Starting phenix.real_space_refine on Fri Sep 27 00:24:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/09_2024/6opn_20150.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/09_2024/6opn_20150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/09_2024/6opn_20150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/09_2024/6opn_20150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/09_2024/6opn_20150.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/09_2024/6opn_20150.cif" } resolution = 3.5 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= 0.064 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 90 5.16 5 C 8949 2.51 5 N 2418 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14241 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2753 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 6 Chain: "B" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 760 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" 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: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'N07': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: F, I, E, H, L, N, M, O, D, G Time building chain proxies: 8.11, per 1000 atoms: 0.57 Number of scatterers: 14241 At special positions: 0 Unit cell: (147.29, 150.38, 111.24, 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 90 16.00 O 2784 8.00 N 2418 7.00 C 8949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.21 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN M 4 " - " MAN M 5 " " MAN O 4 " - " MAN O 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 609 " - " ASN A 276 " " NAG A 610 " - " ASN A 295 " " NAG A 611 " - " ASN A 332 " " NAG A 612 " - " ASN A 362 " " NAG A 613 " - " ASN A 386 " " NAG A 614 " - " ASN A 392 " " NAG A 615 " - " ASN A 413 " " NAG A 616 " - " ASN A 448 " " NAG D 601 " - " ASN D 234 " " NAG D 609 " - " ASN D 276 " " NAG D 610 " - " ASN D 295 " " NAG D 611 " - " ASN D 332 " " NAG D 612 " - " ASN D 362 " " NAG D 613 " - " ASN D 386 " " NAG D 614 " - " ASN D 392 " " NAG D 615 " - " ASN D 413 " " NAG D 616 " - " ASN D 448 " " NAG G 601 " - " ASN G 234 " " NAG G 609 " - " ASN G 276 " " NAG G 610 " - " ASN G 295 " " NAG G 611 " - " ASN G 332 " " NAG G 612 " - " ASN G 362 " " NAG G 613 " - " ASN G 386 " " NAG G 614 " - " ASN G 392 " " NAG G 615 " - " ASN G 413 " " NAG G 616 " - " ASN G 448 " " NAG J 1 " - " ASN A 241 " " NAG K 1 " - " ASN A 262 " " NAG L 1 " - " ASN D 241 " " NAG M 1 " - " ASN D 262 " " NAG N 1 " - " ASN G 241 " " NAG O 1 " - " ASN G 262 " Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.6 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3204 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 27 sheets defined 31.0% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.891A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.907A pdb=" N ASN A 98 " --> pdb=" O MET A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.817A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.979A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 547 Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.650A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 659 Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.024A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.891A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.906A pdb=" N ASN D 98 " --> pdb=" O MET D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 116 removed outlier: 3.817A pdb=" N GLN D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.978A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 547 Processing helix chain 'E' and resid 569 through 593 removed outlier: 3.650A pdb=" N ARG E 579 " --> pdb=" O GLN E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 597 Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 659 Processing helix chain 'F' and resid 58 through 64 removed outlier: 4.024A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'G' and resid 64 through 74 removed outlier: 3.892A pdb=" N HIS G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 98 removed outlier: 3.906A pdb=" N ASN G 98 " --> pdb=" O MET G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.817A pdb=" N GLN G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 474 through 484 removed outlier: 3.979A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 547 Processing helix chain 'H' and resid 569 through 593 removed outlier: 3.650A pdb=" N ARG H 579 " --> pdb=" O GLN H 575 " (cutoff:3.500A) Processing