Starting phenix.real_space_refine on Fri Mar 15 06:37:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/03_2024/8j5y_33733.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/03_2024/8j5y_33733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/03_2024/8j5y_33733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/03_2024/8j5y_33733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/03_2024/8j5y_33733.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/03_2024/8j5y_33733.pdb" } resolution = 3.07 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= 0.009 sd= 0.090 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 27 5.16 5 C 7006 2.51 5 N 1856 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 32": "OD1" <-> "OD2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 570": "OD1" <-> "OD2" Residue "B ASP 598": "OD1" <-> "OD2" Residue "B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10905 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4122 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 9, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 489} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1362 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 153} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1352 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 154} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4069 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'CIS': 9, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 488} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 144 Time building chain proxies: 5.79, per 1000 atoms: 0.53 Number of scatterers: 10905 At special positions: 0 Unit cell: (110.7, 140.22, 86.92, 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 27 16.00 O 2016 8.00 N 1856 7.00 C 7006 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=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.9 seconds 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 33.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.094A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 4.280A pdb=" N TYR A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 235 removed outlier: 3.884A pdb=" N THR A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.533A pdb=" N LEU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 270 Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.636A pdb=" N ASP A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.602A pdb=" N LEU A 344 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.619A pdb=" N ILE A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 435 through 449 removed outlier: 3.506A pdb=" N THR A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 494 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.619A pdb=" N GLN A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'C' and resid 11 through 23 removed outlier: 3.643A pdb=" N LEU C 15 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 48 Processing helix chain 'C' and resid 53 through 69 Processing helix chain 'C' and resid 81 through 101 removed outlier: 3.634A pdb=" N ARG C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 99 " --> pdb=" O PHE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.854A pdb=" N GLY C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 159 removed outlier: 3.568A pdb=" N SER C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.763A pdb=" N GLU D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 48 removed outlier: 3.522A pdb=" N ALA D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 43 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 70 removed outlier: 3.524A pdb=" N THR D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU D 70 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 removed outlier: 3.925A pdb=" N ARG D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 140 through 159 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.973A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 235 Proline residue: B 225 - end of helix removed outlier: 3.713A pdb=" N LEU B 229 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 270 Processing helix chain 'B' and resid 333 through 351 removed outlier: 3.690A pdb=" N LEU B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.766A pdb=" N ASN