Starting phenix.real_space_refine on Wed Feb 4 14:29:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9npr_49630/02_2026/9npr_49630.cif Found real_map, /net/cci-nas-00/data/ceres_data/9npr_49630/02_2026/9npr_49630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9npr_49630/02_2026/9npr_49630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9npr_49630/02_2026/9npr_49630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9npr_49630/02_2026/9npr_49630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9npr_49630/02_2026/9npr_49630.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 36 5.16 5 C 7037 2.51 5 N 1779 2.21 5 O 2154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11006 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1591 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 2 Chain: "H" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1598 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 2 Chain: "I" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1591 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 2 Chain: "A" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "D" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 792 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain breaks: 3 Chain: "B" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1118 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 805 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 3 Chain: "C" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1118 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "F" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 798 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 3 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: "L" 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: "M" 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" 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: "R" 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: "S" 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 Time building chain proxies: 2.99, per 1000 atoms: 0.27 Number of scatterers: 11006 At special positions: 0 Unit cell: (130.144, 140.768, 107.125, 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 36 16.00 O 2154 8.00 N 1779 7.00 C 7037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS G 468 " - pdb=" SG CYS G 479 " distance=2.03 Simple disulfide: pdb=" SG CYS G 516 " - pdb=" SG CYS G 533 " distance=2.03 Simple disulfide: pdb=" SG CYS H 468 " - pdb=" SG CYS H 479 " distance=2.03 Simple disulfide: pdb=" SG CYS H 516 " - pdb=" SG CYS H 533 " distance=2.03 Simple disulfide: pdb=" SG CYS I 468 " - pdb=" SG CYS I 479 " distance=2.03 Simple disulfide: pdb=" SG CYS I 516 " - pdb=" SG CYS I 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS D 512 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 119 " distance=2.03 Simple disulfide: pdb=" SG CYS E 512 " - pdb=" SG CYS E 557 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 119 " distance=2.03 Simple disulfide: pdb=" SG CYS F 512 " - pdb=" SG CYS F 557 " 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 ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA M 3 " - " MAN M 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG K 1 " - " ASN G 557 " " NAG L 1 " - " ASN H 557 " " NAG M 1 " - " ASN I 557 " " NAG N 1 " - " ASN A 94 " " NAG O 1 " - " ASN B 94 " " NAG P 1 " - " ASN C 94 " " NAG Q 1 " - " ASN D 564 " " NAG R 1 " - " ASN E 564 " " NAG S 1 " - " ASN F 564 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 567.1 milliseconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 19 sheets defined 24.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'G' and resid 391 through 396 removed outlier: 4.038A pdb=" N PHE G 395 " --> pdb=" O GLU G 391 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP G 396 " --> pdb=" O LYS G 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 391 through 396' Processing helix chain 'G' and resid 439 through 453 removed outlier: 4.019A pdb=" N VAL G 443 " --> pdb=" O ILE G 439 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU G 451 " --> pdb=" O GLN G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 489 Processing helix chain 'G' and resid 491 through 496 Processing helix chain 'G' and resid 554 through 558 removed outlier: 3.684A pdb=" N ASN G 557 " --> pdb=" O ASN G 554 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA G 558 " --> pdb=" O TYR G 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 554 through 558' Processing helix chain 'G' and resid 576 through 582 removed outlier: 3.627A pdb=" N ALA G 580 " --> pdb=" O LYS G 576 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 593 removed outlier: 3.811A pdb=" N GLU G 586 " --> pdb=" O ALA G 582 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE G 587 " --> pdb=" O TRP G 583 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS G 592 " --> pdb=" O ILE G 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 449 removed outlier: 3.843A pdb=" N LEU H 446 " --> pdb=" O GLN H 442 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLN H 447 " --> pdb=" O VAL H 443 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA H 449 " --> pdb=" O ASP H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 468 Processing helix chain 'H' and resid 484 through 489 Processing helix chain 'H' and resid 491 through 496 removed outlier: 3.520A pdb=" N LEU H 495 " --> pdb=" O SER H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 583 through 593 removed outlier: 3.929A pdb=" N PHE H 587 " --> pdb=" O TRP H 583 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN H 589 " --> pdb=" O LYS H 585 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS H 592 " --> pdb=" O ILE H 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 