Starting phenix.real_space_refine on Fri Feb 16 05:19:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/02_2024/8fww_29521_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/02_2024/8fww_29521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/02_2024/8fww_29521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/02_2024/8fww_29521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/02_2024/8fww_29521_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/02_2024/8fww_29521_updated.pdb" } resolution = 3.1 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= 0.034 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 7 4.78 5 C 9478 2.51 5 N 2196 2.21 5 O 2688 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 ARG 503": "NH1" <-> "NH2" 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 800": "NH1" <-> "NH2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "C ARG 503": "NH1" <-> "NH2" 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 800": "NH1" <-> "NH2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 503": "NH1" <-> "NH2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14471 Number of models: 1 Model: "" Number of chains: 14 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: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 338 Unusual residues: {' CL': 1, ' NA': 4, '2J9': 2, '6ZP': 1, 'NAG': 1, 'POV': 5} Classifications: {'undetermined': 14} Link IDs: {None: 13} 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: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 189 Unusual residues: {' NA': 1, '2J9': 2, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 251 Unusual residues: {' CL': 1, ' NA': 1, '6ZP': 1, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 209 Unusual residues: {' NA': 1, 'POV': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 8.68, per 1000 atoms: 0.60 Number of scatterers: 14471 At special positions: 0 Unit cell: (87.36, 131.456, 138.944, 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 7 11.00 F 4 9.00 O 2688 8.00 N 2196 7.00 C 9478 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=2.14 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=1.92 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 A1005 " - " ASN A 751 " " NAG C1004 " - " 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: 6.48 Conformation dependent library (CDL) restraints added in 2.7 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: 58 helices and 12 sheets defined 43.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.787A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.607A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) 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 557 removed outlier: 3.688A pdb=" N ASN A 557 " --> pdb=" O SER A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 557' Processing helix chain 'A' and resid 561 through 584 removed outlier: 3.685A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 583 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 619 removed outlier: 3.575A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 664 removed outlier: 3.850A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.605A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 711 removed outlier: 3.592A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 730 removed outlier: 3.510A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.700A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 787 Processing helix chain 'A' and resid 790 through 799 removed outlier: 3.758A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 849 removed outlier: 3.583A pdb=" N LYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 473 removed outlier: 3.623A pdb=" N LEU B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 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 583 removed outlier: 3.656A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 619 Processing helix chain 'B' and resid 631 through 658 removed outlier: 3.886A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.705A 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: 3.704A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 711 removed outlier: 3.603A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 729 removed outlier: 3.547A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 747 removed outlier: 4.014A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 788 removed outlier: 3.545A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 798 Processing helix chain 'B' and resid 823 through 849 removed outlier: 3.556A pdb=" N LEU B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 472 removed outlier: 3.787A pdb=" N LEU C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.608A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) 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 557 removed outlier: 3.687A pdb=" N ASN C 557 " --> pdb=" O SER C 