245 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG C 265 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.631A pdb=" N ARG C 494 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C 481 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 52 through 55 removed outlier: 3.647A pdb=" N ILE E 14 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 93 through 97 removed outlier: 3.553A pdb=" N GLY E 60 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA E 73 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU E 58 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 186 through 193 removed outlier: 3.815A pdb=" N ASN E 382 " --> pdb=" O HIS E 368 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL E 370 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE E 380 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 204 through 207 Processing sheet with id= M, first strand: chain 'E' and resid 263 through 266 Processing sheet with id= N, first strand: chain 'E' and resid 386 through 390 removed outlier: 6.408A pdb=" N ASP E 298 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG E 389 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR E 300 " --> pdb=" O ARG E 389 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN E 303 " --> pdb=" O VAL E 333 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 76 through 82 removed outlier: 6.872A pdb=" N PHE E 87 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG E 81 " --> pdb=" O HIS E 85 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N HIS E 85 " --> pdb=" O ARG E 81 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 591 through 597 removed outlier: 3.816A pdb=" N GLY E 605 " --> pdb=" O THR E 596 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1758 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: 4.84 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4994 1.34 - 1.46: 3622 1.46 - 1.58: 7375 1.58 - 1.70: 6 1.70 - 1.82: 98 Bond restraints: 16095 Sorted by residual: bond pdb=" C04 Q7G A 303 " pdb=" C05 Q7G A 303 " ideal model delta sigma weight residual 1.836 1.529 0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" C13 Q7G A 303 " pdb=" C14 Q7G A 303 " ideal model delta sigma weight residual 1.599 1.323 0.276 2.00e-02 2.50e+03 1.90e+02 bond pdb=" C07 Q7G A 303 " pdb=" C15 Q7G A 303 " ideal model delta sigma weight residual 1.779 1.521 0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C07 Q7G A 303 " pdb=" C08 Q7G A 303 " ideal model delta sigma weight residual 1.323 1.539 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C03 Q7G A 303 " pdb=" C04 Q7G A 303 " ideal model delta sigma weight residual 1.332 1.541 -0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 16090 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.38: 474 106.38 - 113.49: 8794 113.49 - 120.59: 6818 120.59 - 127.69: 5615 127.69 - 134.80: 162 Bond angle restraints: 21863 Sorted by residual: angle pdb=" N ILE C 118 " pdb=" CA ILE C 118 " pdb=" C ILE C 118 " ideal model delta sigma weight residual 111.88 107.27 4.61 1.06e+00 8.90e-01 1.89e+01 angle pdb=" N VAL E 537 " pdb=" CA VAL E 537 " pdb=" C VAL E 537 " ideal model delta sigma weight residual 113.16 108.39 4.77 1.49e+00 4.50e-01 1.03e+01 angle pdb=" C HIS C 96 " pdb=" N ASP C 97 " pdb=" CA ASP C 97 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.72e+00 angle pdb=" C20 ERG B 601 " pdb=" C22 ERG B 601 " pdb=" C23 ERG B 601 " ideal model delta sigma weight residual 125.47 134.80 -9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" C02 Q7G A 303 " pdb=" C03 Q7G A 303 " pdb=" C74 Q7G A 303 " ideal model delta sigma weight residual 111.60 120.23 -8.63 3.00e+00 1.11e-01 8.28e+00 ... (remaining 21858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 9218 26.09 - 52.19: 470 52.19 - 78.28: 35 78.28 - 104.38: 17 104.38 - 130.47: 8 Dihedral angle restraints: 9748 sinusoidal: 4081 harmonic: 5667 Sorted by residual: dihedral pdb=" C5A PLP C 601 " pdb=" O4P PLP C 601 " pdb=" P PLP C 601 " pdb=" O1P PLP C 601 " ideal model delta sinusoidal sigma weight residual 76.43 -162.96 -120.62 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" C1 ERG A 301 " pdb=" C2 ERG A 301 " pdb=" C3 ERG A 301 " pdb=" O1 ERG A 301 " ideal model delta sinusoidal sigma weight residual 182.38 51.91 130.47 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C1 ERG A 301 " pdb=" C2 ERG A 301 " pdb=" C3 ERG A 301 " pdb=" C4 ERG A 301 " ideal model delta sinusoidal sigma weight residual 60.21 -69.09 129.30 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 9745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 2440 0.160 - 0.320: 18 0.320 - 0.481: 0 0.481 - 0.641: 0 0.641 - 0.801: 1 Chirality restraints: 2459 Sorted by residual: chirality pdb=" C02 Q7G A 303 " pdb=" C03 Q7G A 303 " pdb=" C06 Q7G A 303 " pdb=" C10 Q7G A 303 " both_signs ideal model delta sigma weight residual False 2.14 2.94 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C04 Q7G A 303 " pdb=" C03 Q7G A 303 " pdb=" C05 Q7G A 303 " pdb=" O72 Q7G A 303 " both_signs ideal model delta sigma weight residual False 2.98 2.68 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C14 ERG B 602 " pdb=" C13 ERG B 602 " pdb=" C15 ERG B 602 " pdb=" C8 ERG B 602 " both_signs ideal model delta sigma weight residual False -2.26 -1.97 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 2456 not shown) Planarity restraints: 2759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 259 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO E 260 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 260 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 260 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 155 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 156 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 492 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.43e+00 pdb=" N PRO E 493 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 493 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 493 " 0.022 5.00e-02 4.00e+02 ... (remaining 2756 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2375 2.76 - 3.29: 14074 3.29 - 3.83: 23695 3.83 - 4.36: 25679 4.36 - 4.90: 48916 Nonbonded interactions: 114739 Sorted by model distance: nonbonded pdb=" OE2 GLU C 517 " pdb=" OG1 THR D 13 " model vdw 2.225 2.440 nonbonded pdb=" O ASN A 74 " pdb=" OG1 THR A 78 " model vdw 2.248 2.440 nonbonded pdb=" OG SER B 476 " pdb=" OD2 ASP C 238 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR B 460 " pdb=" OE1 GLU B 488 " model vdw 2.253 2.440 nonbonded pdb=" O SER D 7 " pdb=" OG SER D 7 " model vdw 2.261 2.440 ... (remaining 114734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 18.330 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 42.660 Find NCS groups from input model: 0.580 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.307 16095 Z= 0.492 Angle : 0.635 9.327 21863 Z= 0.316 Chirality : 0.050 0.801 2459 Planarity : 0.004 0.049 2759 Dihedral : 15.204 130.469 6098 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1922 helix: 2.26 (0.19), residues: 777 sheet: 0.38 (0.30), residues: 302 loop : -1.40 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 346 HIS 0.004 0.001 HIS E 331 PHE 0.015 0.001 PHE C 168 TYR 0.020 0.001 TYR C 510 ARG 0.005 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.826 Fit side-chains REVERT: E 366 PHE cc_start: 0.7357 (p90) cc_final: 0.6854 (p90) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2619 time to fit residues: 58.7848 Evaluate side-chains 122 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN D 21 ASN E 254 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16095 Z= 0.202 Angle : 0.546 9.031 21863 Z= 0.272 Chirality : 0.043 0.244 2459 Planarity : 0.004 0.045 2759 Dihedral : 9.899 107.666 2401 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.53 % Allowed : 5.26 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1922 helix: 2.43 (0.19), residues: 774 sheet: 0.43 (0.30), residues: 302 loop : -1.42 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 