Starting phenix.real_space_refine on Sat Jul 20 12:12:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k53_36896/07_2024/8k53_36896.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k53_36896/07_2024/8k53_36896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k53_36896/07_2024/8k53_36896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k53_36896/07_2024/8k53_36896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k53_36896/07_2024/8k53_36896.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k53_36896/07_2024/8k53_36896.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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 44 5.16 5 C 6663 2.51 5 N 1852 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 233": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5998 Classifications: {'peptide': 777} Link IDs: {'PCIS': 8, 'PTRANS': 48, 'TRANS': 720} Chain: "B" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4439 Classifications: {'peptide': 573} Link IDs: {'PCIS': 6, 'PTRANS': 31, 'TRANS': 535} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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: "E" 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: "F" 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: "A" 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: "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: 7.61, per 1000 atoms: 0.72 Number of scatterers: 10602 At special positions: 0 Unit cell: (106.72, 168.36, 207.92, 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 44 16.00 O 2043 8.00 N 1852 7.00 C 6663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 440 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 587 " 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 C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1101 " - " ASN A 76 " " NAG A1102 " - " ASN A 477 " " NAG B1101 " - " ASN B 76 " " NAG C 1 " - " ASN A 461 " " NAG D 1 " - " ASN A 498 " " NAG E 1 " - " ASN B 461 " " NAG F 1 " - " ASN B 498 " Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 2.1 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 44 sheets defined 3.0% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.684A pdb=" N LEU A 202 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.863A pdb=" N GLU A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.739A pdb=" N ASP A 482 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 483' Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.118A pdb=" N ALA B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.616A pdb=" N LEU B 202 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.845A pdb=" N GLU B 301 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.596A pdb=" N GLU B 483 " --> pdb=" O ARG B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41 removed outlier: 5.690A pdb=" N GLY A 36 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SER A 66 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG A 62 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.297A pdb=" N VAL A 46 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLY A 130 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE A 48 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LEU A 132 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59 Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 145 removed outlier: 6.277A pdb=" N VAL A 143 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 203 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 145 removed outlier: 6.277A pdb=" N VAL A 143 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 203 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA8, first strand: chain 'A' and resid 237 through 243 removed outlier: 5.682A pdb=" N ALA A 238 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASN A 266 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE A 262 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 248 through 252 removed outlier: 6.471A pdb=" N THR A 249 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN A 324 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA A 251 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260 Processing sheet with id=AB2, first strand: chain 'A' and resid 328 through 331 removed outlier: 6.457A pdb=" N ALA A 349 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AB4, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AB5, first strand: chain 'A' and resid 430 through 431 removed outlier: 6.863A pdb=" N ALA A 430 " --> pdb=" O ARG A 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 435 through 438 Processing sheet with id=AB7, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AB8, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.311A pdb=" N HIS A 531 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 518 through 520 removed outlier: 3.615A pdb=" N VAL A 602 " --> pdb=" O GLY A 583 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 583 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.687A pdb=" N LEU A 526 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 612 through 617 removed outlier: 3.621A pdb=" N GLY A 612 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 614 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 627 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 616 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN A 625 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.311A pdb=" N VAL A 685 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA A 687 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 663 through 664 removed outlier: 4.671A pdb=" N ILE A 663 " --> pdb=" O TYR A 641 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 703 " --> pdb=" O TYR A 681 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AC6, first strand: chain 'A' and resid 759 through 764 removed outlier: 6.437A pdb=" N ILE A 788 " --> pdb=" O GLU A 799 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 799 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N SER A 790 " --> pdb=" O GLY A 797 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 759 through 764 Processing sheet with id=AC8, first strand: chain 'B' and resid 35 through 41 removed outlier: 5.948A pdb=" N GLY B 36 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER B 66 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B 62 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.275A pdb=" N VAL B 46 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY B 130 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE B 48 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LEU B 132 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.504A pdb=" N THR B 78 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.664A pdb=" N VAL B 96 " --> pdb=" O GLN B 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.063A pdb=" N VAL B 143 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 203 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.063A pdb=" N VAL B 143 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 203 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 151 through 153 Processing sheet with id=AD6, first strand: chain 'B' and resid 237 through 243 removed outlier: 5.571A pdb=" N ALA B 238 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ASN B 266 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 262 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 248 through 252 removed outlier: 3.689A pdb=" N ILE B 322 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 248 through 252 removed outlier: 3.689A pdb=" N ILE B 322 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLN B 326 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LYS B 353 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 349 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 257 through 260 Processing sheet with id=AE1, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.491A pdb=" N THR B 336 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLN B 413 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA B 338 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 343 through 347 Processing sheet with id=AE3, first strand: chain 'B' and resid 415 through 418 removed outlier: 5.513A pdb=" N ALA B 416 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ALA B 445 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 427 through 431 removed outlier: 7.016A pdb=" N ILE B 428 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ARG B 506 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA B 430 " --> pdb=" O ARG B 506 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 436 through 438 Processing sheet with id=AE6, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.196A pdb=" N HIS B 531 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 518 through 521 Processing sheet with id=AE8, first strand: chain 'B' and resid 526 through 528 391 hydrogen bonds defined for protein. 906 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: 7.49 Time building geometry restraints manager: 4.31 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: 3525 1.34 - 1.46: 2407 1.46 - 1.58: 4858 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 10854 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" C1 NAG A1102 " pdb=" O5 NAG A1102 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" CB PRO B 469 " pdb=" CG PRO B 469 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.56e+00 bond pdb=" C1 NAG B1101 " pdb=" O5 NAG B1101 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 10849 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.22: 397 106.22 - 113.19: 5896 113.19 - 120.16: 3502 120.16 - 127.13: 4821 127.13 - 134.10: 159 Bond angle restraints: 14775 Sorted by residual: angle pdb=" CA PRO B 469 " pdb=" N PRO B 469 " pdb=" CD PRO B 469 " ideal model delta sigma weight residual 112.00 104.14 7.86 1.40e+00 5.10e-01 3.15e+01 angle pdb=" C ASN A 498 " pdb=" CA ASN A 498 " pdb=" CB ASN A 498 " ideal model delta sigma weight residual 109.72 115.30 -5.58 1.61e+00 3.86e-01 1.20e+01 angle pdb=" CA GLN B 318 " pdb=" CB GLN B 318 " pdb=" CG GLN B 318 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CB GLN B 318 " pdb=" CG GLN B 318 " pdb=" CD GLN B 318 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.70e+00 3.46e-01 1.08e+01 angle pdb=" C SER B 86 " pdb=" N ARG B 87 " pdb=" CA ARG B 87 " ideal model delta sigma weight residual 120.99 127.11 -6.12 1.86e+00 2.89e-01 1.08e+01 ... (remaining 14770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 6193 21.45 - 42.90: 415 42.90 - 64.35: 78 64.35 - 85.81: 17 85.81 - 107.26: 6 Dihedral angle restraints: 