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 554 through 557' Processing helix chain 'C' and resid 561 through 584 removed outlier: 3.686A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 583 " --> pdb=" O PHE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 619 removed outlier: 3.575A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 664 removed outlier: 3.849A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 689 through 695 removed outlier: 3.604A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 711 removed outlier: 3.592A pdb=" N MET C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 730 removed outlier: 3.511A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 748 removed outlier: 3.700A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 787 Processing helix chain 'C' and resid 790 through 799 removed outlier: 3.758A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 849 removed outlier: 3.584A pdb=" N LYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 473 removed outlier: 3.622A pdb=" N LEU D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 506 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 583 removed outlier: 3.656A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 619 Processing helix chain 'D' and resid 631 through 658 removed outlier: 3.887A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 676 removed outlier: 3.705A 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: 3.704A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 711 removed outlier: 3.602A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 729 removed outlier: 3.546A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 747 removed outlier: 4.013A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 788 removed outlier: 3.545A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 798 Processing helix chain 'D' and resid 823 through 849 removed outlier: 3.554A pdb=" N LEU D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 433 through 437 removed outlier: 3.555A 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: 3.967A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 736 through 738 removed outlier: 4.060A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 432 through 435 removed outlier: 6.592A pdb=" N THR B 477 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 435 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU B 479 " --> pdb=" O VAL B 435 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 534 through 536 removed outlier: 3.969A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 735 through 738 Processing sheet with id= G, first strand: chain 'C' and resid 433 through 437 removed outlier: 3.555A pdb=" N THR C 437 " --> pdb=" O ARG C 481 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.967A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 736 through 738 removed outlier: 4.060A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 432 through 435 removed outlier: 6.592A pdb=" N THR D 477 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL D 435 " --> pdb=" O THR D 477 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU D 479 " --> pdb=" O VAL D 435 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 534 through 536 removed outlier: 3.969A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 735 through 738 478 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: 3.93 Time building geometry restraints manager: 6.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2226 1.28 - 1.41: 3591 1.41 - 1.55: 8495 1.55 - 1.68: 324 1.68 - 1.82: 132 Bond restraints: 14768 Sorted by residual: bond pdb=" OAA 2J9 A1001 " pdb=" SAP 2J9 A1001 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAA 2J9 A1009 " pdb=" SAP 2J9 A1009 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" OAA 2J9 B1004 " pdb=" SAP 2J9 B1004 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" OAA 2J9 B1001 " pdb=" SAP 2J9 B1001 " ideal model delta sigma weight residual 1.452 1.651 -0.199 2.00e-02 2.50e+03 9.95e+01 bond pdb=" OAB 2J9 A1009 " pdb=" SAP 2J9 A1009 " ideal model delta sigma weight residual 1.452 1.647 -0.195 2.00e-02 2.50e+03 9.55e+01 ... (remaining 14763 not shown) Histogram of bond angle deviations from ideal: 59.79 - 82.99: 12 82.99 - 106.20: 391 106.20 - 129.40: 19355 129.40 - 152.60: 104 152.60 - 175.80: 2 Bond angle restraints: 19864 Sorted by residual: angle pdb=" CAH 2J9 B1001 " pdb=" CAN 2J9 B1001 " pdb=" NAO 2J9 B1001 " ideal model delta sigma weight residual 117.67 150.47 -32.80 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CAH 2J9 A1009 " pdb=" CAN 2J9 A1009 " pdb=" NAO 2J9 A1009 " ideal model delta sigma weight residual 117.67 150.29 -32.62 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CAG 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 118.82 150.78 -31.96 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CAG 2J9 B1004 " pdb=" CAN 2J9 