Starting phenix.real_space_refine on Sat Mar 16 11:03:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwu_29519/03_2024/8fwu_29519_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwu_29519/03_2024/8fwu_29519.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwu_29519/03_2024/8fwu_29519_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwu_29519/03_2024/8fwu_29519_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwu_29519/03_2024/8fwu_29519_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwu_29519/03_2024/8fwu_29519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwu_29519/03_2024/8fwu_29519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwu_29519/03_2024/8fwu_29519_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwu_29519/03_2024/8fwu_29519_updated.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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: 8 Type Number sf(0) Gaussians P 16 5.49 5 S 80 5.16 5 Cl 2 4.86 5 Na 8 4.78 5 C 9464 2.51 5 N 2206 2.21 5 O 2716 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 727": "NH1" <-> "NH2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C ARG 727": "NH1" <-> "NH2" Residue "C ARG 800": "NH1" <-> "NH2" Residue "D PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 503": "NH1" <-> "NH2" Residue "D PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14496 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3318 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 402} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 349 Unusual residues: {' CL': 1, ' NA': 4, 'DNQ': 1, 'NAG': 1, 'POV': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 156 Unusual residues: {' NA': 2, '2J9': 2, 'DNQ': 1, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 398 Unusual residues: {' CL': 1, ' NA': 1, 'DNQ': 1, 'NAG': 1, 'POV': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Unusual residues: {' NA': 1, '2J9': 2, 'DNQ': 1, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 8.17, per 1000 atoms: 0.56 Number of scatterers: 14496 At special positions: 0 Unit cell: (107.07, 118.69, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 2 17.00 S 80 16.00 P 16 15.00 Na 8 11.00 F 4 9.00 O 2716 8.00 N 2206 7.00 C 9464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS B 595 " distance=1.99 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS D 595 " distance=2.06 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " " BMA I 3 " - " BMA I 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1006 " - " ASN A 751 " " NAG C1006 " - " ASN C 751 " " NAG E 1 " - " ASN A 546 " " NAG F 1 " - " ASN B 546 " " NAG G 1 " - " ASN B 751 " " NAG H 1 " - " ASN C 546 " " NAG I 1 " - " ASN D 546 " " NAG J 1 " - " ASN D 751 " Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 2.4 seconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 10 sheets defined 42.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.683A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 563 through 584 removed outlier: 3.530A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 631 through 664 removed outlier: 3.776A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 674 No H-bonds generated for 'chain 'A' and resid 671 through 674' Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 702 through 711 removed outlier: 3.917A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.699A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 787 Processing helix chain 'A' and resid 790 through 799 removed outlier: 3.608A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 849 removed outlier: 3.774A pdb=" N VAL A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 473 removed outlier: 3.565A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 524 No H-bonds generated for 'chain 'B' and resid 521 through 524' Processing helix chain 'B' and resid 561 through 584 removed outlier: 3.509A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 580 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 619 removed outlier: 3.588A pdb=" N PHE B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 660 removed outlier: 3.907A pdb=" N THR B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.575A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 