6709 sinusoidal: 2836 harmonic: 3873 Sorted by residual: dihedral pdb=" CA ALA A 497 " pdb=" C ALA A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TRP A 678 " pdb=" C TRP A 678 " pdb=" N MET A 679 " pdb=" CA MET A 679 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.55 107.26 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 6706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1657 0.151 - 0.301: 7 0.301 - 0.452: 1 0.452 - 0.603: 0 0.603 - 0.753: 1 Chirality restraints: 1666 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 461 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.81 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1663 not shown) Planarity restraints: 1937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 468 " -0.071 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 469 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 469 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 469 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 498 " 0.038 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" CG ASN A 498 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 498 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 498 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 498 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" CG ASN A 498 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 498 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 498 " 0.012 2.00e-02 2.50e+03 ... (remaining 1934 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 313 2.70 - 3.25: 9310 3.25 - 3.80: 15472 3.80 - 4.35: 19189 4.35 - 4.90: 33322 Nonbonded interactions: 77606 Sorted by model distance: nonbonded pdb=" NZ LYS B 218 " pdb=" O SER B 219 " model vdw 2.149 2.520 nonbonded pdb=" N GLU B 55 " pdb=" OE1 GLU B 55 " model vdw 2.251 2.520 nonbonded pdb=" OG SER A 165 " pdb=" OG1 THR A 210 " model vdw 2.256 2.440 nonbonded pdb=" NH2 ARG A 464 " pdb=" OD2 ASP A 482 " model vdw 2.294 2.520 nonbonded pdb=" NH2 ARG A 355 " pdb=" O MET B 538 " model vdw 2.295 2.520 ... (remaining 77601 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 'D' selection = chain 'E' selection = chain 'F' } 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: 4.860 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: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 38.770 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 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 : 0.003 0.080 10854 Z= 0.213 Angle : 0.625 8.364 14775 Z= 0.319 Chirality : 0.049 0.753 1666 Planarity : 0.005 0.103 1930 Dihedral : 15.218 107.256 4183 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 0.18 % Allowed : 17.13 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1346 helix: None (None), residues: 0 sheet: 0.86 (0.20), residues: 657 loop : -0.82 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 73 HIS 0.008 0.001 HIS B 534 PHE 0.022 0.001 PHE A 173 TYR 0.014 0.001 TYR B 166 ARG 0.003 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 1.187 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.2248 time to fit residues: 19.5195 Evaluate side-chains 54 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 306 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 50.0000 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10854 Z= 0.279 Angle : 0.591 6.375 14775 Z= 0.302 Chirality : 0.046 0.570 1666 Planarity : 0.005 0.066 1930 Dihedral : 7.633 59.932 1721 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.09 % Favored : 93.76 % Rotamer: Outliers : 3.19 % Allowed : 16.50 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1346 helix: -5.44 (0.23), residues: 6 sheet: 0.85 (0.20), residues: 642 loop : -0.92 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 346 HIS 0.007 0.001 HIS B 534 PHE 0.030 0.002 PHE B 184 TYR 0.013 0.001 TYR A 109 ARG 0.002 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 61 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7746 (ppp) cc_final: 0.7133 (ppp) REVERT: A 346 TRP cc_start: 0.9147 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: A 468 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (m) REVERT: A 679 MET cc_start: 0.1814 (mpp) cc_final: 0.1484 (tpt) REVERT: B 74 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8424 (ttpp) REVERT: B 152 MET cc_start: 0.6935 (tmm) cc_final: 0.6644 (tmm) outliers start: 36 outliers final: 21 residues processed: 89 average time/residue: 0.1847 time to fit residues: 25.5063 Evaluate side-chains 79 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 55 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 450 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 0.0570 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 121 optimal weight: 0.6980 chunk 131 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10854 Z= 0.166 Angle : 0.538 6.053 14775 Z= 0.273 Chirality : 0.044 0.550 1666 Planarity : 0.004 0.067 1930 Dihedral : 6.502 59.239 1720 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 2.84 % Allowed : 17.92 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1346 helix: -5.42 (0.24), residues: 6 sheet: 0.92 (0.20), residues: 642 loop : -0.83 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 273 HIS 0.003 0.001 HIS B 146 PHE 0.027 0.001 PHE A 493 TYR 0.010 0.001 TYR B 405 ARG 0.002 