B 374 " --> pdb=" O MET B 370 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 removed outlier: 4.647A pdb=" N SER B 393 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 448 removed outlier: 3.780A pdb=" N PHE B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.597A pdb=" N ILE B 495 " --> pdb=" O ASN B 491 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS B 496 " --> pdb=" O PRO B 492 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER B 497 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 169 Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169 removed outlier: 4.325A pdb=" N ILE A 305 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 360 removed outlier: 7.247A pdb=" N ARG A 241 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N LEU A 386 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET A 243 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 281 removed outlier: 6.050A pdb=" N LYS A 299 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR A 319 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 467 through 470 removed outlier: 6.944A pdb=" N ILE A 551 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ILE A 545 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN A 553 " --> pdb=" O HIS A 543 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE A 536 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR A 508 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 538 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 572 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN A 482 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 518 through 520 Processing sheet with id=AA8, first strand: chain 'A' and resid 605 through 606 removed outlier: 3.502A pdb=" N THR A 606 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 5 " --> pdb=" O THR A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'B' and resid 168 through 169 Processing sheet with id=AB2, first strand: chain 'B' and resid 168 through 169 Processing sheet with id=AB3, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.527A pdb=" N ILE B 104 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 241 through 244 removed outlier: 3.679A pdb=" N VAL B 244 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 278 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASN B 360 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU B 280 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 295 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN B 322 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 297 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 468 through 470 removed outlier: 6.754A pdb=" N ILE B 551 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE B 545 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B 553 " --> pdb=" O HIS B 543 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE B 536 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR B 508 " --> pdb=" O PHE B 536 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 538 " --> pdb=" O ILE B 506 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TRP B 573 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 480 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 517 through 520 348 hydrogen bonds defined for protein. 975 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: 3.25 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3536 1.34 - 1.46: 2635 1.46 - 1.58: 4981 1.58 - 1.70: 1 1.70 - 1.82: 40 Bond restraints: 11193 Sorted by residual: bond pdb=" CB PRO C 122 " pdb=" CG PRO C 122 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.27e+00 bond pdb=" CB PRO D 122 " pdb=" CG PRO D 122 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.00e+00 bond pdb=" N ASP A 74 " pdb=" CA ASP A 74 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.94e+00 bond pdb=" CG LEU C 128 " pdb=" CD2 LEU C 128 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.72e+00 bond pdb=" CG LEU C 155 " pdb=" CD1 LEU C 155 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 ... (remaining 11188 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.35: 268 105.35 - 112.54: 5849 112.54 - 119.73: 3607 119.73 - 126.91: 5315 126.91 - 134.10: 214 Bond angle restraints: 15253 Sorted by residual: angle pdb=" N PRO B 416 " pdb=" CA