676' Processing helix chain 'B' and resid 689 through 695 removed outlier: 3.677A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 711 removed outlier: 3.520A pdb=" N TRP B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 739 through 748 removed outlier: 3.894A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 788 removed outlier: 3.520A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 798 Processing helix chain 'B' and resid 823 through 849 removed outlier: 3.560A pdb=" N ALA B 828 " --> pdb=" O PHE B 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 474 removed outlier: 3.684A pdb=" N LEU C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 506 Processing helix chain 'C' and resid 521 through 524 No H-bonds generated for 'chain 'C' and resid 521 through 524' Processing helix chain 'C' and resid 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 563 through 584 removed outlier: 3.530A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 619 Processing helix chain 'C' and resid 631 through 664 removed outlier: 3.776A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 674 No H-bonds generated for 'chain 'C' and resid 671 through 674' Processing helix chain 'C' and resid 689 through 695 Processing helix chain 'C' and resid 702 through 711 removed outlier: 3.916A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 711 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 730 Processing helix chain 'C' and resid 739 through 748 removed outlier: 3.698A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 748 " --> pdb=" O PHE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 787 Processing helix chain 'C' and resid 790 through 799 removed outlier: 3.608A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 849 removed outlier: 3.774A pdb=" N VAL C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 473 removed outlier: 3.565A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 524 No H-bonds generated for 'chain 'D' and resid 521 through 524' Processing helix chain 'D' and resid 561 through 584 removed outlier: 3.509A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 580 " --> pdb=" O CYS D 576 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 619 removed outlier: 3.588A pdb=" N PHE D 614 " --> pdb=" O ASN D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 660 removed outlier: 3.907A pdb=" N THR D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 676 removed outlier: 3.575A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 672 through 676' Processing helix chain 'D' and resid 689 through 695 removed outlier: 3.677A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 711 removed outlier: 3.520A pdb=" N TRP D 706 " --> pdb=" O TYR D 702 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 739 through 748 removed outlier: 3.895A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 788 removed outlier: 3.520A pdb=" N ILE D 778 " --> pdb=" O TYR D 774 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 798 Processing helix chain 'D' and resid 823 through 849 removed outlier: 3.561A pdb=" N ALA D 828 " --> pdb=" O PHE D 824 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 433 through 437 removed outlier: 3.760A pdb=" N THR A 437 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.927A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 752 through 754 removed outlier: 5.074A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 534 through 536 removed outlier: 3.736A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 735 through 738 removed outlier: 4.037A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 433 through 437 removed outlier: 3.761A pdb=" N THR C 437 " --> pdb=" O ARG C 481 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.926A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 752 through 754 removed outlier: 5.075A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 534 through 536 removed outlier: 3.736A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 735 through 738 removed outlier: 4.037A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 6.