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 60 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: A 98 MET cc_start: 0.7734 (ppp) cc_final: 0.7180 (ppp) REVERT: A 152 MET cc_start: 0.7664 (tmm) cc_final: 0.7416 (tmm) REVERT: A 468 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8319 (m) REVERT: A 679 MET cc_start: 0.1839 (mpp) cc_final: 0.1556 (tpt) REVERT: B 74 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8811 (mtpp) outliers start: 32 outliers final: 19 residues processed: 86 average time/residue: 0.2098 time to fit residues: 27.1206 Evaluate side-chains 77 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 55 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 0.0030 chunk 63 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.0570 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 115 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 overall best weight: 0.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10854 Z= 0.123 Angle : 0.516 7.253 14775 Z= 0.260 Chirality : 0.044 0.545 1666 Planarity : 0.004 0.073 1930 Dihedral : 5.331 54.574 1718 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 2.57 % Allowed : 17.39 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1346 helix: -5.36 (0.26), residues: 6 sheet: 1.00 (0.20), residues: 641 loop : -0.69 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 273 HIS 0.003 0.001 HIS B 183 PHE 0.026 0.001 PHE A 493 TYR 0.008 0.000 TYR B 405 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 60 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7613 (ppp) cc_final: 0.7372 (ppp) REVERT: A 355 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8154 (mpt-90) REVERT: A 679 MET cc_start: 0.2010 (mpp) cc_final: 0.1713 (tpt) outliers start: 29 outliers final: 18 residues processed: 83 average time/residue: 0.1964 time to fit residues: 25.0061 Evaluate side-chains 74 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 20.0000 chunk 1 optimal weight: 0.0670 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.0370 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 43 optimal weight: 0.9980 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10854 Z= 0.148 Angle : 0.521 8.023 14775 Z= 0.263 Chirality : 0.044 0.557 1666 Planarity : 0.004 0.072 1930 Dihedral : 5.041 53.336 1718 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.39 % Rotamer: Outliers : 2.75 % Allowed : 17.48 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1346 helix: -5.36 (0.26), residues: 6 sheet: 1.04 (0.20), residues: 641 loop : -0.65 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 273 HIS 0.002 0.000 HIS A 160 PHE 0.025 0.001 PHE A 493 TYR 0.008 0.001 TYR B 405 ARG 0.002 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 63 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7649 (ppp) cc_final: 0.7446 (ppp) REVERT: A 355 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8139 (mpt-90) REVERT: A 679 MET cc_start: 0.2244 (mpp) cc_final: 0.1948 (tpt) outliers start: 31 outliers final: 25 residues processed: 87 average time/residue: 0.2017 time to fit residues: 26.8332 Evaluate side-chains 82 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 56 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 30.0000 chunk 31 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 60 optimal weight: 0.0370 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 50.0000 chunk 124 optimal weight: 0.1980 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10854 Z= 0.159 Angle : 0.525 7.272 14775 Z= 0.265 Chirality : 0.044 0.556 1666 Planarity : 0.004 0.074 1930 Dihedral : 4.858 52.399 1718 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 3.64 % Allowed : 17.39 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1346 helix: -5.37 (0.26), residues: 6 sheet: 1.07 (0.20), residues: 639 loop : -0.62 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 273 HIS 0.002 0.001 HIS A 160 PHE 0.029 0.001 PHE A 493 TYR 0.009 0.001 TYR B 405 ARG 0.002 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 60 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: A 355 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8162 (mpt-90) REVERT: A 579 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7497 (mm) outliers start: 41 outliers final: 31 residues processed: 95 average time/residue: 0.2147 time to fit residues: 30.4815 Evaluate side-chains 89 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 55 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 0.0470 chunk 129 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10854 Z= 0.182 Angle : 0.550 11.155 14775 Z= 0.274 Chirality : 0.044 0.560 1666 Planarity : 0.004 0.077 1930 Dihedral : 4.812 52.119 1718 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.90 % Favored : 95.02 % Rotamer: Outliers : 3.55 % Allowed : 17.66 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1346 helix: -5.38 (0.25), residues: 6 sheet: 1.02 (0.20), residues: 641 loop : -0.59 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 273 HIS 0.002 0.001 HIS A 160 PHE 0.029 0.001 PHE A 493 TYR 0.010 0.001 TYR B 405 ARG 0.003 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 59 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: A 355 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8162 (mpt-90) REVERT: A 579 