PRO B 416 " pdb=" CB PRO B 416 " ideal model delta sigma weight residual 103.25 111.91 -8.66 1.05e+00 9.07e-01 6.81e+01 angle pdb=" N PRO A 416 " pdb=" CA PRO A 416 " pdb=" CB PRO A 416 " ideal model delta sigma weight residual 103.25 111.80 -8.55 1.05e+00 9.07e-01 6.62e+01 angle pdb=" N PRO B 422 " pdb=" CA PRO B 422 " pdb=" CB PRO B 422 " ideal model delta sigma weight residual 103.25 111.23 -7.98 1.05e+00 9.07e-01 5.77e+01 angle pdb=" N PRO B 466 " pdb=" CA PRO B 466 " pdb=" CB PRO B 466 " ideal model delta sigma weight residual 103.25 111.09 -7.84 1.05e+00 9.07e-01 5.57e+01 angle pdb=" CA PRO D 122 " pdb=" N PRO D 122 " pdb=" CD PRO D 122 " ideal model delta sigma weight residual 112.00 103.93 8.07 1.40e+00 5.10e-01 3.32e+01 ... (remaining 15248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5989 17.53 - 35.05: 524 35.05 - 52.58: 85 52.58 - 70.11: 15 70.11 - 87.63: 11 Dihedral angle restraints: 6624 sinusoidal: 2556 harmonic: 4068 Sorted by residual: dihedral pdb=" CA HIS D 130 " pdb=" C HIS D 130 " pdb=" N TRP D 131 " pdb=" CA TRP D 131 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU A 388 " pdb=" C LEU A 388 " pdb=" N GLU A 389 " pdb=" CA GLU A 389 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASP D 101 " pdb=" C ASP D 101 " pdb=" N PRO D 102 " pdb=" CA PRO D 102 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 6621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1183 0.040 - 0.080: 374 0.080 - 0.120: 120 0.120 - 0.160: 26 0.160 - 0.201: 8 Chirality restraints: 1711 Sorted by residual: chirality pdb=" CA PRO A 416 " pdb=" N PRO A 416 " pdb=" C PRO A 416 " pdb=" CB PRO A 416 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA PRO B 416 " pdb=" N PRO B 416 " pdb=" C PRO B 416 " pdb=" CB PRO B 416 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA PRO B 422 " pdb=" N PRO B 422 " pdb=" C PRO B 422 " pdb=" CB PRO B 422 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 1708 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 121 " -0.087 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO D 122 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO D 122 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO D 122 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 286 " -0.078 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO B 287 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 121 " -0.070 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 122 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 122 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 122 " -0.056 5.00e-02 4.00e+02 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 326 2.70 - 3.25: 11259 3.25 - 3.80: 16965 3.80 - 4.35: 21951 4.35 - 4.90: 36280 Nonbonded interactions: 86781 Sorted by model distance: nonbonded pdb=" O GLU A 77 " pdb=" OH TYR A 204 " model vdw 2.153 2.440 nonbonded pdb=" O GLU B 77 " pdb=" OH TYR B 204 " model vdw 2.159 2.440 nonbonded pdb=" OE1 GLU C 17 " pdb=" NH1 ARG C 40 " model vdw 2.167 2.520 nonbonded pdb=" O GLY B 247 " pdb=" OG SER B 250 " model vdw 2.193 2.440 nonbonded pdb=" O SER B 590 " pdb=" OG1 THR B 593 " model vdw 2.205 2.440 ... (remaining 86776 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 65 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 70 or (resid 71 through 72 and (na \ me N or name CA or name C or name O or name CB )) or resid 73 through 74 or (res \ id 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 82 or (resid 83 through 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 105 or (resid 106 and (name N or name CA or name C or \ name O or name CB )) or resid 107 through 167 or (resid 168 and (name N or name \ CA or name C or name O or name CB )) or resid 169 through 192 or (resid 193 and \ (name N or name CA or name C or name O or name CB )) or resid 194 through 197 o \ r (resid 198 through 201 and (name N or name CA or name C or name O or name CB ) \ ) or resid 202 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB )) or resid 227 through 275 or (resid 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 302 or resid 304 through \ 367 or (resid 368 and (name N or name CA or name C or name O or name CB )) or re \ sid 369 through 405 or (resid 406 through 417 and (name N or name CA or name C o \ r name O or name CB )) or