400 removed outlier: 3.884A pdb=" N GLY I 400 " --> pdb=" O GLN I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 453 removed outlier: 3.562A pdb=" N ILE I 453 " --> pdb=" O ALA I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 489 Processing helix chain 'I' and resid 491 through 496 Processing helix chain 'I' and resid 542 through 545 Processing helix chain 'I' and resid 576 through 584 removed outlier: 4.635A pdb=" N GLU I 584 " --> pdb=" O ALA I 580 " (cutoff:3.500A) Processing helix chain 'I' and resid 586 through 591 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 55 through 58 removed outlier: 3.652A pdb=" N LYS A 58 " --> pdb=" O SER A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 554 through 577 removed outlier: 3.762A pdb=" N ARG D 558 " --> pdb=" O ASN D 554 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 559 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 562 " --> pdb=" O ARG D 558 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA D 563 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN D 564 " --> pdb=" O ARG D 560 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER D 569 " --> pdb=" O GLN D 565 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 571 " --> pdb=" O ALA D 567 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU D 572 " --> pdb=" O LYS D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 596 Processing helix chain 'D' and resid 597 through 600 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 55 through 58 removed outlier: 3.725A pdb=" N LYS B 58 " --> pdb=" O SER B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'E' and resid 533 through 537 Processing helix chain 'E' and resid 555 through 577 removed outlier: 3.830A pdb=" N LEU E 559 " --> pdb=" O LEU E 555 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 567 " --> pdb=" O ALA E 563 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS E 568 " --> pdb=" O ASN E 564 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER E 569 " --> pdb=" O GLN E 565 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU E 571 " --> pdb=" O ALA E 567 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU E 572 " --> pdb=" O LYS E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 596 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 65 through 68 Processing helix chain 'C' and resid 171 through 180 removed outlier: 3.795A pdb=" N MET C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 577 removed outlier: 3.708A pdb=" N ARG F 561 " --> pdb=" O CYS F 557 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU F 562 " --> pdb=" O ARG F 558 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN F 564 " --> pdb=" O ARG F 560 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN F 565 " --> pdb=" O ARG F 561 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS F 568 " --> pdb=" O ASN F 564 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER F 569 " --> pdb=" O GLN F 565 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU F 571 " --> pdb=" O ALA F 567 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 572 " --> pdb=" O LYS F 568 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 598 removed outlier: 3.651A pdb=" N TRP F 598 " --> pdb=" O LEU F 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 561 through 565 removed outlier: 3.755A pdb=" N LEU G 408 " --> pdb=" O ILE G 563 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE G 565 " --> pdb=" O GLU G 406 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU G 406 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG G 411 " --> pdb=" O THR G 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 418 through 420 removed outlier: 3.855A pdb=" N HIS G 418 " --> pdb=" O PHE G 431 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 547 through 548 removed outlier: 3.792A pdb=" N LEU H 561 " --> pdb=" O ILE H 410 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE H 563 " --> pdb=" O LEU H 408 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 408 " --> pdb=" O ILE H 563 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE H 565 " --> pdb=" O GLU H 406 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU H 406 " --> pdb=" O PHE H 565 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 418 through 420 removed outlier: 3.626A pdb=" N HIS H 418 " --> pdb=" O PHE H 431 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 499 through 500 Processing sheet with id=AA6, first strand: chain 'I' and resid 547 through 548 Processing sheet with id=AA7, first strand: chain 'I' and resid 419 through 420 Processing sheet with id=AA8, first strand: chain 'A' and resid 143 through 145 removed outlier: 7.611A pdb=" N GLU A 85 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU A 49 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU A 87 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY A 51 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 86 " --> pdb=" O TRP D 519 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 516 " --> pdb=" O ILE D 549 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 547 " --> pdb=" O ILE D 518 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 70 through 73 Processing sheet with id=AB1, first strand: chain 'A' and resid 80 through 82 Processing sheet with id=AB2, first strand: chain 'A' and resid 89 through 93 removed outlier: 6.374A pdb=" N LYS A 90 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N HIS A 123 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS A 92 " --> pdb=" O HIS A 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 47 through 53 Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 73 Processing sheet with id=AB5, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.626A