helix chain 'H' and resid 594 through 597 Processing helix chain 'H' and resid 611 through 615 Processing helix chain 'H' and resid 618 through 626 Processing helix chain 'H' and resid 627 through 635 Processing helix chain 'H' and resid 638 through 659 Processing helix chain 'I' and resid 58 through 64 removed outlier: 4.024A pdb=" N ASP I 63 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 199 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.533A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.431A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 420 Processing sheet with id=AA8, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.799A pdb=" N LYS C 2 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 91 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS C 35 " --> pdb=" O ASN C 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AB1, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AB5, first strand: chain 'D' and resid 199 through 202 Processing sheet with id=AB6, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.534A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N LEU D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N LEU D 288 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 284 through 298 current: chain 'D' and resid 358 through 361 Processing sheet with id=AB7, first strand: chain 'D' and resid 271 through 273 removed outlier: 10.431A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N LEU D 288 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N LEU D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 443 through 456 current: chain 'D' and resid 413 through 420 Processing sheet with id=AB8, first strand: chain 'F' and resid 2 through 3 removed outlier: 6.799A pdb=" N LYS F 2 " --> pdb=" O GLN F 94 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 91 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN F 30 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS F 35 " --> pdb=" O ASN F 30 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 12 through 17 Processing sheet with id=AC1, first strand: chain 'G' and resid 494 through 499 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 56 Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'G' and resid 199 through 202 Processing sheet with id=AC6, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.532A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 298 current: chain 'G' and resid 358 through 361 Processing sheet with id=AC7, first strand: chain 'G' and resid 271 through 273 removed outlier: 10.432A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 443 through 456 current: chain 'G' and resid 413 through 420 Processing sheet with id=AC8, first strand: chain 'I' and resid 2 through 3 removed outlier: 6.799A pdb=" N LYS I 2 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU I 91 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN I 30 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS I 35 " --> pdb=" O ASN I 30 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 12 through 17 600 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3296 1.32 - 1.45: 3933 1.45 - 1.58: 7125 1.58 - 1.71: 31 1.71 - 1.84: 117 Bond restraints: 14502 Sorted by residual: bond pdb=" C1 NAG D 601 " pdb=" O5 NAG D 601 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C1 NAG G 601 " pdb=" O5 NAG G 601 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C1 NAG A 615 " pdb=" O5 NAG A 615 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C1 NAG D 615 " pdb=" O5 NAG D 615 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 14497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 18185 3.17 - 6.34: 1312 6.34 - 9.50: 135 9.50 - 12.67: 12 12.67 - 15.84: 3 Bond angle restraints: 19647 Sorted by residual: angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 120.03 128.18 -8.15 9.90e-01 1.02e+00 6.78e+01 angle pdb=" C PRO G 437 " pdb=" N PRO G 438 " pdb=" CA PRO G 438 " ideal model delta sigma weight residual 120.03 128.17 -8.14 9.90e-01 1.02e+00 6.75e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 120.03 128.15 -8.12 9.90e-01 1.02e+00 6.73e+01 angle pdb=" C ALA G 436 " pdb=" N PRO G 437 " pdb=" CA PRO G 437 " ideal model delta sigma weight residual 120.38 128.28 -7.90 1.03e+00 9.43e-01 5.88e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 120.38 128.26 -7.88 1.03e+00 9.43e-01 5.85e+01 ... (remaining 19642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.20: 8986 