resid 418 through 421 or (resid 422 through 423 and (n \ ame N or name CA or name C or name O or name CB )) or resid 424 through 465 or ( \ resid 466 and (name N or name CA or name C or name O or name CB )) or resid 467 \ through 526 or (resid 527 and (name N or name CA or name C or name O or name CB \ )) or resid 528 through 618)) selection = (chain 'B' and (resid 65 through 261 or (resid 262 and (name N or name CA or nam \ e C or name O or name CB )) or resid 263 through 369 or (resid 370 and (name N o \ r name CA or name C or name O or name CB )) or resid 371 through 399 or (resid 4 \ 00 and (name N or name CA or name C or name O or name CB )) or resid 401 through \ 517 or (resid 518 and (name N or name CA or name C or name O or name CB )) or r \ esid 519 through 569 or (resid 570 through 571 and (name N or name CA or name C \ or name O or name CB )) or resid 572 through 611 or (resid 612 and (name N or na \ me CA or name C or name O or name CB )) or resid 613 through 618)) } ncs_group { reference = (chain 'C' and (resid 2 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 or (resid 29 throug \ h 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throug \ h 167)) selection = (chain 'D' and (resid 2 through 134 or (resid 135 and (name N or name CA or name \ C or name O or name CB )) or resid 136 through 167)) } 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: 1.700 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: 6.210 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 30.280 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0038 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 : 0.004 0.090 11193 Z= 0.296 Angle : 0.842 13.621 15253 Z= 0.475 Chirality : 0.046 0.201 1711 Planarity : 0.006 0.126 1953 Dihedral : 13.879 87.632 3986 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.04 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % 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: -1.55 (0.21), residues: 1375 helix: -0.28 (0.26), residues: 386 sheet: -1.64 (0.36), residues: 192 loop : -1.23 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP C 21 HIS 0.014 0.001 HIS C 54 PHE 0.025 0.002 PHE A 263 TYR 0.028 0.002 TYR A 230 ARG 0.006 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.194 Fit side-chains REVERT: C 114 THR cc_start: -0.0995 (t) cc_final: -0.2581 (p) REVERT: D 126 VAL cc_start: -0.1066 (t) cc_final: -0.1311 (p) REVERT: B 188 LEU cc_start: 0.3229 (tt) cc_final: 0.2813 (mt) REVERT: B 301 LEU cc_start: 0.1475 (pt) cc_final: 0.0297 (tp) REVERT: B 552 MET cc_start: 0.0198 (mtm) cc_final: -0.0168 (ppp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2317 time to fit residues: 34.0317 Evaluate side-chains 60 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 20.0000 chunk 69 optimal weight: 40.0000 chunk 55 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 40.0000 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 578 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN D 113 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN B 371 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0321 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 11193 Z= 0.210 Angle : 0.683 8.713 15253 Z= 0.344 Chirality : 0.044 0.176 1711 Planarity : 0.005 0.076 1953 Dihedral : 4.738 23.466 1484 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.82 % Favored : 93.96 % Rotamer: Outliers : 1.04 % Allowed : 6.74 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % 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: -1.08 (0.22), residues: 1375 helix: 0.42 (0.26), residues: 392 sheet: -1.12 (0.34), residues: 223 loop : -1.19 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 21 HIS 0.008 0.001 HIS C 54 PHE 0.018 0.001 PHE B 434 TYR 0.016 0.002 TYR B 230 ARG 0.006 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1381 (pt) cc_final: 0.1149 (pt) REVERT: A 485 MET cc_start: 0.4047 (mmm) cc_final: 0.2984 (mtm) REVERT: A 489 ASP cc_start: 0.3278 (t0) cc_final: 0.2104 (p0) REVERT: A 581 GLU cc_start: -0.0223 (tt0) cc_final: -0.2902 (pp20) REVERT: C 5 ARG cc_start: -0.0364 (mtm110) cc_final: -0.1290 (ptt90) REVERT: C 114 THR cc_start: -0.0574 (t) cc_final: -0.2172 (p) REVERT: B 268 ARG cc_start: 0.0865 (OUTLIER) cc_final: -0.0458 (ttt180) REVERT: B 301 LEU cc_start: 0.1601 (pt) cc_final: 0.0424 (tp) outliers start: 12 outliers final: 6 residues processed: 74 average time/residue: 0.2058 time to fit residues: 23.8062 Evaluate side-chains 63 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 386 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 34 optimal weight: 30.0000 chunk 123 optimal weight: 9.9990 chunk 133 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 40.0000 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN A 449 HIS A 453 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 435 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0580 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11193 Z= 0.210 Angle : 0.665 9.985 15253 Z= 0.337 Chirality : 0.044 0.198 1711 Planarity : 0.005 0.070 1953 Dihedral : 4.712 24.764 1484 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.75 % Favored : 94.11 % Rotamer: Outliers : 1.73 % Allowed : 11.24 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % 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: -1.04 (0.22), residues: 1375 helix: 0.51 (0.26), residues: 400 sheet: -0.95 (0.35), residues: 220 loop : -1.27 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 121 HIS 0.005 0.001 HIS A 615 PHE 0.020 0.001 PHE B 442 TYR 0.017 0.002 TYR B 182 ARG 0.005 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 53 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1297 (pt) cc_final: 0.0764 (tt) REVERT: A 261 GLU cc_start: -0.0918 (OUTLIER) cc_final: -0.1401 (tt0) REVERT: A 485 MET cc_start: 0.4255 (mmm) cc_final: 0.3029 (mtm) REVERT: A 489 ASP cc_start: 0.3282 (t0) cc_final: 0.2065 (p0) REVERT: C 9 TRP cc_start: 0.0026 (p90) cc_final: -0.0839 (p90) REVERT: D 51 TYR cc_start: -0.0154 (m-80) cc_final: -0.0361 (m-10) REVERT: B 268 ARG cc_start: 0.1318 (OUTLIER) cc_final: -0.2168 (mmp80) REVERT: B 301 LEU cc_start: 0.1872 (pt) cc_final: 0.0746 (tp) outliers start: 20 outliers final: 13 residues processed: 71 average time/residue: 0.1917 time to fit residues: 21.8345 Evaluate side-chains 61 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 30.0000 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.0070 chunk 83 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 0.0470 chunk 35 optimal weight: 50.0000 chunk 109 optimal weight: 9.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0666 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11193 Z= 0.173 Angle : 0.618 9.536 15253 Z= 0.312 Chirality : 0.043 0.163 1711 Planarity : 0.005 0.062 1953 Dihedral : 4.480 22.445 1484 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 2.07 % Allowed : 13.57 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % 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: -1.08 (0.22), residues: 1375 helix: 0.53 (0.26), residues: 403 sheet: -0.73 (0.35), residues: 211 loop : -1.43 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 121 HIS 0.005 0.001 HIS C 158 PHE 0.020 0.001 PHE B 434 TYR 0.015 0.001 TYR B 182 ARG 0.007 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 56 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1249 (pt) cc_final: 0.0719 (tt) REVERT: A 261 GLU cc_start: -0.1122 (OUTLIER) cc_final: -0.1570 (tt0) REVERT: A 485 MET cc_start: 0.4435 (mmm) cc_final: 0.3193 (mtm) REVERT: C 9 TRP cc_start: 0.0225 (p90) cc_final: -0.0748 (p90) REVERT: C 15 LEU cc_start: -0.1614 (tp) cc_final: -0.2997 (mt) REVERT: C 114 THR cc_start: -0.0085 (t) cc_final: -0.1557 (p) REVERT: D 51 TYR cc_start: -0.0129 (m-80) cc_final: -0.0549 (m-10) REVERT: B 124 LEU cc_start: -0.1244 (OUTLIER) cc_final: -0.2613 (mt) REVERT: B 166 ARG cc_start: -0.0905 (OUTLIER) cc_final: -0.2969 (tpp80) REVERT: B 268 ARG cc_start: 0.1096 (OUTLIER) cc_final: -0.0742 (tpp-160) REVERT: B 301 LEU cc_start: 0.2012 (pt) cc_final: 0.1308 (tp) outliers start: 24 outliers final: 14 residues processed: 77 average time/residue: 0.2451 time to fit residues: 28.1722 Evaluate side-chains 68 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 441 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 117 optimal weight: 0.0980 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN B 90 HIS ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 265 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0964 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11193 Z= 