pdb=" N GLY B 86 " --> pdb=" O TRP E 519 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 93 removed outlier: 5.756A pdb=" N CYS B 92 " --> pdb=" O HIS B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 47 through 53 removed outlier: 3.701A pdb=" N PHE F 583 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 82 " --> pdb=" O PHE F 583 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AB9, first strand: chain 'C' and resid 86 through 87 removed outlier: 4.019A pdb=" N LEU F 516 " --> pdb=" O ILE F 549 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 89 through 93 removed outlier: 7.320A pdb=" N LYS C 90 " --> pdb=" O CYS C 119 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 609 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3387 1.34 - 1.46: 2863 1.46 - 1.58: 4975 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 11273 Sorted by residual: bond pdb=" N ILE I 437 " pdb=" CA ILE I 437 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.78e+00 bond pdb=" N ILE H 437 " pdb=" CA ILE H 437 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.54e+00 bond pdb=" N ASP I 436 " pdb=" CA ASP I 436 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.27e-02 6.20e+03 8.34e+00 bond pdb=" N ILE I 439 " pdb=" CA ILE I 439 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.24e+00 bond pdb=" N VAL I 443 " pdb=" CA VAL I 443 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.23e-02 6.61e+03 7.75e+00 ... (remaining 11268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 14778 2.01 - 4.01: 433 4.01 - 6.02: 82 6.02 - 8.03: 22 8.03 - 10.04: 4 Bond angle restraints: 15319 Sorted by residual: angle pdb=" N LEU I 444 " pdb=" CA LEU I 444 " pdb=" C LEU I 444 " ideal model delta sigma weight residual 111.07 106.14 4.93 1.07e+00 8.73e-01 2.13e+01 angle pdb=" N GLN I 442 " pdb=" CA GLN I 442 " pdb=" C GLN I 442 " ideal model delta sigma weight residual 111.71 106.42 5.29 1.15e+00 7.56e-01 2.11e+01 angle pdb=" N VAL I 443 " pdb=" CA VAL I 443 " pdb=" C VAL I 443 " ideal model delta sigma weight residual 111.00 106.59 4.41 1.09e+00 8.42e-01 1.64e+01 angle pdb=" CB LYS A 172 " pdb=" CG LYS A 172 " pdb=" CD LYS A 172 " ideal model delta sigma weight residual 111.30 120.28 -8.98 2.30e+00 1.89e-01 1.52e+01 angle pdb=" C ASN F 553 " pdb=" N ASN F 554 " pdb=" CA ASN F 554 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 ... (remaining 15314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.72: 6586 24.72 - 49.44: 369 49.44 - 74.15: 71 74.15 - 98.87: 39 98.87 - 123.59: 69 Dihedral angle restraints: 7134 sinusoidal: 3327 harmonic: 3807 Sorted by residual: dihedral pdb=" CB CYS G 516 " pdb=" SG CYS G 516 " pdb=" SG CYS G 533 " pdb=" CB CYS G 533 " ideal model delta sinusoidal sigma weight residual -86.00 -146.01 60.01 1 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" CB CYS H 516 " pdb=" SG CYS H 516 " pdb=" SG CYS H 533 " pdb=" CB CYS H 533 " ideal model delta sinusoidal sigma weight residual 93.00 144.03 -51.03 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA LYS C 43 " pdb=" C LYS C 43 " pdb=" N THR C 44 " pdb=" CA THR C 44 " ideal model delta harmonic sigma weight residual -180.00 -153.27 -26.73 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 7131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1701 0.101 - 0.203: 108 0.203 - 0.304: 4 0.304 - 0.406: 0 0.406 - 0.507: 1 Chirality restraints: 1814 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN F 564 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A 94 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN I 557 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1811 not shown) Planarity restraints: 1911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 503 " 0.020 2.00e-02 2.50e+03 2.05e-02 7.34e+00 pdb=" CG PHE G 503 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE G 503 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE G 503 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE G 503 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 503 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 503 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 564 " -0.019 2.00e-02 2.50e+03 1.85e-02 4.27e+00 pdb=" CG ASN E 564 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN E 564 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN E 564 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 109 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO B 110 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.027 5.00e-02 4.00e+02 ... (remaining 1908 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 298 2.69 - 3.24: 10516 3.24 - 3.80: 16493 3.80 - 4.35: 21338 4.35 - 4.90: 35302 Nonbonded interactions: 83947 Sorted by model distance: nonbonded pdb=" OD1 ASP D 592 " pdb=" OG1 THR C 44 " model vdw 2.140 3.040 nonbonded pdb=" O GLU C 87 " pdb=" OH TYR C 116 " model vdw 2.177 3.040 nonbonded pdb=" O PHE G 503 " pdb=" ND2 ASN A 129 " model vdw 2.192 3.120 nonbonded pdb=" OD2 ASP H 501 " pdb=" OH TYR H 506 " model vdw 2.198 3.040 nonbonded pdb=" OE1 GLU B 82 " pdb=" OG1 THR F 578 " model vdw 2.205 3.040 ... (remaining 83942 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 'B' and resid 39 through 180) selection = (chain 'C' and resid 39 through 180) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 469 through 477 or resid 490 through 600)) selection = (chain 'F' and (resid 469 through 477 or resid 490 through 600)) } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 390 through 469 or resid 478 through 604)) selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.860 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11324 Z= 0.191 Angle : 0.889 21.393 15460 Z= 0.414 Chirality : 0.051 0.507 1814 Planarity : 0.005 0.050 1902 Dihedral : 