B1004 " pdb=" NAO 2J9 B1004 " ideal model delta sigma weight residual 118.82 150.59 -31.77 3.00e+00 1.11e-01 1.12e+02 angle pdb=" CAH 2J9 B1004 " pdb=" CAN 2J9 B1004 " pdb=" NAO 2J9 B1004 " ideal model delta sigma weight residual 117.67 149.36 -31.69 3.00e+00 1.11e-01 1.12e+02 ... (remaining 19859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 8569 30.70 - 61.40: 467 61.40 - 92.09: 97 92.09 - 122.79: 39 122.79 - 153.49: 6 Dihedral angle restraints: 9178 sinusoidal: 4338 harmonic: 4840 Sorted by residual: dihedral pdb=" CB CYS D 750 " pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " pdb=" CB CYS D 804 " ideal model delta sinusoidal sigma weight residual 93.00 176.48 -83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS B 750 " pdb=" SG CYS B 750 " pdb=" SG CYS B 804 " pdb=" CB CYS B 804 " ideal model delta sinusoidal sigma weight residual 93.00 176.43 -83.43 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS C 750 " pdb=" SG CYS C 750 " pdb=" SG CYS C 804 " pdb=" CB CYS C 804 " ideal model delta sinusoidal sigma weight residual 93.00 157.23 -64.23 1 1.00e+01 1.00e-02 5.43e+01 ... (remaining 9175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.463: 2154 0.463 - 0.926: 0 0.926 - 1.390: 0 1.390 - 1.853: 0 1.853 - 2.316: 4 Chirality restraints: 2158 Sorted by residual: chirality pdb=" CAN 2J9 B1001 " pdb=" CAG 2J9 B1001 " pdb=" CAH 2J9 B1001 " pdb=" NAO 2J9 B1001 " both_signs ideal model delta sigma weight residual True 2.32 0.00 2.32 2.00e-01 2.50e+01 1.34e+02 chirality pdb=" CAN 2J9 A1009 " pdb=" CAG 2J9 A1009 " pdb=" CAH 2J9 A1009 " pdb=" NAO 2J9 A1009 " both_signs ideal model delta sigma weight residual True 2.32 -0.01 2.31 2.00e-01 2.50e+01 1.33e+02 chirality pdb=" CAN 2J9 B1004 " pdb=" CAG 2J9 B1004 " pdb=" CAH 2J9 B1004 " pdb=" NAO 2J9 B1004 " both_signs ideal model delta sigma weight residual True 2.32 -0.03 2.29 2.00e-01 2.50e+01 1.31e+02 ... (remaining 2155 not shown) Planarity restraints: 2406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 553 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C PHE B 553 " -0.047 2.00e-02 2.50e+03 pdb=" O PHE B 553 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B 554 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 553 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C PHE D 553 " -0.047 2.00e-02 2.50e+03 pdb=" O PHE D 553 " 0.018 2.00e-02 2.50e+03 pdb=" N SER D 554 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 716 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C VAL C 716 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL C 716 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU C 717 " -0.014 2.00e-02 2.50e+03 ... (remaining 2403 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1808 2.74 - 3.28: 12874 3.28 - 3.82: 22709 3.82 - 4.36: 28920 4.36 - 4.90: 49006 Nonbonded interactions: 115317 Sorted by model distance: nonbonded pdb=" OG SER A 834 " pdb=" O SER D 632 " model vdw 2.206 2.440 nonbonded pdb=" NH2 ARG D 543 " pdb=" O LEU D 729 " model vdw 2.249 2.520 nonbonded pdb=" NH2 ARG B 543 " pdb=" O LEU B 729 " model vdw 2.250 2.520 nonbonded pdb=" OG SER A 585 " pdb=" OE1 GLU B 841 " model vdw 2.263 2.440 nonbonded pdb=" NH2 ARG B 634 " pdb=" OE2 GLU C 625 " model vdw 2.278 2.520 ... (remaining 115312 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 1002 through 1003)) selection = (chain 'B' and (resid 431 through 850 or resid 1002 through 1003)) selection = (chain 'C' and (resid 431 through 850 or resid 1002 through 1003)) selection = (chain 'D' and (resid 431 through 850 or resid 1002 through 1003)) } 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: 3.120 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: 0.220 Set scattering table: 0.150 Process input model: 43.850 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.290 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:3.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.013 0.202 14768 Z= 0.773 Angle : 1.645 32.801 19864 Z= 0.759 Chirality : 0.118 2.316 2158 Planarity : 0.007 0.054 2398 Dihedral : 20.284 153.489 6064 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 1.17 % Allowed : 3.66 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -5.95 (0.13), residues: 1672 helix: -4.16 (0.09), residues: 842 sheet: -3.04 (0.36), residues: 150 loop : -3.68 (0.17), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 799 HIS 0.003 0.001 HIS A 508 PHE 0.037 0.003 PHE D 584 TYR 0.024 0.003 TYR C 733 ARG 0.017 0.002 ARG D 543 *********************** 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 298 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 281 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7012 (tt0) cc_final: 0.6686 (tt0) REVERT: A 487 LYS cc_start: 0.8323 (mtpp) cc_final: 0.8032 (mttt) REVERT: A 531 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7381 (ttmm) REVERT: A 629 LYS cc_start: 0.7826 (ttmp) cc_final: 