Starting phenix.real_space_refine on Wed Jan 17 21:06:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t23_40979/01_2024/8t23_40979.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t23_40979/01_2024/8t23_40979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t23_40979/01_2024/8t23_40979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t23_40979/01_2024/8t23_40979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t23_40979/01_2024/8t23_40979.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t23_40979/01_2024/8t23_40979.pdb" } resolution = 3.87 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= -0.001 sd= 0.019 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 37 5.16 5 C 4121 2.51 5 N 1075 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6451 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Chain: "B" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1467 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 11, 'TRANS': 173} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.84, per 1000 atoms: 0.60 Number of scatterers: 6451 At special positions: 0 Unit cell: (103.23, 75.48, 135.42, 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 37 16.00 O 1218 8.00 N 1075 7.00 C 4121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.02 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " BETA1-6 " NAG H 1 " - " FUC H 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 53 " " NAG B 601 " - " ASN B 343 " " NAG G 1 " - " ASN A 322 " " NAG H 1 " - " ASN A 216 " Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 45.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.534A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 66 through 83 removed outlier: 3.646A pdb=" N THR A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR A 83 " --> pdb=" O HIS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.610A pdb=" N ALA A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 4.873A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N MET A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.616A pdb=" N GLY A 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 157 through 163 removed outlier: 4.367A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.577A pdb=" N LEU A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 236 through 248 removed outlier: 4.855A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 removed outlier: 3.973A pdb=" N TYR A 252 " --> pdb=" O MET A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.388A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.956A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 382 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 413 removed outlier: 3.628A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 446 through 452 removed outlier: 4.238A pdb=" N THR A 449 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 450 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Proline residue: A 451 - end of helix No H-bonds generated for 'chain 'A' and resid 446 through 452' Processing helix chain 'A' and resid 453 through 464 removed outlier: 4.725A pdb=" N ARG A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 removed outlier: 4.026A pdb=" N GLU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 6.677A pdb=" N PHE A 504 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS A 505 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 506 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 507 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.646A pdb=" N GLN A 522 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.946A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.840A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.536A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.588A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.008A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.941A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 396 through 403 removed outlier: 3.898A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) 173 hydrogen bonds defined for protein. 