0.286 Angle : 0.785 11.564 15253 Z= 0.399 Chirality : 0.046 0.242 1711 Planarity : 0.006 0.129 1953 Dihedral : 5.331 30.714 1484 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.55 % Favored : 93.31 % Rotamer: Outliers : 2.59 % Allowed : 15.21 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % 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: -1.27 (0.22), residues: 1375 helix: 0.26 (0.26), residues: 395 sheet: -0.79 (0.35), residues: 215 loop : -1.47 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 222 HIS 0.012 0.001 HIS C 158 PHE 0.045 0.002 PHE B 434 TYR 0.022 0.002 TYR C 51 ARG 0.014 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 50 time to evaluate : 1.182 Fit side-chains REVERT: A 216 LEU cc_start: 0.1329 (pt) cc_final: 0.0809 (tt) REVERT: A 261 GLU cc_start: -0.0957 (OUTLIER) cc_final: -0.1494 (tt0) REVERT: A 485 MET cc_start: 0.4474 (mmm) cc_final: 0.3188 (mtm) REVERT: C 9 TRP cc_start: 0.0100 (p90) cc_final: -0.0610 (p90) REVERT: C 19 LYS cc_start: -0.0600 (ttpt) cc_final: -0.1396 (ttpt) REVERT: D 51 TYR cc_start: 0.0185 (m-80) cc_final: -0.0416 (m-10) REVERT: B 78 THR cc_start: -0.1980 (OUTLIER) cc_final: -0.3835 (p) REVERT: B 124 LEU cc_start: -0.1019 (OUTLIER) cc_final: -0.1353 (mm) REVERT: B 135 HIS cc_start: 0.0107 (OUTLIER) cc_final: -0.0626 (p90) REVERT: B 165 LEU cc_start: 0.0696 (OUTLIER) cc_final: 0.0235 (mt) REVERT: B 166 ARG cc_start: -0.0771 (OUTLIER) cc_final: -0.3330 (mmm-85) REVERT: B 170 SER cc_start: 0.0133 (OUTLIER) cc_final: -0.0080 (t) outliers start: 30 outliers final: 15 residues processed: 78 average time/residue: 0.2385 time to fit residues: 27.2308 Evaluate side-chains 70 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 441 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 40.0000 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN B 172 HIS B 180 HIS B 286 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1134 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11193 Z= 0.348 Angle : 0.839 12.376 15253 Z= 0.429 Chirality : 0.050 0.365 1711 Planarity : 0.007 0.123 1953 Dihedral : 5.837 35.502 1484 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.15 % Favored : 91.71 % Rotamer: Outliers : 3.54 % Allowed : 15.82 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % Twisted General : 0.08 % 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: -1.63 (0.22), residues: 1375 helix: -0.13 (0.26), residues: 391 sheet: -0.49 (0.39), residues: 182 loop : -1.77 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 222 HIS 0.011 0.001 HIS A 615 PHE 0.061 0.002 PHE B 434 TYR 0.020 0.002 TYR C 51 ARG 0.012 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 53 time to evaluate : 1.174 Fit side-chains REVERT: A 216 LEU cc_start: 0.1049 (pt) cc_final: 0.0684 (tp) REVERT: A 261 GLU cc_start: -0.1049 (OUTLIER) cc_final: -0.1561 (tt0) REVERT: A 485 MET cc_start: 0.4584 (mmm) cc_final: 0.3361 (mtm) REVERT: A 495 ILE cc_start: 0.0296 (OUTLIER) cc_final: -0.0046 (mp) REVERT: C 9 TRP cc_start: 0.0058 (p90) cc_final: -0.0940 (p-90) REVERT: C 19 LYS cc_start: -0.0358 (ttpt) cc_final: -0.1104 (ttpt) REVERT: D 99 LEU cc_start: 0.2979 (OUTLIER) cc_final: 0.2547 (tp) REVERT: B 95 PHE cc_start: 0.1707 (p90) cc_final: 0.1489 (p90) REVERT: B 124 LEU cc_start: -0.0961 (OUTLIER) cc_final: -0.1391 (mm) REVERT: B 135 HIS cc_start: 0.0067 (OUTLIER) cc_final: -0.1323 (m170) REVERT: B 166 ARG cc_start: -0.0318 (OUTLIER) cc_final: -0.2840 (mmm-85) REVERT: B 453 GLN cc_start: 0.0104 (OUTLIER) cc_final: -0.0660 (pt0) outliers start: 41 outliers final: 26 residues processed: 89 average time/residue: 0.2360 time to fit residues: 30.8330 Evaluate side-chains 85 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 52 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 584 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 30.0000 chunk 74 optimal weight: 40.0000 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 79 optimal weight: 0.0970 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 0.