441 HIS 0.004 0.001 HIS E 331 PHE 0.017 0.001 PHE D 67 TYR 0.021 0.001 TYR C 510 ARG 0.003 0.000 ARG E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 1.905 Fit side-chains revert: symmetry clash REVERT: E 366 PHE cc_start: 0.7814 (p90) cc_final: 0.7339 (p90) outliers start: 9 outliers final: 6 residues processed: 132 average time/residue: 0.2713 time to fit residues: 55.0592 Evaluate side-chains 124 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN D 21 ASN E 355 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16095 Z= 0.395 Angle : 0.647 8.729 21863 Z= 0.332 Chirality : 0.047 0.249 2459 Planarity : 0.004 0.048 2759 Dihedral : 9.820 111.654 2401 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.11 % Allowed : 7.89 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1922 helix: 2.14 (0.19), residues: 778 sheet: 0.33 (0.31), residues: 286 loop : -1.60 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 441 HIS 0.007 0.001 HIS C 203 PHE 0.018 0.002 PHE B 364 TYR 0.036 0.002 TYR E 318 ARG 0.003 0.001 ARG E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.941 Fit side-chains REVERT: A 81 ASP cc_start: 0.8616 (t70) cc_final: 0.8376 (t0) REVERT: A 211 SER cc_start: 0.8952 (t) cc_final: 0.8743 (t) REVERT: E 245 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7110 (tm-30) REVERT: E 366 PHE cc_start: 0.7926 (p90) cc_final: 0.7520 (p90) REVERT: E 483 ARG cc_start: 0.7513 (ttm170) cc_final: 0.7269 (ttm170) outliers start: 19 outliers final: 15 residues processed: 133 average time/residue: 0.2817 time to fit residues: 56.8857 Evaluate side-chains 130 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 184 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN D 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16095 Z= 0.218 Angle : 0.548 8.485 21863 Z= 0.278 Chirality : 0.043 0.248 2459 Planarity : 0.004 0.046 2759 Dihedral : 9.384 109.354 2401 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.11 % Allowed : 9.82 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1922 helix: 2.30 (0.19), residues: 775 sheet: 0.31 (0.30), residues: 304 loop : -1.52 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.006 0.001 HIS E 331 PHE 0.013 0.001 PHE B 256 TYR 0.022 0.001 TYR C 510 ARG 0.002 0.000 ARG E 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.902 Fit side-chains REVERT: A 81 ASP cc_start: 0.8596 (t70) cc_final: 0.8345 (t0) REVERT: A 211 SER cc_start: 0.8877 (t) cc_final: 0.8669 (t) REVERT: B 127 MET cc_start: 0.8402 (mtp) cc_final: 0.8091 (mtp) REVERT: E 245 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7168 (tm-30) REVERT: E 366 PHE cc_start: 0.7910 (p90) cc_final: 0.7361 (p90) REVERT: E 414 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7573 (mm-30) outliers start: 19 outliers final: 16 residues processed: 142 average time/residue: 0.2776 time to fit residues: 59.4942 Evaluate side-chains 139 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 ASN D 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16095 Z= 0.179 Angle : 0.524 8.469 21863 Z= 0.263 Chirality : 0.042 0.247 2459 Planarity : 0.004 0.046 2759 Dihedral : 9.072 107.813 2401 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.23 % Allowed : 10.64 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1922 helix: 2.39 (0.19), residues: 779 sheet: 0.44 (0.30), residues: 306 loop : -1.47 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.005 0.001 HIS E 331 PHE 0.018 0.001 PHE D 67 TYR 0.020 0.001 TYR C 510 ARG 0.003 0.000 ARG C 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.978 Fit side-chains REVERT: A 81 ASP cc_start: 0.8598 (t70) cc_final: 0.8330 (t0) REVERT: A 211 SER cc_start: 0.8861 (t) cc_final: 0.8647 (t) REVERT: E 170 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6952 (t70) REVERT: E 245 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7164 (tm-30) REVERT: E 366 PHE cc_start: 0.7919 (p90) cc_final: 0.7309 (p90) REVERT: E 414 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7453 (mm-30) outliers start: 21 outliers final: 16 residues processed: 145 average time/residue: 0.2797 time to fit residues: 61.3855 Evaluate side-chains 143 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 ASN D 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16095 Z= 0.393 Angle : 0.624 8.189 21863 Z= 0.320 Chirality : 0.046 0.254 2459 Planarity : 0.004 0.047 2759 Dihedral : 9.342 111.350 2401 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.58 % Allowed : 11.92 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 1922 helix: 2.16 (0.19), residues: 778 sheet: 0.27 (0.30), residues: 309 loop : -1.62 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.006 0.001 HIS C 203 PHE 0.017 0.002 PHE B 256 TYR 0.027 0.002 TYR E 318 ARG 0.003 0.000 ARG C 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 2.004 Fit side-chains REVERT: A 81 ASP cc_start: 0.8636 (t70) cc_final: 0.8348 (t0) REVERT: A 211 SER cc_start: 0.8953 (t) cc_final: 0.8751 (t) REVERT: C 476 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7953 (mpt90) REVERT: E 170 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6987 (t70) REVERT: E 245 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7406 (tm-30) REVERT: E 366 PHE cc_start: 0.8000 (p90) cc_final: 0.7506 (p90) REVERT: E 414 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7564 (mm-30) outliers start: 27 outliers final: 20 residues processed: 140 average time/residue: 0.2992 time to fit residues: 62.9885 Evaluate side-chains 146 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 155 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN D 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16095 Z= 0.145 Angle : 0.510 8.436 21863 Z= 0.255 Chirality : 0.042 0.244 2459 Planarity : 0.004 0.046 2759 Dihedral : 8.821 107.574 2401 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.99 % Allowed : 12.62 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1922 helix: 2.37 (0.19), residues: 779 sheet: 0.47 (0.30), residues: 307 loop : -1.45 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 188 HIS 0.006 0.001 HIS E 331 PHE 0.020 0.001 PHE D 67 TYR 0.019 0.001 TYR C 510 ARG 0.004 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.722 Fit side-chains REVERT: A 81 ASP cc_start: 0.8553 (t70) cc_final: 0.8303 (t0) REVERT: A 211 SER cc_start: 0.8849 (t) cc_final: 0.8638 (t) REVERT: B 127 MET cc_start: 0.8430 (mtp) cc_final: 0.8157 (mtp) REVERT: C 138 ASP cc_start: 0.8362 (t0) cc_final: 0.8104 (t0) REVERT: D 51 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8337 (mtp) REVERT: E 170 HIS cc_start: 0.7225 (OUTLIER) cc_final: 0.7014 (t70) REVERT: E 245 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7191 (tm-30) REVERT: E 366 PHE cc_start: 0.7934 (p90) cc_final: 0.7367 (p90) REVERT: E 414 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7501 (mm-30) outliers start: 17 outliers final: 13 residues processed: 147 average time/residue: 0.2843 time to fit residues: 63.0668 Evaluate side-chains 142 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN D 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16095 Z= 0.173 Angle : 0.517 7.970 21863 Z= 0.259 Chirality : 0.042 0.247 2459 Planarity : 0.004 0.044 2759 Dihedral : 8.657 107.295 2401 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.23 % Allowed : 12.86 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1922 helix: 2.45 (0.19), residues: 779 sheet: 0.41 (0.31), residues: 293 loop : -1.40 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.005 0.001 HIS E 368 PHE 0.023 0.001 PHE E 337 TYR 0.020 0.001 TYR C 510 ARG 0.003 0.000 ARG C 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.960 Fit side-chains REVERT: A 70 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: A 81 ASP cc_start: 0.8546 (t70) cc_final: 0.8292 (t0) REVERT: A 211 SER cc_start: 0.8880 (t) cc_final: 0.8671 (t) REVERT: B 127 MET cc_start: 0.8365 (mtp) cc_final: 0.8105 (mtp) REVERT: C 138 ASP cc_start: 0.8379 (t0) cc_final: 0.8116 (t0) REVERT: E 245 