468 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: 1.48 Time building geometry restraints manager: 2.66 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: 2064 1.34 - 1.46: 1660 1.46 - 1.58: 2852 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6635 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CB PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.92e+00 bond pdb=" CG PRO A 389 " pdb=" CD PRO A 389 " ideal model delta sigma weight residual 1.503 1.431 0.072 3.40e-02 8.65e+02 4.45e+00 bond pdb=" CA LYS A 441 " pdb=" CB LYS A 441 " ideal model delta sigma weight residual 1.526 1.559 -0.033 1.70e-02 3.46e+03 3.83e+00 bond pdb=" N PRO A 389 " pdb=" CA PRO A 389 " ideal model delta sigma weight residual 1.469 1.444 0.024 1.28e-02 6.10e+03 3.66e+00 ... (remaining 6630 not shown) Histogram of bond angle deviations from ideal: 94.54 - 102.45: 36 102.45 - 110.36: 1458 110.36 - 118.27: 3409 118.27 - 126.18: 3957 126.18 - 134.09: 152 Bond angle restraints: 9012 Sorted by residual: angle pdb=" CA PRO A 389 " pdb=" N PRO A 389 " pdb=" CD PRO A 389 " ideal model delta sigma weight residual 112.00 95.27 16.73 1.40e+00 5.10e-01 1.43e+02 angle pdb=" C ALA A 212 " pdb=" N ASP A 213 " pdb=" CA ASP A 213 " ideal model delta sigma weight residual 122.35 132.59 -10.24 1.46e+00 4.69e-01 4.92e+01 angle pdb=" N PRO A 389 " pdb=" CD PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 103.20 94.54 8.66 1.50e+00 4.44e-01 3.33e+01 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 113.71 108.86 4.85 9.50e-01 1.11e+00 2.61e+01 angle pdb=" CA LEU A 45 " pdb=" CB LEU A 45 " pdb=" CG LEU A 45 " ideal model delta sigma weight residual 116.30 132.29 -15.99 3.50e+00 8.16e-02 2.09e+01 ... (remaining 9007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.55: 3535 23.55 - 47.09: 388 47.09 - 70.64: 62 70.64 - 94.19: 10 94.19 - 117.74: 6 Dihedral angle restraints: 4001 sinusoidal: 1708 harmonic: 2293 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 168.30 -75.30 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 167.32 -74.32 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.83 48.17 1 1.00e+01 1.00e-02 3.20e+01 ... (remaining 3998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 828 0.077 - 0.154: 113 0.154 - 0.231: 3 0.231 - 0.308: 1 0.308 - 0.385: 1 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 216 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CB VAL A 318 " pdb=" CA VAL A 318 " pdb=" CG1 VAL A 318 " pdb=" CG2 VAL A 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 943 not shown) Planarity restraints: 1168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " 0.144 5.00e-02 4.00e+02 2.00e-01 6.39e+01 pdb=" N PRO A 389 " -0.344 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.113 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " -0.017 2.00e-02 2.50e+03 1.96e-02 9.57e+00 pdb=" CG TRP A 168 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 564 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO A 565 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " 0.039 5.00e-02 4.00e+02 ... (remaining 1165 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 191 2.69 - 3.24: 6608 3.24 - 3.79: 9892 3.79 - 4.35: 12329 4.35 - 4.90: 18650 Nonbonded interactions: 47670 Sorted by model distance: nonbonded pdb=" OH TYR A 180 " pdb=" O THR A 496 " model vdw 2.136 2.440 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.226 2.440 nonbonded pdb=" O GLU A 166 " pdb=" OG SER A 170 " model vdw 2.228 2.440 nonbonded pdb=" O ARG A 305 " pdb=" NZ LYS A 309 " model vdw 2.233 2.520 nonbonded pdb=" NH2 ARG B 355 " pdb=" OD2 ASP B 398 " model vdw 2.239 2.520 ... (remaining 47665 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 'G' and resid 1) selection = (chain 'H' and resid 1) } 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 group one per residue 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: 11.610 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: 0.000 Extract box with map and model: 27.350 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.380 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 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 : 0.005 0.149 6635 Z= 0.293 Angle : 1.004 16.729 9012 Z= 0.535 Chirality : 0.051 0.385 946 Planarity : 0.009 0.200 1164 Dihedral : 19.217 117.737 2511 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 0.59 % Allowed : 31.48 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.28), residues: 775 helix: -1.63 (0.31), residues: 257 sheet: 2.48 (1.14), residues: 24 loop : -2.66 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 168 HIS 0.008 0.001 HIS A 505 PHE 0.020 0.002 PHE B 338 TYR 0.015 0.001 TYR A 510 ARG 0.008 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6107 (mt) cc_final: 0.5829 (mm) REVERT: A 62 MET cc_start: 0.4429 (mpp) cc_final: 0.4108 (pmm) REVERT: A 123 MET cc_start: -0.0391 (tpt) cc_final: -0.0686 (tpt) REVERT: A 202 TYR cc_start: 0.7222 (m-10) cc_final: 0.6390 (t80) REVERT: A 379 ILE cc_start: 0.8955 (tt) cc_final: 0.8683 (mm) REVERT: A 382 ASP cc_start: 0.8908 (t70) cc_final: 0.8393 (p0) REVERT: A 408 MET cc_start: 