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2224 1.31 - 1.43: 3964 1.43 - 1.56: 8402 1.56 - 1.68: 62 1.68 - 1.81: 132 Bond restraints: 14784 Sorted by residual: bond pdb=" C3 DNQ C1001 " pdb=" C4 DNQ C1001 " ideal model delta sigma weight residual 2.767 1.362 1.405 2.00e-02 2.50e+03 4.93e+03 bond pdb=" C3 DNQ A1001 " pdb=" C4 DNQ A1001 " ideal model delta sigma weight residual 2.767 1.363 1.404 2.00e-02 2.50e+03 4.93e+03 bond pdb=" C3 DNQ D1003 " pdb=" C4 DNQ D1003 " ideal model delta sigma weight residual 2.767 1.364 1.403 2.00e-02 2.50e+03 4.92e+03 bond pdb=" C3 DNQ B1002 " pdb=" C4 DNQ B1002 " ideal model delta sigma weight residual 2.767 1.365 1.402 2.00e-02 2.50e+03 4.91e+03 bond pdb=" C7 DNQ C1001 " pdb=" C8 DNQ C1001 " ideal model delta sigma weight residual 0.516 1.410 -0.894 2.00e-02 2.50e+03 2.00e+03 ... (remaining 14779 not shown) Histogram of bond angle deviations from ideal: 59.69 - 77.98: 12 77.98 - 96.28: 0 96.28 - 114.57: 9141 114.57 - 132.87: 10693 132.87 - 151.16: 48 Bond angle restraints: 19894 Sorted by residual: angle pdb=" C6 DNQ B1002 " pdb=" C4 DNQ B1002 " pdb=" N2 DNQ B1002 " ideal model delta sigma weight residual 180.00 117.72 62.28 3.00e+00 1.11e-01 4.31e+02 angle pdb=" C6 DNQ D1003 " pdb=" C4 DNQ D1003 " pdb=" N2 DNQ D1003 " ideal model delta sigma weight residual 180.00 117.74 62.26 3.00e+00 1.11e-01 4.31e+02 angle pdb=" C6 DNQ C1001 " pdb=" C4 DNQ C1001 " pdb=" N2 DNQ C1001 " ideal model delta sigma weight residual 180.00 117.77 62.23 3.00e+00 1.11e-01 4.30e+02 angle pdb=" C6 DNQ A1001 " pdb=" C4 DNQ A1001 " pdb=" N2 DNQ A1001 " ideal model delta sigma weight residual 180.00 117.98 62.02 3.00e+00 1.11e-01 4.27e+02 angle pdb=" C5 DNQ A1001 " pdb=" C3 DNQ A1001 " pdb=" N1 DNQ A1001 " ideal model delta sigma weight residual 180.00 121.59 58.41 3.00e+00 1.11e-01 3.79e+02 ... (remaining 19889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8683 35.43 - 70.86: 368 70.86 - 106.30: 80 106.30 - 141.73: 13 141.73 - 177.16: 4 Dihedral angle restraints: 9148 sinusoidal: 4308 harmonic: 4840 Sorted by residual: dihedral pdb=" CA ASP D 732 " pdb=" C ASP D 732 " pdb=" N TYR D 733 " pdb=" CA TYR D 733 " ideal model delta harmonic sigma weight residual 180.00 110.45 69.55 0 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CA ASP B 732 " pdb=" C ASP B 732 " pdb=" N TYR B 733 " pdb=" CA TYR B 733 " ideal model delta harmonic sigma weight residual 180.00 110.53 69.47 0 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CA GLU D 811 " pdb=" C GLU D 811 " pdb=" N ALA D 812 " pdb=" CA ALA D 812 " ideal model delta harmonic sigma weight residual -180.00 -135.50 -44.50 0 5.00e+00 4.00e-02 7.92e+01 ... (remaining 9145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.460: 2152 0.460 - 0.919: 2 0.919 - 1.379: 0 1.379 - 1.838: 0 1.838 - 2.298: 4 Chirality restraints: 2158 Sorted by residual: chirality pdb=" CAN 2J9 D1001 " pdb=" CAG 2J9 D1001 " pdb=" CAH 2J9 D1001 " pdb=" NAO 2J9 D1001 " both_signs ideal model delta sigma weight residual True 2.32 -0.02 2.30 2.00e-01 2.50e+01 1.32e+02 chirality pdb=" CAN 2J9 D1002 " pdb=" CAG 2J9 D1002 " pdb=" CAH 2J9 D1002 " pdb=" NAO 2J9 D1002 " both_signs ideal model delta sigma weight residual True 2.32 -0.02 2.30 2.00e-01 2.50e+01 1.32e+02 chirality pdb=" CAN 2J9 B1005 " pdb=" CAG 2J9 B1005 " pdb=" CAH 2J9 B1005 " pdb=" NAO 2J9 B1005 " both_signs ideal model delta sigma weight residual True 2.32 -0.02 2.29 2.00e-01 2.50e+01 1.32e+02 ... (remaining 2155 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 478 " 0.031 2.00e-02 2.50e+03 1.77e-02 6.23e+00 pdb=" CG TYR D 478 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR D 478 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR D 478 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 478 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 478 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 478 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 478 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 478 " -0.031 2.00e-02 2.50e+03 1.76e-02 6.22e+00 pdb=" CG TYR B 478 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 478 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 478 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 478 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 478 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 