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 172 HIS B 265 GLN ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1003 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11193 Z= 0.188 Angle : 0.650 9.902 15253 Z= 0.332 Chirality : 0.044 0.163 1711 Planarity : 0.005 0.081 1953 Dihedral : 5.069 30.023 1484 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.55 % Favored : 93.31 % Rotamer: Outliers : 2.42 % Allowed : 16.85 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % 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: -1.25 (0.22), residues: 1375 helix: 0.42 (0.27), residues: 393 sheet: -0.44 (0.37), residues: 200 loop : -1.65 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 131 HIS 0.009 0.001 HIS B 310 PHE 0.031 0.001 PHE B 434 TYR 0.020 0.001 TYR D 88 ARG 0.010 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 56 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 GLU cc_start: -0.1136 (OUTLIER) cc_final: -0.1648 (tt0) REVERT: A 608 GLU cc_start: 0.2049 (pp20) cc_final: 0.1236 (mt-10) REVERT: C 9 TRP cc_start: 0.0026 (p90) cc_final: -0.1100 (p-90) REVERT: C 19 LYS cc_start: -0.0455 (ttpt) cc_final: -0.1062 (ttpt) REVERT: D 99 LEU cc_start: 0.3026 (OUTLIER) cc_final: 0.2634 (tp) REVERT: B 89 LEU cc_start: -0.1440 (OUTLIER) cc_final: -0.1952 (tt) REVERT: B 135 HIS cc_start: -0.0016 (OUTLIER) cc_final: -0.0926 (m-70) REVERT: B 166 ARG cc_start: -0.0596 (OUTLIER) cc_final: -0.3181 (mmt180) outliers start: 28 outliers final: 18 residues processed: 83 average time/residue: 0.2449 time to fit residues: 29.7547 Evaluate side-chains 72 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 49 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 83 optimal weight: 40.0000 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 0.0670 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1036 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11193 Z= 0.189 Angle : 0.656 9.981 15253 Z= 0.331 Chirality : 0.043 0.165 1711 Planarity : 0.005 0.060 1953 Dihedral : 4.893 29.762 1484 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.56 % Favored : 92.29 % Rotamer: Outliers : 2.77 % Allowed : 17.11 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % 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: -1.17 (0.22), residues: 1375 helix: 0.54 (0.27), residues: 393 sheet: -0.40 (0.39), residues: 183 loop : -1.61 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 131 HIS 0.012 0.001 HIS B 310 PHE 0.029 0.001 PHE B 434 TYR 0.022 0.001 TYR D 88 ARG 0.007 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 50 time to evaluate : 1.126 Fit side-chains REVERT: A 261 GLU cc_start: -0.1145 (OUTLIER) cc_final: -0.1661 (tt0) REVERT: A 485 MET cc_start: 0.3482 (mpp) cc_final: 0.2704 (mtm) REVERT: A 495 ILE cc_start: -0.0009 (OUTLIER) cc_final: -0.0216 (mp) REVERT: C 2 ILE cc_start: -0.0902 (OUTLIER) cc_final: -0.1586 (pt) REVERT: C 9 TRP cc_start: -0.0049 (p90) cc_final: -0.1044 (p90) REVERT: C 19 LYS cc_start: -0.0593 (ttpt) cc_final: -0.1054 (ttpt) REVERT: D 99 LEU cc_start: 0.2939 (OUTLIER) cc_final: 0.2578 (tp) REVERT: B 89 LEU cc_start: -0.1429 (OUTLIER) cc_final: -0.1940 (tt) REVERT: B 135 HIS cc_start: 0.0280 (OUTLIER) cc_final: -0.0681 (m170) REVERT: B 166 ARG cc_start: -0.0357 (OUTLIER) cc_final: -0.2750 (mmt90) REVERT: B 453 GLN cc_start: 0.0450 (OUTLIER) cc_final: -0.1817 (mp10) outliers start: 32 outliers final: 22 residues processed: 79 average time/residue: 0.2084 time to fit residues: 25.2781 Evaluate side-chains 78 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 48 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 50.0000 chunk 125 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 0.0170 chunk 80 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 overall best weight: 3.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 286 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1249 moved from start: 0.7709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11193 Z= 0.366 Angle : 0.863 14.552 15253 Z= 0.444 Chirality : 0.050 0.288 1711 Planarity : 0.007 0.084 1953 Dihedral : 5.975 38.474 1484 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.80 % Favored : 91.05 % Rotamer: Outliers : 3.03 % Allowed : 17.29 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % 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: -1.51 (0.22), residues: 1375 helix: 0.16 (0.26), residues: 384 sheet: 0.03 (0.44), residues: 150 loop : -1.86 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 131 HIS 0.016 0.002 HIS B 172 PHE 0.061 0.002 PHE B 434 TYR 0.029 0.002 