0.3341 (mmp) cc_final: 0.2561 (mmm) REVERT: A 474 MET cc_start: -0.1394 (ptt) cc_final: -0.2041 (ptt) REVERT: A 497 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6257 (t80) REVERT: A 515 TYR cc_start: 0.6070 (m-80) cc_final: 0.5712 (m-80) REVERT: A 539 LEU cc_start: 0.6118 (tp) cc_final: 0.5859 (mp) outliers start: 4 outliers final: 1 residues processed: 127 average time/residue: 0.1990 time to fit residues: 33.7145 Evaluate side-chains 82 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 23 optimal weight: 0.0010 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5114 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6635 Z= 0.196 Angle : 0.768 12.227 9012 Z= 0.383 Chirality : 0.050 0.509 946 Planarity : 0.006 0.069 1164 Dihedral : 11.530 103.930 982 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 4.10 % Allowed : 28.26 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.30), residues: 775 helix: -1.19 (0.32), residues: 259 sheet: 1.66 (1.14), residues: 24 loop : -2.49 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 168 HIS 0.006 0.001 HIS A 505 PHE 0.023 0.002 PHE B 490 TYR 0.015 0.001 TYR A 41 ARG 0.006 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ILE cc_start: 0.6829 (mm) cc_final: 0.6569 (mt) REVERT: A 171 GLU cc_start: 0.8921 (pp20) cc_final: 0.8553 (pm20) REVERT: A 211 TRP cc_start: 0.3791 (p90) cc_final: 0.2473 (m100) REVERT: A 252 TYR cc_start: 0.2765 (OUTLIER) cc_final: 0.1923 (p90) REVERT: A 279 TYR cc_start: 0.5292 (OUTLIER) cc_final: 0.4801 (m-10) REVERT: A 345 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7184 (t70) REVERT: A 376 MET cc_start: 0.8854 (tpt) cc_final: 0.8181 (ptt) REVERT: A 382 ASP cc_start: 0.9036 (t70) cc_final: 0.8368 (p0) REVERT: A 462 MET cc_start: 0.7032 (ppp) cc_final: 0.6716 (ppp) REVERT: A 474 MET cc_start: -0.1596 (ptt) cc_final: -0.1924 (ptt) REVERT: A 566 TRP cc_start: 0.7401 (p-90) cc_final: 0.6908 (p-90) REVERT: A 579 MET cc_start: 0.6878 (ppp) cc_final: 0.5721 (ppp) outliers start: 28 outliers final: 15 residues processed: 109 average time/residue: 0.1709 time to fit residues: 25.1143 Evaluate side-chains 90 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.0670 chunk 70 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5159 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6635 Z= 0.179 Angle : 0.731 14.729 9012 Z= 0.362 Chirality : 0.049 0.518 946 Planarity : 0.006 0.067 1164 Dihedral : 10.876 100.123 980 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 4.69 % Allowed : 28.40 % Favored : 66.91 % 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: -2.60 (0.30), residues: 775 helix: -0.98 (0.33), residues: 258 sheet: 1.40 (1.01), residues: 24 loop : -2.46 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 168 HIS 0.006 0.001 HIS A 555 PHE 0.036 0.002 PHE A 72 TYR 0.011 0.001 TYR A 613 ARG 0.003 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8855 (pp20) cc_final: 0.8377 (pm20) REVERT: A 203 TRP cc_start: 0.5983 (t-100) cc_final: 0.4677 (m-10) REVERT: A 211 TRP cc_start: 0.3736 (p90) cc_final: 0.2599 (m100) REVERT: A 249 MET cc_start: 0.5975 (mmm) cc_final: 0.5625 (mmt) REVERT: A 252 TYR cc_start: 0.2697 (OUTLIER) cc_final: 0.1911 (p90) REVERT: A 279 TYR cc_start: 0.5499 (OUTLIER) cc_final: 0.4873 (m-10) REVERT: A 345 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.7201 (t70) REVERT: A 376 MET cc_start: 0.8903 (tpt) cc_final: 0.8015 (ptp) REVERT: A 381 TYR cc_start: 0.5571 (OUTLIER) cc_final: 0.3883 (p90) REVERT: A 400 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7273 (t80) REVERT: A 462 MET cc_start: 0.7047 (ppp) cc_final: 0.6629 (ppp) REVERT: A 474 MET cc_start: -0.1662 (ptt) cc_final: -0.1886 (ptt) REVERT: A 566 TRP cc_start: 0.7241 (p-90) cc_final: 0.7020 (p-90) REVERT: A 579 MET cc_start: 0.6984 (ppp) cc_final: 0.5615 (tpp) outliers start: 32 outliers final: 21 residues processed: 99 average time/residue: 0.1892 time to fit residues: 25.0675 Evaluate side-chains 98 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 36 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.0040 chunk 47 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 20 optimal weight: 0.0010 chunk 61 optimal weight: 4.