22.20 - 44.39: 238 44.39 - 66.59: 60 66.59 - 88.78: 28 88.78 - 110.98: 12 Dihedral angle restraints: 9324 sinusoidal: 4404 harmonic: 4920 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -171.85 85.85 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" O4 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C5 BMA K 3 " pdb=" O5 BMA K 3 " ideal model delta sinusoidal sigma weight residual 288.71 177.73 110.98 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual 288.71 177.74 110.97 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 9321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1732 0.110 - 0.220: 554 0.220 - 0.330: 60 0.330 - 0.440: 9 0.440 - 0.550: 3 Chirality restraints: 2358 Sorted by residual: chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.60e+01 chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.59e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.52e+01 ... (remaining 2355 not shown) Planarity restraints: 2460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 332 " -0.060 2.00e-02 2.50e+03 6.50e-02 5.28e+01 pdb=" CG ASN G 332 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN G 332 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN G 332 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG G 611 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 392 " -0.062 2.00e-02 2.50e+03 6.49e-02 5.27e+01 pdb=" CG ASN D 392 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN D 392 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN D 392 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG D 614 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 332 " -0.060 2.00e-02 2.50e+03 6.49e-02 5.27e+01 pdb=" CG ASN A 332 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 332 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 332 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG A 611 " -0.079 2.00e-02 2.50e+03 ... (remaining 2457 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 205 2.60 - 3.17: 12372 3.17 - 3.75: 21544 3.75 - 4.32: 30996 4.32 - 4.90: 48840 Nonbonded interactions: 113957 Sorted by model distance: nonbonded pdb=" SG CYS D 296 " pdb=" SG CYS D 331 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS G 296 " pdb=" SG CYS G 331 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS D 218 " pdb=" SG CYS D 247 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS G 218 " pdb=" SG CYS G 247 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS F 16 " pdb=" SG CYS F 84 " model vdw 2.027 3.760 ... (remaining 113952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } 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: 1.410 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 32.010 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.022 0.169 14502 Z= 1.387 Angle : 1.781 15.840 19647 Z= 1.152 Chirality : 0.103 0.550 2358 Planarity : 0.009 0.057 2427 Dihedral : 12.345 110.976 6090 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1653 helix: 0.40 (0.22), residues: 405 sheet: 1.27 (0.24), residues: 381 loop : 0.08 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.010 TRP C 28 HIS 0.007 0.002 HIS A 330 PHE 0.029 0.007 PHE A 353 TYR 0.028 0.006 TYR D 484 ARG 0.007 0.001 ARG D 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.7717 (ttm) cc_final: 0.7513 (ttm) REVERT: B 530 MET cc_start: 0.7404 (mtm) cc_final: 0.6759 (mtp) REVERT: D 371 ILE cc_start: 0.8266 (pt) cc_final: 0.7815 (pt) REVERT: E 530 MET cc_start: 0.7434 (mtm) cc_final: 0.6814 (mtp) REVERT: F 1 LYS cc_start: 0.7755 (pttm) cc_final: 0.7500 (pttp) REVERT: G 371 ILE cc_start: 0.8274 (pt) cc_final: 0.7771 (pt) REVERT: H 530 MET cc_start: 0.7459 (mtm) cc_final: 0.6892 (mtp) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.2846 time to fit residues: 163.0082 Evaluate side-chains 183 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN F 40 GLN I 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14502 Z= 0.244 Angle : 0.829 9.554 19647 Z= 0.432 Chirality : 0.049 0.173 2358 Planarity : 0.005 0.055 2427 Dihedral : 9.107 64.872 2805 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.10 % Allowed : 9.77 % Favored : 87.13 % 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: 0.52 (0.19), residues: 1653 helix: 1.44 (0.26), residues: 405 sheet: 0.48 (0.25), residues: 318 loop : -0.14 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 631 HIS 0.008 0.002 HIS E 641 PHE 0.019 0.003 PHE G 233 TYR 0.015 0.002 TYR D 486 ARG 0.005 0.001 