21.311 123.590 4638 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 0.95 % Allowed : 0.35 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.22), residues: 1263 helix: -2.00 (0.28), residues: 254 sheet: -0.66 (0.35), residues: 223 loop : -1.54 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 517 TYR 0.015 0.001 TYR A 83 PHE 0.048 0.002 PHE G 503 TRP 0.030 0.002 TRP D 532 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00370 (11273) covalent geometry : angle 0.80646 (15319) SS BOND : bond 0.00101 ( 12) SS BOND : angle 0.80419 ( 24) hydrogen bonds : bond 0.28616 ( 239) hydrogen bonds : angle 8.22887 ( 609) link_ALPHA1-3 : bond 0.00729 ( 6) link_ALPHA1-3 : angle 1.53785 ( 18) link_ALPHA1-6 : bond 0.00486 ( 6) link_ALPHA1-6 : angle 1.48483 ( 18) link_BETA1-4 : bond 0.00851 ( 18) link_BETA1-4 : angle 3.37970 ( 54) link_NAG-ASN : bond 0.01330 ( 9) link_NAG-ASN : angle 7.57125 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 260 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 551 ASP cc_start: 0.7571 (p0) cc_final: 0.7311 (p0) REVERT: H 435 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7651 (mt) REVERT: I 406 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6966 (mm-30) REVERT: I 440 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7482 (tp) outliers start: 11 outliers final: 1 residues processed: 265 average time/residue: 0.1246 time to fit residues: 44.1093 Evaluate side-chains 129 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 440 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 0.0070 overall best weight: 2.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 407 GLN G 441 HIS ** G 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 510 HIS G 581 GLN G 589 ASN G 598 ASN ** H 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 ASN A 129 ASN ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.126478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.091264 restraints weight = 33220.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.093609 restraints weight = 16822.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.095019 restraints weight = 11514.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.095813 restraints weight = 9351.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.096196 restraints weight = 8366.764| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11324 Z= 0.218 Angle : 0.906 20.404 15460 Z= 0.405 Chirality : 0.050 0.317 1814 Planarity : 0.006 0.063 1902 Dihedral : 18.870 112.445 2181 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 1.47 % Allowed : 11.77 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.22), residues: 1263 helix: -1.66 (0.28), residues: 286 sheet: -0.54 (0.36), residues: 213 loop : -1.67 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 156 TYR 0.018 0.002 TYR A 83 PHE 0.028 0.002 PHE I 504 TRP 0.015 0.002 TRP F 519 HIS 0.010 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00505 (11273) covalent geometry : angle 0.83016 (15319) SS BOND : bond 0.00172 ( 12) SS BOND : angle 0.86582 ( 24) hydrogen bonds : bond 0.05647 ( 239) hydrogen bonds : angle 5.82655 ( 609) link_ALPHA1-3 : bond 0.00797 ( 6) link_ALPHA1-3 : angle 2.28151 ( 18) link_ALPHA1-6 : bond 0.00602 ( 6) link_ALPHA1-6 : angle 2.67202 ( 18) link_BETA1-4 : bond 0.00669 ( 18) link_BETA1-4 : angle 3.20760 ( 54) link_NAG-ASN : bond 0.01005 ( 9) link_NAG-ASN : angle 7.00659 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.453 Fit side-chains REVERT: G 406 GLU cc_start: 0.7830 (tp30) cc_final: 0.7348 (tm-30) REVERT: H 408 LEU cc_start: 0.8608 (tt) cc_final: 0.8025 (mm) REVERT: I 406 GLU cc_start: 0.8690 (mm-30) cc_final: 0.7947 (mm-30) REVERT: I 408 LEU cc_start: 0.9068 (mm) cc_final: 0.8839 (mm) REVERT: A 82 GLU cc_start: 0.7710 (pp20) cc_final: 0.7228 (pp20) REVERT: A 168 MET cc_start: 0.8140 (ppp) cc_final: 0.7833 (ttp) REVERT: C 98 THR cc_start: 0.8465 (p) cc_final: 0.8222 (t) REVERT: C 115 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7521 (m-30) outliers start: 17 outliers final: 8 residues processed: 152 average time/residue: 0.1067 time to fit residues: 23.0970 Evaluate side-chains 127 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 594 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain E residue 494 TYR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 510 HIS A 112 ASN ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.123544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.088050 restraints weight = 33231.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.090284 restraints weight = 17296.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.091656 restraints weight = 11916.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.092409 restraints weight = 9659.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.092922 restraints weight = 8588.316| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11324 Z= 0.138 Angle : 0.811 19.647 15460 Z= 0.353 Chirality : 0.046 0.270 1814 Planarity : 0.005 0.045 1902 Dihedral : 15.766 110.218 2177 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.23 % Favored : 94.62 % Rotamer: Outliers : 1.47 % Allowed : 13.42 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.23), residues: 1263 helix: -1.36 (0.29), residues: 285 sheet: -0.39 (0.36), residues: 217 loop : -1.62 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 579 TYR 0.014 0.001 TYR H 509 PHE 0.024 0.001 PHE I 504 TRP 0.014 0.001 TRP G 583 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00311 (11273) covalent geometry : angle 0.72832 (15319) SS BOND : bond 0.00129 ( 12) SS BOND : angle 0.68540 ( 24) hydrogen bonds : bond 0.04554 ( 239) hydrogen bonds : angle 5.34559 ( 609) link_ALPHA1-3 : bond 0.01129 ( 6) link_ALPHA1-3 : angle 2.32755 ( 18) link_ALPHA1-6 : bond 0.00980 ( 6) link_ALPHA1-6 : angle 2.50497 ( 18) link_BETA1-4 : bond 0.00687 ( 18) link_BETA1-4 : angle 3.15175 ( 54) link_NAG-ASN : bond 0.01012 ( 9) link_NAG-ASN : angle 6.88804 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: G 406 GLU cc_start: 0.7725 (tp30) cc_final: 0.7111 (tp30) REVERT: H 408 LEU cc_start: 0.8705 (tt) cc_final: 0.8090 (mm) REVERT: H 438 GLN cc_start: 0.8376 (mm110) cc_final: 0.8153 (mm-40) REVERT: I 406 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8099 (mm-30) REVERT: C 115 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: C 168 MET cc_start: 0.7715 (ptt) cc_final: 0.7482 (ptt) outliers start: 17 outliers final: 8 residues processed: 140 average time/residue: 0.1038 time to fit residues: 20.4729 Evaluate side-chains 121 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 594 TYR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 16 optimal weight: 0.0060 chunk 53 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 589 ASN H 438 GLN ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.122521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.086875 restraints weight = 33079.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.089102 restraints weight = 17010.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.090517 restraints weight = 11659.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.091235 restraints weight = 9413.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.091771 restraints weight = 8409.079| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11324 Z= 0.141 Angle : 0.803 18.757 15460 Z= 0.345 Chirality : 0.046 0.259 1814 Planarity : 0.004 0.043 1902 Dihedral : 14.556 107.757 2177 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.25 % Favored : 93.67 % Rotamer: Outliers : 1.65 % Allowed : 13.94 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.23), residues: 1263 helix: -1.11 (0.30), residues: 288 sheet: -0.39 (0.40), residues: 195 loop : -1.70 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 176 TYR 0.011 0.001 TYR H 509 PHE 0.018 0.001 PHE I 504 TRP 0.019 0.001 TRP D 532 HIS 0.008 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00320 (11273) covalent geometry : angle 0.72199 (15319) SS BOND : bond 0.00086 ( 12) SS BOND : angle 0.64297 ( 24) hydrogen bonds : bond 0.04098 ( 239) hydrogen bonds : angle 5.03951 ( 609) link_ALPHA1-3 : bond 0.01214 ( 6) link_ALPHA1-3 : angle 2.43819 ( 18) link_ALPHA1-6 : bond 0.01092 ( 6) link_ALPHA1-6 : angle 2.79589 ( 18) link_BETA1-4 : bond 0.00697 ( 18) link_BETA1-4 : angle 3.14697 ( 54) link_NAG-ASN : bond 0.00987 ( 9) link_NAG-ASN : angle 6.61593 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.411 Fit side-chains REVERT: H 408 LEU cc_start: 0.8693 (tt) cc_final: 0.8057 (mm) REVERT: A 50 MET cc_start: 0.6748 (mtt) cc_final: 0.6015 (mtt) REVERT: A 125 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7439 (mt) REVERT: A 168 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7928 (ttp) REVERT: B 168 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8085 (ptm) REVERT: E 473 SER cc_start: 0.8475 (m) cc_final: 0.7740 (t) REVERT: E 555 LEU cc_start: 0.8135 (tp) cc_final: 0.7522 (mt) REVERT: C 115 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7651 (m-30) outliers start: 19 outliers final: 8 residues processed: 140 average time/residue: 0.1126 time to fit residues: 22.0000 Evaluate side-chains 125 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain H residue 583 TRP Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 594 TYR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 115 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 568 ASN G 578 GLN G 581 GLN ** I 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.120481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.085191 restraints weight = 33059.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.088358 restraints weight = 18310.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.087981 restraints weight = 10549.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.088431 restraints weight = 11916.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.088950 restraints weight = 10438.583| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11324 Z= 0.183 Angle : 0.825 17.559 15460 Z= 0.361 Chirality : 0.046 0.236 1814 Planarity : 0.005 0.043 1902 Dihedral : 13.899 108.779 2177 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 1.90 % Allowed : 15.58 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.23), residues: 1263 helix: -0.90 (0.31), residues: 277 sheet: -0.60 (0.38), residues: 207 loop : -1.69 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 579 TYR 0.012 0.001 TYR H 506 PHE 0.019 0.001 PHE I 504 TRP 0.011 0.001 TRP I 583 HIS 0.012 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00422 (11273) covalent geometry : angle 0.74654 (15319) SS BOND : bond 0.00112 ( 12) SS BOND : angle 0.63754 ( 24) hydrogen bonds : bond 0.04234 ( 239) hydrogen bonds : angle 5.14425 ( 609) link_ALPHA1-3 : bond 0.01232 ( 6) link_ALPHA1-3 : angle 2.44148 ( 18) link_ALPHA1-6 : bond 0.01105 ( 6) link_ALPHA1-6 : angle 3.11862 ( 18) link_BETA1-4 : bond 0.00721 ( 18) link_BETA1-4 : angle 3.20928 ( 54) link_NAG-ASN : bond 0.00915 ( 9) link_NAG-ASN : angle 6.46987 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.467 Fit side-chains REVERT: G 404 ARG cc_start: 0.8381 (tpt90) cc_final: 0.8031 (tpt90) REVERT: G 495 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6534 (tt) REVERT: H 408 LEU cc_start: 0.8737 (tt) cc_final: 0.8123 (mm) REVERT: H 442 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8476 (mm-40) REVERT: A 50 MET cc_start: 0.7025 (mtt) cc_final: 0.6510 (mtt) REVERT: A 82 GLU cc_start: 0.7823 (pp20) cc_final: 