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5204 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6635 Z= 0.168 Angle : 0.703 10.822 9012 Z= 0.346 Chirality : 0.048 0.509 946 Planarity : 0.005 0.060 1164 Dihedral : 9.995 92.441 980 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 5.12 % Allowed : 28.99 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.30), residues: 775 helix: -0.68 (0.35), residues: 246 sheet: 1.66 (1.05), residues: 24 loop : -2.37 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.006 0.001 HIS A 555 PHE 0.012 0.001 PHE B 490 TYR 0.013 0.001 TYR A 41 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 75 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6843 (mmmt) REVERT: A 61 LYS cc_start: -0.0721 (OUTLIER) cc_final: -0.0958 (pttm) REVERT: A 93 ILE cc_start: 0.6839 (mm) cc_final: 0.6271 (pt) REVERT: A 171 GLU cc_start: 0.8923 (pp20) cc_final: 0.8164 (pm20) REVERT: A 249 MET cc_start: 0.5992 (mmm) cc_final: 0.5608 (mmt) REVERT: A 252 TYR cc_start: 0.2936 (OUTLIER) cc_final: 0.2284 (p90) REVERT: A 279 TYR cc_start: 0.5861 (OUTLIER) cc_final: 0.5022 (m-10) REVERT: A 345 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7334 (t70) REVERT: A 381 TYR cc_start: 0.5640 (OUTLIER) cc_final: 0.3774 (p90) REVERT: A 400 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7239 (t80) REVERT: A 462 MET cc_start: 0.7168 (ppp) cc_final: 0.6856 (ppp) REVERT: A 579 MET cc_start: 0.6932 (ppp) cc_final: 0.5550 (tpp) REVERT: B 484 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6683 (tm-30) REVERT: B 486 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6272 (t80) outliers start: 35 outliers final: 20 residues processed: 100 average time/residue: 0.1816 time to fit residues: 24.5331 Evaluate side-chains 100 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.0370 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 0.0040 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.0060 overall best weight: 0.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5166 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6635 Z= 0.156 Angle : 0.683 11.538 9012 Z= 0.335 Chirality : 0.047 0.487 946 Planarity : 0.005 0.063 1164 Dihedral : 8.393 80.125 980 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 4.69 % Allowed : 30.31 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.31), residues: 775 helix: -0.54 (0.35), residues: 246 sheet: 2.04 (1.08), residues: 24 loop : -2.33 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 566 HIS 0.004 0.001 HIS A 555 PHE 0.045 0.001 PHE A 72 TYR 0.013 0.001 TYR A 41 ARG 0.002 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 80 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.6781 (mm) cc_final: 0.6264 (pt) REVERT: A 171 GLU cc_start: 0.8840 (pp20) cc_final: 0.8327 (pm20) REVERT: A 203 TRP cc_start: 0.5767 (t-100) cc_final: 0.4502 (m-10) REVERT: A 252 TYR cc_start: 0.2846 (OUTLIER) cc_final: 0.2411 (p90) REVERT: A 279 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.5057 (m-10) REVERT: A 345 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7396 (t70) REVERT: A 381 TYR cc_start: 0.5384 (OUTLIER) cc_final: 0.3559 (p90) REVERT: A 400 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7191 (t80) REVERT: A 462 MET cc_start: 0.7139 (ppp) cc_final: 0.6892 (ppp) REVERT: A 579 MET cc_start: 0.7044 (ppp) cc_final: 0.5407 (tpp) REVERT: B 484 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6746 (tm-30) REVERT: B 486 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6522 (t80) outliers start: 32 outliers final: 19 residues processed: 102 average time/residue: 0.2113 time to fit residues: 28.7808 Evaluate side-chains 94 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 69 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.0570 chunk 39 optimal weight: 0.0040 chunk 71 optimal weight: 3.9990 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5238 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6635 Z= 0.169 Angle : 0.706 16.425 9012 Z= 0.343 Chirality : 0.047 0.498 946 Planarity : 0.005 0.059 1164 Dihedral : 7.850 69.182 980 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 4.69 % Allowed : 30.60 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.31), residues: 775 helix: -0.53 (0.35), residues: 247 sheet: 2.17 (1.05), residues: 24 loop : -2.36 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 566 HIS 0.013 0.001 HIS A 79 PHE 0.009 0.001 PHE B 497 TYR 0.011 0.001 TYR A 41 ARG 0.002 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: -0.1804 (tpt) cc_final: -0.2151 (tpt) REVERT: A 171 GLU cc_start: 0.8974 (pp20) cc_final: 0.8467 (pm20) REVERT: A 203 TRP cc_start: 0.5906 (t-100) cc_final: 0.4531 (m-10) REVERT: A 252 TYR cc_start: 0.3491 (OUTLIER) cc_final: 0.3055 (p90) REVERT: A 279 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.4954 (m-10) REVERT: A 295 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8131 (p0) REVERT: A 381 TYR cc_start: 0.5442 (OUTLIER) cc_final: 0.3566 (p90) REVERT: A 400 