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 245 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 CYS cc_start: 0.6534 (t) cc_final: 0.6259 (m) REVERT: A 257 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7719 (m) REVERT: B 530 MET cc_start: 0.7341 (mtm) cc_final: 0.6863 (mtm) REVERT: C 1 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7057 (pptt) REVERT: C 51 LEU cc_start: 0.8166 (mm) cc_final: 0.7855 (mp) REVERT: C 73 ASN cc_start: 0.8924 (t0) cc_final: 0.8581 (t0) REVERT: D 257 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7576 (m) REVERT: D 373 THR cc_start: 0.7854 (t) cc_final: 0.7503 (t) REVERT: D 482 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6621 (tp30) REVERT: E 530 MET cc_start: 0.7527 (mtm) cc_final: 0.6828 (mtm) REVERT: G 40 TYR cc_start: 0.6332 (t80) cc_final: 0.6104 (t80) REVERT: G 373 THR cc_start: 0.7852 (t) cc_final: 0.7533 (t) REVERT: G 482 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6563 (mm-30) REVERT: H 530 MET cc_start: 0.7343 (mtm) cc_final: 0.6759 (mtm) REVERT: I 1 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6764 (pptt) REVERT: I 73 ASN cc_start: 0.8861 (t0) cc_final: 0.8563 (t0) outliers start: 47 outliers final: 23 residues processed: 279 average time/residue: 0.2740 time to fit residues: 109.5115 Evaluate side-chains 197 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 620 ASN Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 1 LYS Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 0.0040 chunk 122 optimal weight: 5.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN B 652 GLN C 25 GLN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 ASN I 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14502 Z= 0.315 Angle : 0.777 8.100 19647 Z= 0.401 Chirality : 0.048 0.239 2358 Planarity : 0.005 0.051 2427 Dihedral : 8.026 54.097 2805 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.22 % Allowed : 10.89 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 1653 helix: 1.26 (0.25), residues: 405 sheet: 0.09 (0.25), residues: 327 loop : -0.46 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 96 HIS 0.011 0.002 HIS F 27 PHE 0.021 0.003 PHE G 53 TYR 0.015 0.003 TYR D 384 ARG 0.006 0.001 ARG H 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 195 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7499 (pt) REVERT: B 530 MET cc_start: 0.7764 (mtm) cc_final: 0.7507 (mtp) REVERT: C 92 GLU cc_start: 0.7849 (mp0) cc_final: 0.7629 (pm20) REVERT: D 217 TYR cc_start: 0.5783 (m-80) cc_final: 0.5511 (m-80) REVERT: D 449 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7518 (pt) REVERT: D 482 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6638 (mm-30) REVERT: E 530 MET cc_start: 0.7828 (mtm) cc_final: 0.7369 (mtm) REVERT: F 63 ASP cc_start: 0.8747 (t0) cc_final: 0.8436 (p0) REVERT: F 92 GLU cc_start: 0.8096 (mp0) cc_final: 0.7770 (pm20) REVERT: G 69 TRP cc_start: 0.7635 (t60) cc_final: 0.7133 (t60) REVERT: G 97 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8164 (pptt) REVERT: G 279 ASP cc_start: 0.7442 (t70) cc_final: 0.7240 (t70) REVERT: G 449 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7594 (pt) REVERT: G 482 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6600 (mm-30) REVERT: I 15 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7731 (t) REVERT: I 25 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7653 (pp30) REVERT: I 92 GLU cc_start: 0.8092 (mp0) cc_final: 0.7799 (pm20) outliers start: 64 outliers final: 36 residues processed: 240 average time/residue: 0.2710 time to fit residues: 93.4918 Evaluate side-chains 204 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain H residue 657 GLU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 249 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN G 203 GLN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14502 Z= 0.216 Angle : 0.687 8.102 19647 Z= 0.349 Chirality : 0.045 0.157 2358 Planarity : 0.004 0.046 2427 Dihedral : 7.430 59.548 2805 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.70 % Allowed : 13.00 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1653 helix: 1.48 (0.26), residues: 405 sheet: 0.16 (0.26), residues: 327 loop : -0.54 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 338 HIS 0.004 0.001 HIS B 641 PHE 0.023 0.002 PHE D 233 TYR 0.013 0.002 TYR D 486 ARG 0.009 0.001 ARG H 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 190 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.6923 (OUTLIER) cc_final: 