0.7164 (pp20) REVERT: A 125 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7561 (mt) REVERT: E 473 SER cc_start: 0.8547 (m) cc_final: 0.7760 (t) REVERT: E 493 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8449 (m) REVERT: C 115 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: F 522 GLN cc_start: 0.6365 (tm-30) cc_final: 0.5942 (tm-30) outliers start: 22 outliers final: 11 residues processed: 136 average time/residue: 0.1198 time to fit residues: 22.7295 Evaluate side-chains 125 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain H residue 583 TRP Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 512 HIS Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 115 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 7 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 HIS H 512 HIS ** I 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.117891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.082068 restraints weight = 33271.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.083940 restraints weight = 17607.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.085127 restraints weight = 12433.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.085813 restraints weight = 10240.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.086225 restraints weight = 9186.347| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11324 Z= 0.251 Angle : 0.888 16.561 15460 Z= 0.399 Chirality : 0.049 0.203 1814 Planarity : 0.005 0.046 1902 Dihedral : 13.581 113.713 2177 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.79 % Rotamer: Outliers : 2.51 % Allowed : 15.76 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.22), residues: 1263 helix: -0.97 (0.31), residues: 278 sheet: -0.97 (0.39), residues: 174 loop : -1.78 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 575 TYR 0.015 0.002 TYR A 83 PHE 0.024 0.002 PHE A 52 TRP 0.014 0.002 TRP I 583 HIS 0.015 0.002 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00577 (11273) covalent geometry : angle 0.81613 (15319) SS BOND : bond 0.00569 ( 12) SS BOND : angle 0.85613 ( 24) hydrogen bonds : bond 0.04956 ( 239) hydrogen bonds : angle 5.37191 ( 609) link_ALPHA1-3 : bond 0.01003 ( 6) link_ALPHA1-3 : angle 2.33390 ( 18) link_ALPHA1-6 : bond 0.01222 ( 6) link_ALPHA1-6 : angle 3.03069 ( 18) link_BETA1-4 : bond 0.00808 ( 18) link_BETA1-4 : angle 3.34189 ( 54) link_NAG-ASN : bond 0.00848 ( 9) link_NAG-ASN : angle 6.42725 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 404 ARG cc_start: 0.8468 (tpt90) cc_final: 0.8025 (tpt90) REVERT: G 495 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6549 (tt) REVERT: G 503 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.4175 (t80) REVERT: H 408 LEU cc_start: 0.8701 (tt) cc_final: 0.8137 (mm) REVERT: I 406 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 45 GLU cc_start: 0.8054 (pp20) cc_final: 0.7498 (pp20) REVERT: A 50 MET cc_start: 0.7034 (mtt) cc_final: 0.6579 (mtt) REVERT: A 61 ASP cc_start: 0.7001 (m-30) cc_final: 0.6590 (m-30) REVERT: A 125 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7402 (mt) REVERT: B 168 MET cc_start: 0.8647 (ptm) cc_final: 0.8350 (ptm) REVERT: E 473 SER cc_start: 0.8606 (m) cc_final: 0.7876 (t) REVERT: E 493 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8588 (m) REVERT: C 115 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7784 (m-30) REVERT: F 522 GLN cc_start: 0.6493 (tm-30) cc_final: 0.6137 (tm-30) outliers start: 29 outliers final: 18 residues processed: 137 average time/residue: 0.1099 time to fit residues: 21.0995 Evaluate side-chains 127 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 PHE Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain H residue 583 TRP Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 441 HIS Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 512 HIS Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 115 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 HIS ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 598 ASN I 441 HIS ** I 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.118296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.082689 restraints weight = 33191.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.084715 restraints weight = 17618.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.085984 restraints weight = 12329.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.086723 restraints weight = 10129.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.087092 restraints weight = 9048.343| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11324 Z= 0.206 Angle : 0.844 16.627 15460 Z= 0.374 Chirality : 0.047 0.238 1814 Planarity : 0.005 0.045 1902 Dihedral : 13.116 111.073 2177 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.10 % Favored : 93.82 % Rotamer: Outliers : 2.42 % Allowed : 16.88 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.22), residues: 1263 helix: -0.93 (0.31), residues: 278 sheet: -0.97 (0.38), residues: 174 loop : -1.71 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 176 TYR 0.016 0.001 TYR H 506 PHE 0.019 0.002 PHE I 504 TRP 0.014 0.001 TRP I 583 HIS 0.010 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00480 (11273) covalent geometry : angle 0.77039 (15319) SS BOND : bond 0.00592 ( 12) SS BOND : angle 0.94397 ( 24) hydrogen bonds : bond 0.04373 ( 239) hydrogen bonds : angle 5.18681 ( 609) link_ALPHA1-3 : bond 0.01002 ( 6) link_ALPHA1-3 : angle 2.14998 ( 18) link_ALPHA1-6 : bond 0.01210 ( 6) link_ALPHA1-6 : angle 2.75033 ( 18) link_BETA1-4 : bond 0.00719 ( 18) link_BETA1-4 : angle 3.31051 ( 54) link_NAG-ASN : bond 0.00825 ( 9) link_NAG-ASN : angle 6.37035 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 404 ARG cc_start: 0.8553 (tpt90) cc_final: 0.8335 (tpt90) REVERT: G 495 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6568 (tt) REVERT: H 408 LEU cc_start: 0.8690 (tt) cc_final: 0.8153 (mm) REVERT: A 45 GLU cc_start: 0.8108 (pp20) cc_final: 0.7349 (pp20) REVERT: A 50 MET cc_start: 0.6934 (mtt) cc_final: 0.6599 (mtt) REVERT: A 125 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7494 (mt) REVERT: B 43 LYS cc_start: 0.8588 (pttm) cc_final: 0.8001 (ptpp) REVERT: E 473 SER cc_start: 0.8594 (m) cc_final: 0.7863 (t) REVERT: E 493 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8461 (m) REVERT: F 555 LEU cc_start: 0.8269 (tt) cc_final: 0.7893 (mt) outliers start: 28 outliers final: 19 residues processed: 131 average time/residue: 0.1102 time to fit residues: 20.3494 Evaluate side-chains 125 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain H residue 583 TRP Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 441 HIS Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 512 HIS Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 40 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 110 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 86 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 447 GLN G 490 ASN G 556 ASN H 497 HIS H 578 GLN ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.119249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.083908 restraints weight = 33018.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.086000 restraints weight = 17383.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.087284 restraints weight = 12109.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.088041 restraints weight = 9871.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.088442 restraints weight = 8812.887| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11324 Z= 0.149 Angle : 0.810 16.532 15460 Z= 0.354 Chirality : 0.046 0.246 1814 Planarity : 0.005 0.045 1902 Dihedral : 12.759 110.126 2177 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.10 % Favored : 93.82 % Rotamer: Outliers : 2.08 % Allowed : 17.75 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.23), residues: 1263 helix: -0.78 (0.31), residues: 278 sheet: -0.94 (0.39), residues: 168 loop : -1.67 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 176 TYR 0.013 0.001 TYR H 506 PHE 0.017 0.001 PHE I 504 TRP 0.016 0.001 TRP I 583 HIS 0.012 0.001 HIS I 441 Details of bonding type rmsd covalent geometry : bond 0.00346 (11273) covalent geometry : angle 0.73548 (15319) SS BOND : bond 0.00148 ( 12) SS BOND : angle 0.68958 ( 24) hydrogen bonds : bond 0.03879 ( 239) hydrogen bonds : angle 4.96139 ( 609) link_ALPHA1-3 : bond 0.01027 ( 6) link_ALPHA1-3 : angle 1.99971 ( 18) link_ALPHA1-6 : bond 0.01368 ( 6) link_ALPHA1-6 : angle 2.70721 ( 18) link_BETA1-4 : bond 0.00686 ( 18) link_BETA1-4 : angle 3.28231 ( 54) link_NAG-ASN : bond 0.00853 ( 9) link_NAG-ASN : angle 6.27727 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: G 404 ARG cc_start: 0.8594 (tpt90) cc_final: 0.8334 (tpt90) REVERT: H 408 LEU cc_start: 0.8728 (tt) cc_final: 0.8211 (mm) REVERT: A 45 GLU cc_start: 0.7960 (pp20) cc_final: 0.7218 (pp20) REVERT: A 50 MET cc_start: 0.6895 (mtt) cc_final: 0.6491 (mtt) REVERT: A 125 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7330 (mm) REVERT: A 168 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7901 (ttp) REVERT: E 473 SER cc_start: 0.8511 (m) cc_final: 0.7882 (t) REVERT: F 555 LEU cc_start: 0.8205 (tt) cc_final: 0.7920 (mt) outliers start: 24 outliers final: 19 residues processed: 127 average time/residue: 0.0873 time to fit residues: 15.7112 Evaluate side-chains 125 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 503 PHE Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain H residue 583 TRP Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 509 TYR Chi-restraints excluded: chain I residue 512 HIS Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain E residue 553 ASN Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 40 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 497 HIS I 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.120126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.084877 restraints weight = 32823.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.086958 restraints weight = 17244.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.088272 restraints weight = 12017.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.089042 restraints weight = 9793.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.089436 restraints weight = 8723.650| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11324 Z= 0.133 Angle : 0.797 16.425 15460 Z= 0.346 Chirality : 0.045 0.258 1814 Planarity : 0.004 0.043 1902 Dihedral : 12.380 108.691 2177 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.18 % Favored : 93.75 % Rotamer: Outliers : 1.90 % Allowed : 17.75 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.23), residues: 1263 helix: -0.81 (0.31), residues: 290 sheet: -0.95 (0.39), residues: 178 loop : -1.59 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 579 TYR 0.012 0.001 TYR H 506 PHE 0.016 0.001 PHE A 160 TRP 0.018 0.001 TRP I 583 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00305 (11273) covalent geometry : angle 0.72202 (15319) SS BOND : bond 0.00142 ( 12) SS BOND : angle 0.59693 ( 24) hydrogen bonds : bond 0.03533 ( 239) hydrogen bonds : angle 4.83959 ( 609) link_ALPHA1-3 : bond 0.01062 ( 6) link_ALPHA1-3 : angle 2.00634 ( 18) link_ALPHA1-6 : bond 0.01429 ( 6) link_ALPHA1-6 : angle 2.75357 ( 18) link_BETA1-4 : bond 0.00688 ( 18) link_BETA1-4 : angle 3.26699 ( 54) link_NAG-ASN : bond 0.00877 ( 9) link_NAG-ASN : angle 6.20366 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.277 Fit side-chains REVERT: G 404 ARG cc_start: 0.8624 (tpt90) cc_final: 0.8355 (tpt90) REVERT: H 408 LEU cc_start: 0.8812 (tt) cc_final: 0.8297 (mm) REVERT: A 43 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8602 (ttpt) REVERT: A 45 GLU cc_start: 0.7945 (pp20) cc_final: 0.7537 (pp20) REVERT: A 50 MET cc_start: 0.6724 (mtt) cc_final: 0.6333 (mtt) REVERT: A 168 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7844 (ttp) REVERT: E 473 SER cc_start: 0.8406 (m) cc_final: 0.7799 (t) REVERT: F 555 LEU cc_start: 0.8210 (tt) cc_final: 0.7899 (mt) outliers start: 22 outliers final: 17 residues processed: 129 average time/residue: 0.1014 time to fit residues: 18.1374 Evaluate side-chains 120 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 503 PHE Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain H residue 583 TRP Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 509 TYR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain E residue 553 ASN Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 497 HIS A 112 ASN ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.118844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083461 restraints weight = 33181.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.085533 restraints weight = 17530.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.086770 restraints weight = 12227.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.087500 restraints weight = 9982.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.087985 restraints weight = 8925.753| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11324 Z= 0.171 Angle : 0.829 16.026 15460 Z= 0.364 Chirality : 0.046 0.239 1814 Planarity : 0.005 0.046 1902 Dihedral : 12.249 110.065 2177 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.41 % Favored : 93.51 % Rotamer: Outliers : 1.82 % Allowed : 18.10 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.23), residues: 1263 helix: -0.79 (0.31), residues: 291 sheet: -0.70 (0.41), residues: 162 loop : -1.65 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 575 TYR 0.016 0.001 TYR H 506 PHE 0.015 0.001 PHE I 504 TRP 0.019 0.001 TRP I 583 HIS 0.008 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00401 (11273) covalent geometry : angle 0.75765 (15319) SS BOND : bond 0.00116 ( 12) SS BOND : angle 0.63758 ( 24) hydrogen bonds : bond 0.03888 ( 239) hydrogen bonds : angle 4.90501 ( 609) link_ALPHA1-3 : bond 0.00917 ( 6) link_ALPHA1-3 : angle 1.99352 ( 18) link_ALPHA1-6 : bond 0.01284 ( 6) link_ALPHA1-6 : angle 2.79239 ( 18) link_BETA1-4 : bond 0.00709 ( 18) link_BETA1-4 : angle 3.28211 ( 54) link_NAG-ASN : bond 0.00833 ( 9) link_NAG-ASN : angle 6.16308 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: G 404 ARG cc_start: 0.8661 (tpt90) cc_final: 0.8397 (tpt90) REVERT: G 495 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6647 (tt) REVERT: H 408 LEU cc_start: 0.8731 (tt) cc_final: 0.8227 (mm) REVERT: A 43 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8605 (ttpt) REVERT: A 45 GLU cc_start: 0.7975 (pp20) cc_final: 0.7585 (pp20) REVERT: A 50 MET cc_start: 0.6991 (mtt) cc_final: 0.6522 (mtt) REVERT: A 168 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7829 (ttp) REVERT: E 473 SER cc_start: 0.8527 (m) cc_final: 0.7913 (t) REVERT: C 168 MET cc_start: 0.8156 (ptp) cc_final: 0.7908 (ptm) REVERT: F 555 LEU cc_start: 0.8246 (tt) cc_final: 0.7946 (mt) outliers start: 21 outliers final: 18 residues processed: 123 average time/residue: 0.1072 time to fit residues: 18.3152 Evaluate side-chains 121 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 PHE Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain H residue 583 TRP Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 441 HIS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain E residue 553 ASN Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain C residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 74 optimal weight: 0.0570 chunk 20 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 126 optimal weight: 0.0030 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 497 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.119595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.084367 restraints weight = 33076.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.086430 restraints weight = 17359.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.087748 restraints weight = 12077.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.088468 restraints weight = 9809.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.088903 restraints weight = 8783.934| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11324 Z= 0.146 Angle : 0.812 16.038 15460 Z= 0.354 Chirality : 0.045 0.250 1814 Planarity : 0.004 0.048 1902 Dihedral : 11.980 108.879 2177 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.90 % Rotamer: Outliers : 1.90 % Allowed : 18.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.23), residues: 1263 helix: -0.72 (0.32), residues: 290 sheet: -0.70 (0.41), residues: 156 loop : -1.60 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 579 TYR 0.012 0.001 TYR H 506 PHE 0.016 0.001 PHE G 504 TRP 0.020 0.001 TRP I 583 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00341 (11273) covalent geometry : angle 0.73942 (15319) SS BOND : bond 0.00112 ( 12) SS BOND : angle 0.57983 ( 24) hydrogen bonds : bond 0.03530 ( 239) hydrogen bonds : angle 4.80894 ( 609) link_ALPHA1-3 : bond 0.01034 ( 6) link_ALPHA1-3 : angle 2.01009 ( 18) link_ALPHA1-6 : bond 0.01522 ( 6) link_ALPHA1-6 : angle 2.87270 ( 18) link_BETA1-4 : bond 0.00694 ( 18) link_BETA1-4 : angle 3.26572 ( 54) link_NAG-ASN : bond 0.00852 ( 9) link_NAG-ASN : angle 6.15071 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.51 seconds wall clock time: 37 minutes 10.59 seconds (2230.59 seconds total)