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 462 MET cc_start: 0.7144 (ppp) cc_final: 0.6936 (ppp) REVERT: A 579 MET cc_start: 0.7056 (ppp) cc_final: 0.5650 (tpp) REVERT: B 410 ILE cc_start: 0.8365 (mm) cc_final: 0.8083 (mm) REVERT: B 486 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6570 (t80) REVERT: B 528 LYS cc_start: 0.3551 (OUTLIER) cc_final: 0.1353 (tttt) outliers start: 32 outliers final: 22 residues processed: 94 average time/residue: 0.2054 time to fit residues: 26.1215 Evaluate side-chains 98 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 69 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN A 526 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6635 Z= 0.242 Angle : 0.780 12.966 9012 Z= 0.393 Chirality : 0.050 0.524 946 Planarity : 0.006 0.061 1164 Dihedral : 7.494 55.226 980 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 5.86 % Allowed : 29.43 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.30), residues: 775 helix: -0.80 (0.34), residues: 249 sheet: 2.08 (1.03), residues: 24 loop : -2.54 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 566 HIS 0.010 0.002 HIS A 79 PHE 0.028 0.003 PHE B 377 TYR 0.025 0.002 TYR A 158 ARG 0.005 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 77 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9050 (pp20) cc_final: 0.8564 (pm20) REVERT: A 232 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6624 (mp10) REVERT: A 252 TYR cc_start: 0.4420 (OUTLIER) cc_final: 0.3576 (p90) REVERT: A 279 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.5066 (m-10) REVERT: A 378 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6564 (t-90) REVERT: A 381 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.3706 (p90) REVERT: A 400 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7446 (t80) REVERT: A 464 PHE cc_start: 0.2007 (OUTLIER) cc_final: -0.1021 (t80) REVERT: A 579 MET cc_start: 0.7506 (ppp) cc_final: 0.7016 (ppp) REVERT: B 484 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6689 (tm-30) REVERT: B 486 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6527 (t80) outliers start: 40 outliers final: 26 residues processed: 104 average time/residue: 0.1875 time to fit residues: 26.0750 Evaluate side-chains 104 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 70 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 58 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS A 373 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6635 Z= 0.177 Angle : 0.710 13.546 9012 Z= 0.357 Chirality : 0.048 0.480 946 Planarity : 0.005 0.057 1164 Dihedral : 6.950 53.650 980 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 4.69 % Allowed : 30.75 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.30), residues: 775 helix: -0.71 (0.34), residues: 243 sheet: 2.15 (1.01), residues: 24 loop : -2.46 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 566 HIS 0.016 0.002 HIS A 79 PHE 0.016 0.002 PHE B 377 TYR 0.014 0.002 TYR A 202 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.5626 (m) cc_final: 0.5313 (m) REVERT: A 171 GLU cc_start: 0.8983 (pp20) cc_final: 0.8679 (pm20) REVERT: A 203 TRP cc_start: 0.7355 (t-100) cc_final: 0.7084 (t60) REVERT: A 249 MET cc_start: 0.5601 (mmm) cc_final: 0.5236 (mmt) REVERT: A 252 TYR cc_start: 0.4440 (OUTLIER) cc_final: 0.3707 (p90) REVERT: A 279 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5023 (m-10) REVERT: A 381 TYR cc_start: 0.5670 (OUTLIER) cc_final: 0.3581 (p90) REVERT: A 382 ASP cc_start: 0.9068 (t0) cc_final: 0.8577 (t0) REVERT: A 400 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7407 (t80) REVERT: A 464 PHE cc_start: 0.2041 (OUTLIER) cc_final: -0.1010 (t80) REVERT: A 579 MET cc_start: 0.7612 (ppp) cc_final: 0.7090 (ppp) REVERT: B 484 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6639 (tm-30) REVERT: B 486 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6696 (t80) outliers start: 32 outliers final: 23 residues processed: 97 average time/residue: 0.2477 time to fit residues: 32.5384 Evaluate side-chains 98 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 69 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.9990 chunk 41 optimal weight: 0.0000 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6635 Z= 0.185 Angle : 0.719 16.138 9012 Z= 0.357 Chirality : 0.048 0.497 946 Planarity : 0.005 0.057 1164 Dihedral : 6.866 53.592 980 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.65 % Favored : 87.35 % Rotamer: Outliers : 4.69 % Allowed : 30.45 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.30), residues: 775 helix: -0.71 (0.35), residues: 243 sheet: 