0.6277 (m-10) REVERT: A 97 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8301 (mmtt) REVERT: A 449 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7433 (pt) REVERT: B 530 MET cc_start: 0.7741 (mtm) cc_final: 0.7185 (mtm) REVERT: C 69 LEU cc_start: 0.7393 (mp) cc_final: 0.6819 (tt) REVERT: D 373 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7380 (t) REVERT: D 449 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7437 (pt) REVERT: D 482 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6624 (tp30) REVERT: E 530 MET cc_start: 0.7774 (mtm) cc_final: 0.7387 (mtm) REVERT: F 63 ASP cc_start: 0.8765 (t0) cc_final: 0.8486 (p0) REVERT: G 69 TRP cc_start: 0.7260 (t60) cc_final: 0.7027 (t60) REVERT: G 97 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8011 (pptt) REVERT: G 279 ASP cc_start: 0.7324 (t70) cc_final: 0.7108 (t70) REVERT: G 373 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7395 (t) REVERT: G 449 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7516 (pt) REVERT: G 482 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6540 (mm-30) REVERT: H 530 MET cc_start: 0.7939 (mtm) cc_final: 0.7467 (mtm) outliers start: 56 outliers final: 27 residues processed: 231 average time/residue: 0.2725 time to fit residues: 92.6806 Evaluate side-chains 189 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14502 Z= 0.360 Angle : 0.754 8.360 19647 Z= 0.389 Chirality : 0.047 0.170 2358 Planarity : 0.005 0.047 2427 Dihedral : 7.169 48.488 2805 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.42 % Allowed : 13.86 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 1653 helix: 1.02 (0.25), residues: 408 sheet: 0.00 (0.25), residues: 357 loop : -0.88 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 338 HIS 0.009 0.002 HIS C 27 PHE 0.027 0.003 PHE I 26 TYR 0.016 0.003 TYR A 39 ARG 0.005 0.001 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 176 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7086 (OUTLIER) cc_final: 0.6709 (m-10) REVERT: A 449 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7594 (pt) REVERT: B 530 MET cc_start: 0.8123 (mtm) cc_final: 0.7896 (mtm) REVERT: C 69 LEU cc_start: 0.7457 (mp) cc_final: 0.6771 (tt) REVERT: C 92 GLU cc_start: 0.8002 (mp0) cc_final: 0.7771 (pm20) REVERT: D 373 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7712 (t) REVERT: D 449 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7464 (pt) REVERT: D 482 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6771 (mm-30) REVERT: E 530 MET cc_start: 0.7997 (mtm) cc_final: 0.7636 (mtm) REVERT: E 626 MET cc_start: 0.6960 (ttm) cc_final: 0.6522 (mtp) REVERT: F 63 ASP cc_start: 0.8883 (t0) cc_final: 0.8510 (p0) REVERT: G 45 TRP cc_start: 0.7058 (OUTLIER) cc_final: 0.5633 (m-90) REVERT: G 279 ASP cc_start: 0.7440 (t70) cc_final: 0.7199 (t70) REVERT: G 449 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7541 (pt) REVERT: G 482 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6677 (mm-30) REVERT: H 530 MET cc_start: 0.8206 (mtm) cc_final: 0.7807 (mtm) outliers start: 67 outliers final: 55 residues processed: 226 average time/residue: 0.2519 time to fit residues: 84.5567 Evaluate side-chains 218 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 157 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 445 CYS Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 599 SER Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain H residue 657 GLU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14502 Z= 0.210 Angle : 0.681 8.187 19647 Z= 0.347 Chirality : 0.044 0.155 2358 Planarity : 0.004 0.052 2427 Dihedral : 6.703 47.311 2805 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.03 % Allowed : 15.58 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1653 helix: 1.28 (0.25), residues: 405 sheet: -0.37 (0.26), residues: 390 loop : -0.58 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 338 HIS 0.005 0.001 HIS D 216 PHE 0.023 0.002 PHE I 26 TYR 0.015 0.002 TYR A 486 ARG 0.012 0.001 ARG H 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 171 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.6914 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: A 449 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7501 (pt) REVERT: B 530 MET cc_start: 0.7882 (mtm) cc_final: 0.7616 (mtm) REVERT: C 69 LEU cc_start: 0.6773 (mp) cc_final: 0.6404 (tt) REVERT: D 373 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7341 (t) REVERT: D 449 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7427 (pt) REVERT: D 482 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6666 (tp30) REVERT: E 626 MET cc_start: 0.6846 (ttm) cc_final: 0.6345 (mtp) REVERT: F 63 ASP cc_start: 0.8868 (t0) cc_final: 0.8533 (p0) REVERT: G 279 ASP cc_start: 0.7331 (t70) cc_final: 0.7102 (t70) REVERT: G 449 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7441 (pt) REVERT: G 482 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6591 (mm-30) REVERT: H 530 MET cc_start: 0.8152 (mtm) cc_final: 0.7753 (mtm) outliers start: 61 outliers final: 48 residues processed: 216 average time/residue: 0.2378 time to fit residues: 77.5500 Evaluate side-chains 208 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 155 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 296 CYS Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 445 CYS Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 90 optimal weight: 0.3980 chunk 161 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14502 Z= 0.416 Angle : 0.804 9.792 19647 Z= 0.416 Chirality : 0.048 0.219 2358 Planarity : 0.005 0.049 2427 Dihedral : 7.226 43.840 2805 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.69 % Allowed : 15.31 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1653 helix: 0.65 (0.24), residues: 408 sheet: -0.22 (0.27), residues: 351 loop : -1.18 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP G 112 HIS 0.010 0.002 HIS C 27 PHE 0.030 0.004 PHE B 522 TYR 0.017 0.003 TYR G 39 ARG 0.004 0.001 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 161 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7694 (pt) REVERT: D 482 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6857 (mm-30) REVERT: E 530 MET cc_start: 0.8245 (mtm) cc_final: 0.7745 (mtm) REVERT: E 626 MET cc_start: 0.7310 (ttm) cc_final: 0.6779 (mtp) REVERT: G 45 TRP cc_start: 0.7058 (OUTLIER) cc_final: 0.5579 (m-10) REVERT: G 279 ASP cc_start: 0.7482 (t70) cc_final: 0.7207 (t0) REVERT: G 482 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6822 (mm-30) REVERT: I 92 GLU cc_start: 0.8088 (pm20) cc_final: 0.7863 (pm20) outliers start: 71 outliers final: 62 residues processed: 215 average time/residue: 0.2467 time to fit residues: 79.1082 Evaluate side-chains 219 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 155 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 296 CYS Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 445 CYS Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 599 SER Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14502 Z= 0.196 Angle : 0.698 12.569 19647 Z= 0.355 Chirality : 0.044 0.219 2358 Planarity : 0.004 0.053 2427 Dihedral : 6.502 43.157 2805 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.70 % Allowed : 16.30 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1653 helix: 1.06 (0.25), residues: 408 sheet: -0.04 (0.29), residues: 339 loop : -0.91 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 338 HIS 0.006 0.001 HIS G 105 PHE 0.023 0.002 PHE I 26 TYR 0.016 0.002 TYR A 486 ARG 0.012 0.001 ARG H 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 178 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TRP cc_start: 0.7537 (t-100) cc_final: 0.7263 (t-100) REVERT: A 449 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7490 (pt) REVERT: B 530 MET cc_start: 0.8100 (mtm) cc_final: 0.7896 (mtm) REVERT: D 104 MET cc_start: 0.8571 (tpt) cc_final: 0.7873 (tpt) REVERT: D 373 THR cc_start: 0.7659 (t) cc_final: 0.7251 (t) REVERT: D 482 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6787 (tp30) REVERT: E 530 MET cc_start: 0.8120 (mtm) cc_final: 0.7539 (mtm) REVERT: F 54 ARG cc_start: 0.7647 (mpp80) cc_final: 0.7445 (mpp80) REVERT: F 63 ASP cc_start: 0.8612 (t0) cc_final: 0.8273 (p0) REVERT: G 45 TRP cc_start: 0.6801 (OUTLIER) cc_final: 0.5604 (m-10) REVERT: G 279 ASP cc_start: 0.7376 (t70) cc_final: 0.7152 (t70) REVERT: G 449 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7405 (pt) REVERT: G 482 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6704 (mm-30) outliers start: 56 outliers final: 42 residues processed: 221 average time/residue: 0.2609 time to fit residues: 88.0481 Evaluate side-chains 204 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 296 CYS Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 445 CYS Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 9.9990 chunk 141 optimal weight: 0.0030 chunk 150 optimal weight: 0.0870 chunk 90 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14502 