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7167 (tm-30) REVERT: E 366 PHE cc_start: 0.7928 (p90) cc_final: 0.7424 (p90) outliers start: 21 outliers final: 17 residues processed: 138 average time/residue: 0.2764 time to fit residues: 58.1106 Evaluate side-chains 141 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 170 optimal weight: 0.0060 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN D 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16095 Z= 0.186 Angle : 0.523 7.924 21863 Z= 0.263 Chirality : 0.042 0.248 2459 Planarity : 0.004 0.044 2759 Dihedral : 8.594 107.561 2401 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.23 % Allowed : 13.03 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1922 helix: 2.45 (0.19), residues: 779 sheet: 0.44 (0.31), residues: 293 loop : -1.40 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 188 HIS 0.005 0.001 HIS E 331 PHE 0.023 0.001 PHE E 337 TYR 0.020 0.001 TYR C 510 ARG 0.004 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.842 Fit side-chains REVERT: A 70 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: A 81 ASP cc_start: 0.8553 (t70) cc_final: 0.8305 (t0) REVERT: A 211 SER cc_start: 0.8883 (t) cc_final: 0.8675 (t) REVERT: C 138 ASP cc_start: 0.8380 (t0) cc_final: 0.8116 (t0) REVERT: E 245 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7137 (tm-30) REVERT: E 366 PHE cc_start: 0.7913 (p90) cc_final: 0.7383 (p90) outliers start: 21 outliers final: 18 residues processed: 136 average time/residue: 0.2993 time to fit residues: 62.0116 Evaluate side-chains 140 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 110 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 0.0980 chunk 190 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN D 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16095 Z= 0.167 Angle : 0.516 7.798 21863 Z= 0.259 Chirality : 0.042 0.246 2459 Planarity : 0.003 0.044 2759 Dihedral : 8.489 107.345 2401 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.29 % Allowed : 13.21 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1922 helix: 2.45 (0.19), residues: 781 sheet: 0.47 (0.31), residues: 293 loop : -1.37 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.005 0.001 HIS E 331 PHE 0.023 0.001 PHE E 337 TYR 0.020 0.001 TYR C 510 ARG 0.004 0.000 ARG C 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 2.043 Fit side-chains REVERT: A 70 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: A 81 ASP cc_start: 0.8546 (t70) cc_final: 0.8298 (t0) REVERT: A 211 SER cc_start: 0.8878 (t) cc_final: 0.8667 (t) REVERT: B 127 MET cc_start: 0.8213 (mtp) cc_final: 0.7926 (mtp) REVERT: C 138 ASP cc_start: 0.8377 (t0) cc_final: 0.8113 (t0) REVERT: E 316 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: E 366 PHE cc_start: 0.7936 (p90) cc_final: 0.7422 (p90) outliers start: 22 outliers final: 19 residues processed: 135 average time/residue: 0.2760 time to fit residues: 56.6733 Evaluate side-chains 140 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 155 optimal weight: 0.0070 chunk 19 optimal weight: 0.0570 chunk 27 optimal weight: 0.0370 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN D 21 ASN E 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.101665 restraints weight = 22889.600| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.05 r_work: 0.3070 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16095 Z= 0.122 Angle : 0.492 7.803 21863 Z= 0.244 Chirality : 0.041 0.237 2459 Planarity : 0.003 0.043 2759 Dihedral : 8.147 105.191 2401 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.94 % Allowed : 13.62 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1922 helix: 2.49 (0.19), residues: 791 sheet: 0.71 (0.30), residues: 306 loop : -1.25 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 188 HIS 0.004 0.000 HIS E 331 PHE 0.022 0.001 PHE E 337 TYR 0.015 0.001 TYR C 510 ARG 0.008 0.000 ARG B 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.59 seconds wall clock time: 58 minutes 29.22 seconds (3509.22 seconds total)