1.59 (0.99), residues: 27 loop : -2.46 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 477 HIS 0.014 0.001 HIS A 79 PHE 0.018 0.002 PHE B 377 TYR 0.016 0.002 TYR A 83 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.5706 (m) cc_final: 0.5402 (m) REVERT: A 145 GLU cc_start: 0.6067 (mp0) cc_final: 0.5719 (mp0) REVERT: A 171 GLU cc_start: 0.8959 (pp20) cc_final: 0.8630 (pm20) REVERT: A 203 TRP cc_start: 0.7334 (t-100) cc_final: 0.7121 (t60) REVERT: A 249 MET cc_start: 0.5583 (mmm) cc_final: 0.5222 (mmt) REVERT: A 252 TYR cc_start: 0.4412 (OUTLIER) cc_final: 0.3707 (p90) REVERT: A 279 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5053 (m-10) REVERT: A 366 MET cc_start: 0.7283 (ppp) cc_final: 0.6768 (mtt) REVERT: A 381 TYR cc_start: 0.5687 (OUTLIER) cc_final: 0.3590 (p90) REVERT: A 382 ASP cc_start: 0.9052 (t0) cc_final: 0.8546 (t0) REVERT: A 400 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7412 (t80) REVERT: A 464 PHE cc_start: 0.2055 (OUTLIER) cc_final: -0.1002 (t80) REVERT: A 579 MET cc_start: 0.7656 (ppp) cc_final: 0.7117 (ppp) REVERT: B 484 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6695 (tm-30) REVERT: B 486 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6729 (t80) outliers start: 32 outliers final: 25 residues processed: 89 average time/residue: 0.2295 time to fit residues: 26.8788 Evaluate side-chains 95 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 64 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6635 Z= 0.237 Angle : 0.797 15.896 9012 Z= 0.398 Chirality : 0.050 0.533 946 Planarity : 0.006 0.059 1164 Dihedral : 7.167 54.679 980 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.68 % Favored : 86.32 % Rotamer: Outliers : 4.83 % Allowed : 30.31 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.30), residues: 775 helix: -1.02 (0.34), residues: 249 sheet: 1.18 (1.03), residues: 27 loop : -2.57 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 211 HIS 0.008 0.002 HIS A 79 PHE 0.020 0.002 PHE B 377 TYR 0.024 0.002 TYR A 158 ARG 0.005 0.001 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 64 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.5877 (m) cc_final: 0.5568 (m) REVERT: A 203 TRP cc_start: 0.7463 (t-100) cc_final: 0.7207 (t60) REVERT: A 232 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6650 (mp10) REVERT: A 249 MET cc_start: 0.5805 (mmm) cc_final: 0.5425 (mmt) REVERT: A 252 TYR cc_start: 0.4771 (OUTLIER) cc_final: 0.3921 (p90) REVERT: A 279 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.4915 (m-10) REVERT: A 366 MET cc_start: 0.7293 (ppp) cc_final: 0.6851 (mtt) REVERT: A 381 TYR cc_start: 0.5587 (OUTLIER) cc_final: 0.3500 (p90) REVERT: A 382 ASP cc_start: 0.9111 (t0) cc_final: 0.8588 (t0) REVERT: A 400 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7882 (t80) REVERT: A 464 PHE cc_start: 0.2204 (OUTLIER) cc_final: -0.0865 (t80) REVERT: A 579 MET cc_start: 0.7539 (ppp) cc_final: 0.7019 (ppp) REVERT: B 484 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6877 (tm-30) REVERT: B 486 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6731 (t80) outliers start: 33 outliers final: 21 residues processed: 91 average time/residue: 0.1925 time to fit residues: 23.4155 Evaluate side-chains 87 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 59 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.5980 chunk 9 optimal weight: 0.0170 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 62 optimal weight: 0.0170 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.0040 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.2268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.139557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.121216 restraints weight = 41192.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.123493 restraints weight = 32627.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.124121 restraints weight = 26786.244| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6635 Z= 0.188 Angle : 0.753 15.328 9012 Z= 0.374 Chirality : 0.049 0.479 946 Planarity : 0.005 0.056 1164 Dihedral : 6.883 52.849 980 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 4.10 % Allowed : 31.77 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.30), residues: 775 helix: -0.81 (0.34), residues: 250 sheet: 1.26 (1.04), residues: 27 loop : -2.53 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 211 HIS 0.018 0.002 HIS A 79 PHE 0.017 0.002 PHE B 377 TYR 0.017 0.001 TYR A 202 ARG 0.007 0.000 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.24 seconds wall clock time: 40 minutes 37.67 seconds (2437.67 seconds total)