0.6784 (tptp) REVERT: A 691 MET cc_start: 0.7048 (ptm) cc_final: 0.6318 (ptt) REVERT: A 695 LYS cc_start: 0.6854 (mttt) cc_final: 0.6486 (mtpt) REVERT: A 780 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7152 (mt) REVERT: B 499 ASN cc_start: 0.6914 (m-40) cc_final: 0.6566 (m-40) REVERT: B 509 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7523 (mtmt) REVERT: B 719 LYS cc_start: 0.8335 (pttp) cc_final: 0.7878 (mttp) REVERT: B 722 GLU cc_start: 0.7173 (tp30) cc_final: 0.6890 (tp30) REVERT: B 762 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7979 (mttt) REVERT: B 793 MET cc_start: 0.7149 (mtm) cc_final: 0.6707 (mmm) REVERT: B 797 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7680 (ttpp) REVERT: C 479 GLU cc_start: 0.7987 (tt0) cc_final: 0.7648 (tp30) REVERT: C 487 LYS cc_start: 0.8474 (mtpp) cc_final: 0.7856 (mttt) REVERT: C 531 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7331 (ttmm) REVERT: C 780 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.7020 (mt) REVERT: D 509 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7767 (mttt) REVERT: D 566 TYR cc_start: 0.7796 (m-10) cc_final: 0.7563 (m-80) REVERT: D 662 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7154 (mp0) REVERT: D 719 LYS cc_start: 0.8204 (pttp) cc_final: 0.7763 (mttp) REVERT: D 720 SER cc_start: 0.8186 (t) cc_final: 0.7589 (p) REVERT: D 722 GLU cc_start: 0.7486 (tp30) cc_final: 0.7285 (tp30) REVERT: D 762 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8057 (mttt) REVERT: D 784 GLN cc_start: 0.7586 (tt0) cc_final: 0.7171 (tm-30) REVERT: D 793 MET cc_start: 0.7129 (mtm) cc_final: 0.6572 (mmm) REVERT: D 797 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7932 (ttpt) outliers start: 17 outliers final: 5 residues processed: 295 average time/residue: 0.2992 time to fit residues: 125.1875 Evaluate side-chains 201 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 552 VAL 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: 3.9990 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.0070 chunk 43 optimal weight: 0.0980 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN A 557 ASN A 605 ASN A 849 ASN B 456 ASN B 621 GLN B 622 GLN B 754 GLN B 849 ASN C 557 ASN C 605 ASN C 621 GLN C 849 ASN D 456 ASN D 604 ASN D 621 GLN D 754 GLN D 849 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14768 Z= 0.211 Angle : 0.707 9.669 19864 Z= 0.335 Chirality : 0.044 0.214 2158 Planarity : 0.005 0.041 2398 Dihedral : 22.777 148.012 2945 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.93 % Allowed : 7.94 % Favored : 90.12 % 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: -4.04 (0.16), residues: 1672 helix: -2.13 (0.14), residues: 864 sheet: -2.70 (0.38), residues: 150 loop : -3.31 (0.19), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 706 HIS 0.001 0.000 HIS A 792 PHE 0.020 0.002 PHE C 579 TYR 0.023 0.002 TYR D 590 ARG 0.005 0.001 ARG B 663 *********************** 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 229 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8316 (mtpp) cc_final: 0.7936 (mttt) REVERT: A 531 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7828 (mttp) REVERT: A 629 LYS cc_start: 0.7904 (ttmp) cc_final: 0.6774 (tptp) REVERT: A 723 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.5999 (tp30) REVERT: B 499 ASN cc_start: 0.6739 (m-40) cc_final: 0.6437 (m-40) REVERT: B 509 LYS cc_start: 0.7935 (mtpp) cc_final: 0.7461 (mtmt) REVERT: B 565 MET cc_start: 0.7828 (ttm) cc_final: 0.7607 (ttm) REVERT: B 620 MET cc_start: 0.8410 (mmt) cc_final: 0.7425 (mmt) REVERT: B 669 ASP cc_start: 0.7804 (t0) cc_final: 0.7318 (t0) REVERT: B 719 LYS cc_start: 0.8291 (pttp) cc_final: 0.7826 (mttp) REVERT: B 722 GLU cc_start: 0.6953 (tp30) cc_final: 0.6604 (tp30) REVERT: B 762 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7498 (mttt) REVERT: B 793 MET cc_start: 0.6821 (mtm) cc_final: 0.6285 (mmm) REVERT: B 796 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7137 (mm-30) REVERT: B 798 TRP cc_start: 0.7612 (m100) cc_final: 0.6666 (m100) REVERT: C 487 LYS cc_start: 0.8472 (mtpp) cc_final: 0.7865 (mttt) REVERT: C 531 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7527 (mmtp) REVERT: C 665 GLU cc_start: 0.6328 (pt0) cc_final: 0.6036 (mt-10) REVERT: D 509 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7821 (mtmt) REVERT: D 566 TYR cc_start: 0.7506 (m-10) cc_final: 0.7244 (m-80) REVERT: D 669 ASP cc_start: 0.7776 (t0) cc_final: 0.7468 (t0) REVERT: D 698 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8572 (mttp) REVERT: D 719 LYS cc_start: 0.8167 (pttp) cc_final: 0.7696 (mttp) REVERT: D 722 GLU cc_start: 0.7269 (tp30) cc_final: 0.7021 (tp30) REVERT: D 793 MET cc_start: 0.6960 (mtm) cc_final: 0.6274 (mmm) REVERT: D 796 GLU cc_start: 0.7248 (mm-30) cc_final: 0.7039 (mm-30) REVERT: D 797 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7953 (ttpt) outliers start: 28 