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7535 (mm) outliers start: 40 outliers final: 31 residues processed: 94 average time/residue: 0.1880 time to fit residues: 27.4220 Evaluate side-chains 91 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 57 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.0470 chunk 38 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10854 Z= 0.202 Angle : 0.562 10.200 14775 Z= 0.280 Chirality : 0.044 0.562 1666 Planarity : 0.004 0.076 1930 Dihedral : 4.821 52.380 1718 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 3.37 % Allowed : 17.75 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1346 helix: -5.39 (0.25), residues: 6 sheet: 1.00 (0.20), residues: 641 loop : -0.59 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 273 HIS 0.002 0.001 HIS B 183 PHE 0.029 0.002 PHE A 493 TYR 0.010 0.001 TYR B 405 ARG 0.003 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 57 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: A 355 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8336 (mpt-90) REVERT: A 427 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8540 (mp) REVERT: A 562 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7144 (ttt180) REVERT: A 579 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7556 (mm) REVERT: B 494 MET cc_start: 0.7370 (mmm) cc_final: 0.7093 (mmm) outliers start: 38 outliers final: 30 residues processed: 90 average time/residue: 0.2050 time to fit residues: 28.0639 Evaluate side-chains 88 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 53 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 119 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10854 Z= 0.205 Angle : 0.572 9.735 14775 Z= 0.285 Chirality : 0.044 0.560 1666 Planarity : 0.004 0.080 1930 Dihedral : 4.831 52.564 1718 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 3.46 % Allowed : 18.01 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1346 helix: -5.39 (0.25), residues: 6 sheet: 1.01 (0.20), residues: 643 loop : -0.61 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 273 HIS 0.002 0.001 HIS B 183 PHE 0.031 0.002 PHE A 493 TYR 0.010 0.001 TYR B 405 ARG 0.003 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 54 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: A 355 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8079 (mpt-90) REVERT: A 427 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8529 (mp) REVERT: A 562 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7151 (ttt180) REVERT: A 579 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7607 (mm) REVERT: B 494 MET cc_start: 0.7375 (mmm) cc_final: 0.7092 (mmm) outliers start: 39 outliers final: 33 residues processed: 88 average time/residue: 0.1980 time to fit residues: 26.5430 Evaluate side-chains 90 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 52 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.4980 chunk 60 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 82 optimal weight: 0.0670 chunk 65 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10854 Z= 0.180 Angle : 0.567 9.666 14775 Z= 0.284 Chirality : 0.044 0.555 1666 Planarity : 0.004 0.081 1930 Dihedral : 4.795 51.687 1718 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 3.37 % Allowed : 18.37 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1346 helix: -5.38 (0.25), residues: 6 sheet: 1.03 (0.20), residues: 643 loop : -0.55 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 273 HIS 0.002 0.001 HIS A 160 PHE 0.032 0.002 PHE A 493 TYR 0.009 0.001 TYR B 405 ARG 0.003 0.000 ARG B 506 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 53 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: A 355 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8015 (mpt-90) REVERT: A 427 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8539 (mp) REVERT: A 562 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7182 (ttt180) REVERT: A 579 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7627 (mm) REVERT: B 494 MET cc_start: 0.7350 (mmm) cc_final: 0.7071 (mmm) outliers start: 38 outliers final: 32 residues processed: 86 average time/residue: 0.2045 time to fit residues: 27.1003 Evaluate side-chains 89 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 52 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.190841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.173814 restraints weight = 17389.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.168095 restraints weight = 24799.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.163704 restraints weight = 30854.297| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10854 Z= 0.198 Angle : 0.568 10.142 14775 Z= 0.284 Chirality : 0.044 0.559 1666 Planarity : 0.004 0.082 1930 Dihedral : 4.778 51.344 1718 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.90 % Favored : 95.02 % Rotamer: Outliers : 3.37 % Allowed : 18.46 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1346 helix: -5.39 (0.25), residues: 6 sheet: 1.06 (0.20), residues: 635 loop : -0.60 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 273 HIS 0.002 0.001 HIS A 160 PHE 0.033 0.002 PHE A 493 TYR 0.010 0.001 TYR B 405 ARG 0.003 0.000 ARG B 506 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.50 seconds wall clock time: 38 minutes 56.48 seconds (2336.48 seconds total)