Z= 0.181 Angle : 0.674 11.787 19647 Z= 0.343 Chirality : 0.044 0.192 2358 Planarity : 0.004 0.054 2427 Dihedral : 6.051 40.845 2805 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.97 % Allowed : 17.03 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1653 helix: 1.38 (0.25), residues: 402 sheet: 0.27 (0.29), residues: 327 loop : -0.77 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 112 HIS 0.002 0.001 HIS H 641 PHE 0.026 0.001 PHE I 26 TYR 0.015 0.002 TYR A 486 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 185 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7505 (pt) REVERT: A 475 MET cc_start: 0.5832 (mmp) cc_final: 0.5491 (mmp) REVERT: A 479 TRP cc_start: 0.6850 (m100) cc_final: 0.6434 (m100) REVERT: B 530 MET cc_start: 0.7943 (mtm) cc_final: 0.7430 (mtm) REVERT: D 104 MET cc_start: 0.8525 (tpt) cc_final: 0.7924 (tpt) REVERT: D 373 THR cc_start: 0.7403 (t) cc_final: 0.7027 (t) REVERT: D 449 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7422 (pt) REVERT: D 482 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6701 (tp30) REVERT: E 530 MET cc_start: 0.8054 (mtm) cc_final: 0.7487 (mtm) REVERT: F 63 ASP cc_start: 0.8620 (t0) cc_final: 0.8296 (p0) REVERT: G 45 TRP cc_start: 0.6672 (OUTLIER) cc_final: 0.5765 (m-10) REVERT: G 279 ASP cc_start: 0.7313 (t70) cc_final: 0.7097 (t70) REVERT: G 373 THR cc_start: 0.7585 (t) cc_final: 0.7126 (t) REVERT: G 449 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7415 (pt) REVERT: G 482 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6623 (mm-30) outliers start: 45 outliers final: 37 residues processed: 216 average time/residue: 0.2376 time to fit residues: 77.2232 Evaluate side-chains 209 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 445 CYS Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 0.5980 chunk 133 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14502 Z= 0.217 Angle : 0.680 11.699 19647 Z= 0.344 Chirality : 0.044 0.183 2358 Planarity : 0.005 0.077 2427 Dihedral : 6.000 38.278 2805 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.04 % Allowed : 17.23 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1653 helix: 1.47 (0.26), residues: 402 sheet: 0.23 (0.30), residues: 327 loop : -0.80 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 28 HIS 0.005 0.001 HIS C 27 PHE 0.020 0.002 PHE I 26 TYR 0.014 0.002 TYR A 486 ARG 0.004 0.001 ARG H 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7540 (pt) REVERT: A 479 TRP cc_start: 0.6973 (m100) cc_final: 0.6528 (m100) REVERT: B 530 MET cc_start: 0.7988 (mtm) cc_final: 0.7627 (mtm) REVERT: D 104 MET cc_start: 0.8507 (tpt) cc_final: 0.7907 (tpt) REVERT: D 373 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7233 (t) REVERT: D 482 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6762 (tp30) REVERT: E 530 MET cc_start: 0.8062 (mtm) cc_final: 0.7529 (mtm) REVERT: E 656 ASN cc_start: 0.8619 (m-40) cc_final: 0.8301 (m110) REVERT: F 63 ASP cc_start: 0.8662 (t0) cc_final: 0.8317 (p0) REVERT: G 45 TRP cc_start: 0.6877 (OUTLIER) cc_final: 0.5764 (m-10) REVERT: G 279 ASP cc_start: 0.7375 (t70) cc_final: 0.7078 (t0) REVERT: G 482 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6719 (mm-30) outliers start: 46 outliers final: 36 residues processed: 206 average time/residue: 0.2572 time to fit residues: 79.6728 Evaluate side-chains 202 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 445 CYS Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS ** H 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.116075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.098811 restraints weight = 44869.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.102094 restraints weight = 23235.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.104365 restraints weight = 14673.795| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14502 Z= 0.220 Angle : 0.683 11.531 19647 Z= 0.347 Chirality : 0.044 0.182 2358 Planarity : 0.004 0.071 2427 Dihedral : 5.963 36.980 2805 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.84 % Allowed : 17.89 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1653 helix: 1.40 (0.25), residues: 423 sheet: 0.31 (0.30), residues: 324 loop : -0.89 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 28 HIS 0.005 0.001 HIS C 27 PHE 0.020 0.002 PHE I 26 TYR 0.013 0.002 TYR A 486 ARG 0.004 0.000 ARG I 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.67 seconds wall clock time: 50 minutes 33.43 seconds (3033.43 seconds total)