TYR B 111 ARG 0.011 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 47 time to evaluate : 1.173 Fit side-chains REVERT: A 248 LYS cc_start: -0.0845 (pttt) cc_final: -0.2028 (pttm) REVERT: A 261 GLU cc_start: -0.1108 (OUTLIER) cc_final: -0.1625 (tt0) REVERT: A 495 ILE cc_start: 0.0084 (OUTLIER) cc_final: -0.0149 (mp) REVERT: A 588 LEU cc_start: 0.0755 (OUTLIER) cc_final: 0.0055 (mp) REVERT: C 9 TRP cc_start: -0.0178 (p90) cc_final: -0.1594 (p90) REVERT: C 19 LYS cc_start: -0.0227 (ttpt) cc_final: -0.0654 (ttpt) REVERT: C 90 MET cc_start: 0.2108 (tpp) cc_final: 0.1902 (tpp) REVERT: B 89 LEU cc_start: -0.1257 (OUTLIER) cc_final: -0.1937 (tt) REVERT: B 135 HIS cc_start: 0.0796 (OUTLIER) cc_final: -0.2901 (m170) REVERT: B 166 ARG cc_start: 0.0745 (OUTLIER) cc_final: -0.2239 (mmm-85) REVERT: B 453 GLN cc_start: 0.0070 (OUTLIER) cc_final: -0.1109 (pt0) outliers start: 35 outliers final: 25 residues processed: 78 average time/residue: 0.1994 time to fit residues: 23.7276 Evaluate side-chains 76 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 44 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 584 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 50.0000 chunk 107 optimal weight: 10.0000 chunk 11 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 66 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1187 moved from start: 0.7903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11193 Z= 0.261 Angle : 0.740 13.890 15253 Z= 0.374 Chirality : 0.046 0.213 1711 Planarity : 0.006 0.052 1953 Dihedral : 5.529 34.583 1484 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.29 % Favored : 91.56 % Rotamer: Outliers : 2.33 % Allowed : 18.06 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % 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: -1.45 (0.22), residues: 1375 helix: 0.17 (0.26), residues: 393 sheet: 0.04 (0.44), residues: 145 loop : -1.81 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 131 HIS 0.009 0.001 HIS B 172 PHE 0.045 0.002 PHE B 434 TYR 0.019 0.002 TYR D 88 ARG 0.009 0.001 ARG B 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 52 time to evaluate : 1.203 Fit side-chains REVERT: A 248 LYS cc_start: -0.0719 (pttt) cc_final: -0.1955 (pttm) REVERT: A 261 GLU cc_start: -0.1187 (OUTLIER) cc_final: -0.1700 (tt0) REVERT: A 489 ASP cc_start: 0.2888 (t0) cc_final: 0.2214 (p0) REVERT: C 9 TRP cc_start: -0.0334 (p90) cc_final: -0.1719 (p90) REVERT: C 19 LYS cc_start: -0.0262 (ttpt) cc_final: -0.0661 (ttpt) REVERT: B 89 LEU cc_start: -0.1273 (OUTLIER) cc_final: -0.1944 (tt) REVERT: B 135 HIS cc_start: 0.0703 (OUTLIER) cc_final: -0.2955 (m170) REVERT: B 166 ARG cc_start: 0.0762 (OUTLIER) cc_final: -0.1965 (mmm160) REVERT: B 365 ILE cc_start: -0.1424 (OUTLIER) cc_final: -0.2794 (mm) outliers start: 27 outliers final: 20 residues processed: 77 average time/residue: 0.2075 time to fit residues: 24.8047 Evaluate side-chains 71 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 46 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 584 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.0370 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5210 r_free = 0.5210 target = 0.303122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.267069 restraints weight = 15161.187| |-----------------------------------------------------------------------------| r_work (start): 0.4873 rms_B_bonded: 3.59 r_work: 0.4588 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0560 moved from start: 0.7905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11193 Z= 0.169 Angle : 0.647 15.757 15253 Z= 0.326 Chirality : 0.043 0.169 1711 Planarity : 0.005 0.051 1953 Dihedral : 4.918 29.559 1484 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.49 % Favored : 92.36 % Rotamer: Outliers : 2.42 % Allowed : 18.15 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % 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: -1.26 (0.22), residues: 1375 helix: 0.42 (0.27), residues: 397 sheet: 0.27 (0.45), residues: 142 loop : -1.75 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 131 HIS 0.006 0.001 HIS B 172 PHE 0.028 0.001 PHE B 434 TYR 0.017 0.001 TYR D 88 ARG 0.007 0.000 ARG C 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2173.08 seconds wall clock time: 40 minutes 4.88 seconds (2404.88 seconds total)