478 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 478 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 481 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ARG B 481 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG B 481 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 482 " 0.014 2.00e-02 2.50e+03 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3420 2.78 - 3.31: 12384 3.31 - 3.84: 23130 3.84 - 4.37: 29114 4.37 - 4.90: 48972 Nonbonded interactions: 117020 Sorted by model distance: nonbonded pdb=" OE2 GLU B 787 " pdb=" OG1 THR C 520 " model vdw 2.254 2.440 nonbonded pdb=" OG SER A 834 " pdb=" O SER D 632 " model vdw 2.274 2.440 nonbonded pdb=" OG SER A 554 " pdb=" O ASN A 819 " model vdw 2.294 2.440 nonbonded pdb=" OG SER C 554 " pdb=" O ASN C 819 " model vdw 2.294 2.440 nonbonded pdb=" O3 DNQ A1001 " pdb=" O4 DNQ A1001 " model vdw 2.308 3.040 ... (remaining 117015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 431 through 850 or resid 1004)) selection = (chain 'B' and (resid 431 through 850 or resid 1004)) selection = (chain 'C' and (resid 431 through 850 or resid 1004)) selection = (chain 'D' and (resid 431 through 850 or resid 1004)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.560 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 38.160 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.036 1.405 14784 Z= 2.043 Angle : 2.598 62.285 19894 Z= 1.027 Chirality : 0.119 2.298 2158 Planarity : 0.007 0.056 2402 Dihedral : 20.010 177.161 6034 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.21 % Favored : 90.55 % Rotamer: Outliers : 0.97 % Allowed : 4.14 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.02 (0.14), residues: 1672 helix: -4.25 (0.09), residues: 842 sheet: -3.17 (0.38), residues: 166 loop : -3.63 (0.18), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 706 HIS 0.008 0.002 HIS D 593 PHE 0.028 0.003 PHE B 658 TYR 0.037 0.003 TYR D 478 ARG 0.006 0.001 ARG D 663 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 320 time to evaluate : 1.503 Fit side-chains REVERT: C 780 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7355 (mp) REVERT: D 587 TYR cc_start: 0.8216 (m-80) cc_final: 0.7939 (m-80) REVERT: D 719 LYS cc_start: 0.7619 (mtmm) cc_final: 0.7384 (mmtm) outliers start: 14 outliers final: 2 residues processed: 333 average time/residue: 0.2774 time to fit residues: 132.1717 Evaluate side-chains 179 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain D residue 791 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 GLN B 591 ASN ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN B 621 GLN B 721 ASN C 604 ASN C 621 GLN D 591 ASN D 593 HIS D 610 ASN D 721 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 14784 Z= 0.276 Angle : 0.997 28.602 19894 Z= 0.430 Chirality : 0.047 0.425 2158 Planarity : 0.006 0.050 2402 Dihedral : 22.767 152.822 2900 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.25 % Favored : 91.51 % Rotamer: Outliers : 2.69 % Allowed : 10.64 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.17), residues: 1672 helix: -2.36 (0.14), residues: 836 sheet: -2.31 (0.43), residues: 132 loop : -3.13 (0.19), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 798 HIS 0.007 0.001 HIS D 593 PHE 0.025 0.002 PHE D 842 TYR 0.027 0.002 TYR D 478 ARG 0.003 0.001 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 208 time to evaluate : 1.589 Fit side-chains REVERT: B 672 ASP cc_start: 0.7736 (p0) cc_final: 0.7463 (t0) REVERT: C 670 SER cc_start: 0.8637 (t) cc_final: 0.8302 (m) REVERT: C 780 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7324 (mp) REVERT: D 691 MET cc_start: 0.8002 (ttp) cc_final: 0.7760 (tmm) REVERT: D 719 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7521 (mmtm) REVERT: D 733 TYR cc_start: 0.6204 (t80) cc_final: 0.5670 (t80) outliers start: 39 outliers final: 20 residues processed: 239 average time/residue: 0.2670 time to fit residues: 93.2531 Evaluate side-chains 195 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 791 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 0.1980 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 GLN A 754 GLN B 593 HIS B 621 GLN C 754 GLN C 792 HIS ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 14784 Z= 0.398 Angle : 1.001 28.118 19894 Z= 0.433 Chirality : 0.049 0.439 2158 Planarity : 0.005 0.046 2402 Dihedral : 21.559 140.426 2900 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.75 % Favored : 90.13 % Rotamer: Outliers : 4.28 % Allowed : 12.43 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.19), residues: 1672 helix: -1.17 (0.17), residues: 828 sheet: -2.21 (0.43), residues: 140 loop : -2.88 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 798 HIS 0.003 0.001 HIS B 593 PHE 0.021 0.002 PHE C 735 TYR 0.023 0.002 TYR D 478 ARG 0.004 0.001 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 184 time to evaluate : 1.407 Fit side-chains REVERT: A 780 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7134 (mp) REVERT: B 733 TYR cc_start: 0.6684 (t80) cc_final: 0.6008 (t80) REVERT: C 670 SER cc_start: 0.8652 (t) cc_final: 0.8316 (m) REVERT: C 780 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7280 (mp) REVERT: D 719 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7472 (mmtm) REVERT: D 733 TYR cc_start: 0.6596 (t80) cc_final: 0.5713 (t80) outliers start: 62 outliers final: 34 residues processed: 232 average time/residue: 0.2594 time to fit residues: 87.1956 Evaluate side-chains 202 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 753 THR Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 825 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 16 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14784 Z= 0.212 Angle : 0.917 28.138 19894 Z= 0.385 Chirality : 0.045 0.405 2158 Planarity : 0.004 0.045 2402 Dihedral : 20.034 140.671 2896 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.36 % Favored : 92.52 % Rotamer: Outliers : 2.97 % Allowed : 14.30 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1672 helix: -0.20 (0.18), residues: 838 sheet: -2.16 (0.44), residues: 134 loop : -2.65 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 798 HIS 0.006 0.001 HIS B 593 PHE 0.026 0.001 PHE D 842 TYR 0.018 0.002 TYR C 590 ARG 0.004 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 1.691 Fit side-chains REVERT: B 691 MET cc_start: 0.7738 (ttp) cc_final: 0.7511 (ttp) REVERT: C 670 SER cc_start: 0.8539 (t) cc_final: 0.8221 (m) REVERT: C 780 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7260 (mp) REVERT: D 719 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7461 (mmtm) REVERT: D 733 TYR cc_start: 0.6168 (t80) cc_final: 0.5313 (t80) outliers start: 43 outliers final: 26 residues processed: 201 average time/residue: 0.2621 time to fit residues: 78.0956 Evaluate side-chains 183 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 112 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14784 Z= 0.209 Angle : 0.900 27.920 19894 Z= 0.375 Chirality : 0.044 0.416 2158 Planarity : 0.004 0.045 2402 Dihedral : 19.082 140.857 2896 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.18 % Favored : 92.70 % Rotamer: Outliers : 3.45 % Allowed : 14.09 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.21), residues: 1672 helix: 0.40 (0.19), residues: 820 sheet: -2.06 (0.43), residues: 140 loop : -2.41 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 798 HIS 0.005 0.001 HIS B 593 PHE 0.026 0.001 PHE D 842 TYR 0.016 0.002 TYR B 733 ARG 0.005 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 165 time to evaluate : 1.404 Fit side-chains REVERT: B 499 ASN cc_start: 0.7947 (m110) cc_final: 0.7563 (m110) REVERT: B 691 MET cc_start: 0.7756 (ttp) cc_final: 0.7520 (ttp) REVERT: C 568 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7712 (tt) REVERT: C 670 SER cc_start: 0.8489 (t) cc_final: 0.8187 (m) REVERT: C 780 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7236 (mp) REVERT: D 719 LYS cc_start: 0.7836 (mtmm) cc_final: 0.7439 (mmtm) REVERT: D 733 TYR cc_start: 0.6057 (t80) cc_final: 0.5408 (t80) outliers start: 50 outliers final: 33 residues processed: 200 average time/residue: 0.2637 time to fit residues: 77.4984 Evaluate side-chains 195 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14784 Z= 0.206 Angle : 0.896 27.881 19894 Z= 0.371 Chirality : 0.045 0.476 2158 Planarity : 0.004 0.045 2402 Dihedral : 18.657 140.830 2896 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.18 % Favored : 92.70 % Rotamer: Outliers : 3.25 % Allowed : 14.57 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.21), residues: 1672 helix: 0.69 (0.19), residues: 840 sheet: -2.12 (0.40), residues: 160 loop : -2.49 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 798 HIS 0.003 0.001 HIS B 593 PHE 0.026 0.001 PHE D 842 TYR 0.018 0.001 TYR D 478 ARG 0.004 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 1.514 Fit side-chains REVERT: B 691 MET cc_start: 0.7736 (ttp) cc_final: 0.7465 (ttp) REVERT: C 568 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7671 (tt) REVERT: C 670 SER cc_start: 0.8468 (t) cc_final: 0.8167 (m) REVERT: D 719 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7516 (mptt) REVERT: D 733 TYR cc_start: 0.5883 (t80) cc_final: 0.5275 (t80) REVERT: D 810 LYS cc_start: 0.6300 (ttpt) cc_final: 0.6088 (pttm) outliers start: 47 outliers final: 31 residues processed: 191 average time/residue: 0.2541 time to fit residues: 71.9951 Evaluate side-chains 184 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 0.0980 chunk 118 optimal weight: 0.0970 chunk 91 optimal weight: 0.5980 chunk 136 optimal weight: 0.0170 chunk 90 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 101 optimal weight: 0.0980 chunk 98 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14784 Z= 0.146 Angle : 0.880 28.031 19894 Z= 0.360 Chirality : 0.044 0.571 2158 Planarity : 0.004 0.044 2402 Dihedral : 18.048 140.783 2894 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.64 % Favored : 93.24 % Rotamer: Outliers : 2.35 % Allowed : 15.81 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1672 helix: 0.95 (0.19), residues: 858 sheet: -2.31 (0.43), residues: 134 loop : -2.30 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 798 HIS 0.005 0.001 HIS B 593 PHE 0.030 0.001 PHE B 842 TYR 0.013 0.001 TYR D 733 ARG 0.004 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.599 Fit side-chains REVERT: A 487 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7363 (mmmt) REVERT: A 674 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7600 (mp) REVERT: B 531 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7512 (mttp) REVERT: B 691 MET cc_start: 0.7710 (ttp) cc_final: 0.7440 (ttp) REVERT: C 568 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7666 (tt) REVERT: C 603 GLU cc_start: 0.7254 (mt-10) cc_final: 0.7023 (mt-10) REVERT: C 670 SER cc_start: 0.8342 (t) cc_final: 0.8116 (m) REVERT: D 531 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7239 (mttm) REVERT: D 644 THR cc_start: 0.8480 (m) cc_final: 0.7899 (p) REVERT: D 719 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7510 (mptt) REVERT: D 746 THR cc_start: 0.7989 (m) cc_final: 0.7588 (p) REVERT: D 793 MET cc_start: 0.7717 (mmm) cc_final: 0.7455 (mmm) outliers start: 34 outliers final: 21 residues processed: 185 average time/residue: 0.2683 time to fit residues: 72.5376 Evaluate side-chains 175 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 chunk 48 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14784 Z= 0.174 Angle : 0.876 27.937 19894 Z= 0.359 Chirality : 0.044 0.511 2158 Planarity : 0.004 0.044 2402 Dihedral : 17.727 140.944 2894 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.30 % Favored : 92.58 % Rotamer: Outliers : 2.56 % Allowed : 15.40 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1672 helix: 1.19 (0.19), residues: 852 sheet: -2.02 (0.43), residues: 140 loop : -2.19 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 798 HIS 0.004 0.001 HIS D 593 PHE 0.026 0.001 PHE D 842 TYR 0.016 0.001 TYR D 478 ARG 0.005 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.561 Fit side-chains REVERT: B 531 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7499 (mttp) REVERT: B 691 MET cc_start: 0.7708 (ttp) cc_final: 0.7420 (ttp) REVERT: C 568 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7673 (tt) REVERT: C 603 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6985 (mt-10) REVERT: C 670 SER cc_start: 0.8357 (t) cc_final: 0.8132 (m) REVERT: D 479 GLU cc_start: 0.5211 (tp30) cc_final: 0.4592 (mp0) REVERT: D 531 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7305 (mttm) REVERT: D 719 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7472 (mptt) outliers start: 37 outliers final: 25 residues processed: 187 average time/residue: 0.2644 time to fit residues: 73.1408 Evaluate side-chains 181 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN B 754 GLN ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14784 Z= 0.288 Angle : 0.914 27.840 19894 Z= 0.381 Chirality : 0.046 0.459 2158 Planarity : 0.005 0.046 2402 Dihedral : 17.795 140.872 2894 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.55 % Favored : 91.33 % Rotamer: Outliers : 2.56 % Allowed : 15.61 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1672 helix: 1.09 (0.19), residues: 840 sheet: -2.06 (0.43), residues: 140 loop : -2.19 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 798 HIS 0.005 0.001 HIS B 593 PHE 0.026 0.002 PHE D 842 TYR 0.020 0.002 TYR D 478 ARG 0.006 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 1.433 Fit side-chains REVERT: A 568 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7639 (tt) REVERT: A 817 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8675 (t) REVERT: B 531 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7700 (mttp) REVERT: B 691 MET cc_start: 0.7736 (ttp) cc_final: 0.7439 (ttp) REVERT: C 568 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7747 (tt) REVERT: C 603 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6950 (mt-10) REVERT: C 670 SER cc_start: 0.8455 (t) cc_final: 0.8147 (m) REVERT: D 479 GLU cc_start: 0.5215 (tp30) cc_final: 0.4649 (mp0) REVERT: D 531 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7670 (mttp) outliers start: 37 outliers final: 27 residues processed: 184 average time/residue: 0.2590 time to fit residues: 69.8627 Evaluate side-chains 183 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14784 Z= 0.219 Angle : 0.894 27.878 19894 Z= 0.369 Chirality : 0.046 0.729 2158 Planarity : 0.004 0.045 2402 Dihedral : 17.574 140.827 2894 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.83 % Favored : 92.05 % Rotamer: Outliers : 2.56 % Allowed : 15.61 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1672 helix: 1.25 (0.19), residues: 840 sheet: -2.07 (0.43), residues: 140 loop : -2.17 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 798 HIS 0.004 0.001 HIS B 593 PHE 0.024 0.001 PHE D 842 TYR 0.018 0.001 TYR D 478 ARG 0.009 0.000 ARG C 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 1.623 Fit side-chains REVERT: A 568 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7642 (tt) REVERT: A 817 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8664 (t) REVERT: B 531 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7604 (mttp) REVERT: B 691 MET cc_start: 0.7731 (ttp) cc_final: 0.7439 (ttp) REVERT: C 568 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7711 (tt) REVERT: C 670 SER cc_start: 0.8411 (t) cc_final: 0.8114 (m) REVERT: D 457 ASP cc_start: 0.7621 (t0) cc_final: 0.7312 (t70) REVERT: D 479 GLU cc_start: 0.5304 (tp30) cc_final: 0.4703 (mp0) REVERT: D 531 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7517 (mttp) outliers start: 37 outliers final: 26 residues processed: 182 average time/residue: 0.2666 time to fit residues: 71.7867 Evaluate side-chains 183 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 669 ASP Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 0.0370 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.129120 restraints weight = 15733.231| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.29 r_work: 0.3236 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14784 Z= 0.210 Angle : 0.889 27.909 19894 Z= 0.366 Chirality : 0.045 0.577 2158 Planarity : 0.004 0.045 2402 Dihedral : 17.266 140.864 2894 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.25 % Favored : 91.63 % Rotamer: Outliers : 2.56 % Allowed : 15.54 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1672 helix: 1.32 (0.19), residues: 844 sheet: -1.98 (0.43), residues: 136 loop : -2.18 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 798 HIS 0.004 0.001 HIS D 593 PHE 0.024 0.001 PHE D 842 TYR 0.016 0.001 TYR B 733 ARG 0.008 0.000 ARG C 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.67 seconds wall clock time: 56 minutes 34.56 seconds (3394.56 seconds total)