outliers final: 14 residues processed: 225 average time/residue: 0.2762 time to fit residues: 90.3797 Evaluate side-chains 195 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 698 LYS Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 0.0870 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 784 GLN D 786 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14768 Z= 0.294 Angle : 0.683 10.468 19864 Z= 0.323 Chirality : 0.045 0.230 2158 Planarity : 0.004 0.042 2398 Dihedral : 21.228 144.382 2934 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.90 % Allowed : 10.22 % Favored : 86.88 % 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: -2.80 (0.19), residues: 1672 helix: -0.79 (0.17), residues: 862 sheet: -2.67 (0.38), residues: 150 loop : -3.08 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 706 HIS 0.002 0.001 HIS C 508 PHE 0.019 0.002 PHE A 735 TYR 0.022 0.002 TYR B 844 ARG 0.005 0.000 ARG C 481 *********************** 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 217 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6290 (ttp-170) REVERT: A 487 LYS cc_start: 0.8459 (mtpp) cc_final: 0.7951 (mttt) REVERT: A 629 LYS cc_start: 0.8061 (ttmp) cc_final: 0.6854 (tptp) REVERT: A 691 MET cc_start: 0.7031 (ptm) cc_final: 0.6421 (ptt) REVERT: A 723 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6112 (tp30) REVERT: A 780 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6345 (mp) REVERT: B 499 ASN cc_start: 0.6717 (m-40) cc_final: 0.6495 (m-40) REVERT: B 509 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7503 (mttt) REVERT: B 669 ASP cc_start: 0.7853 (t0) cc_final: 0.7463 (t0) REVERT: B 719 LYS cc_start: 0.8272 (pttp) cc_final: 0.7836 (mttp) REVERT: B 722 GLU cc_start: 0.6996 (tp30) cc_final: 0.6616 (tp30) REVERT: B 798 TRP cc_start: 0.7612 (m100) cc_final: 0.6592 (m100) REVERT: C 487 LYS cc_start: 0.8493 (mtpp) cc_final: 0.7843 (mttt) REVERT: C 665 GLU cc_start: 0.6426 (pt0) cc_final: 0.6113 (mt-10) REVERT: C 695 LYS cc_start: 0.6583 (mttt) cc_final: 0.6215 (mtpt) REVERT: C 780 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6285 (mp) REVERT: D 509 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7726 (mtmt) REVERT: D 669 ASP cc_start: 0.7903 (t0) cc_final: 0.7523 (t0) REVERT: D 682 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.7281 (m-10) REVERT: D 719 LYS cc_start: 0.8248 (pttp) cc_final: 0.7837 (mttp) REVERT: D 722 GLU cc_start: 0.7238 (tp30) cc_final: 0.6871 (tp30) REVERT: D 797 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7875 (ttpt) outliers start: 42 outliers final: 26 residues processed: 211 average time/residue: 0.2638 time to fit residues: 82.5209 Evaluate side-chains 198 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.0030 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 GLN A 792 HIS C 621 GLN C 754 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14768 Z= 0.185 Angle : 0.606 8.904 19864 Z= 0.281 Chirality : 0.043 0.249 2158 Planarity : 0.004 0.039 2398 Dihedral : 19.608 142.427 2926 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.11 % Allowed : 11.40 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.92 (0.20), residues: 1672 helix: 0.11 (0.18), residues: 860 sheet: -2.54 (0.38), residues: 152 loop : -2.86 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 706 HIS 0.002 0.000 HIS A 792 PHE 0.016 0.001 PHE D 584 TYR 0.021 0.001 TYR B 844 ARG 0.003 0.000 ARG A 481 *********************** 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 226 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 1.619 Fit side-chains REVERT: A 468 ARG cc_start: 0.7214 (ttm110) cc_final: 0.6295 (ttp-170) REVERT: A 487 LYS cc_start: 0.8401 (mtpp) cc_final: 0.7892 (mttt) REVERT: A 691 MET cc_start: 0.7035 (ptm) cc_final: 0.6468 (ptt) REVERT: A 695 LYS cc_start: 0.6468 (mttt) cc_final: 0.6156 (mtpp) REVERT: A 723 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.5997 (tp30) REVERT: A 780 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6293 (mp) REVERT: B 509 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7461 (mttt) REVERT: B 565 MET cc_start: 0.7790 (ttm) cc_final: 0.7585 (ttm) REVERT: B 620 MET cc_start: 0.8326 (mmt) cc_final: 0.7574 (mmt) REVERT: B 669 ASP cc_start: 0.7745 (t0) cc_final: 0.7331 (t0) REVERT: B 719 LYS cc_start: 0.8201 (pttp) cc_final: 0.7810 (mttp) REVERT: B 722 GLU cc_start: 0.7038 (tp30) cc_final: 0.6627 (tp30) REVERT: B 796 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6947 (mm-30) REVERT: B 797 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7494 (ttpp) REVERT: B 798 TRP cc_start: 0.7565 (m100) cc_final: 0.6466 (m100) REVERT: C 487 LYS cc_start: 0.8469 (mtpp) cc_final: 0.7832 (mttt) REVERT: C 665 GLU cc_start: 0.6333 (pt0) cc_final: 0.6064 (mt-10) REVERT: C 695 LYS cc_start: 0.6420 (mttt) cc_final: 0.6079 (mtpt) REVERT: C 780 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6230 (mp) REVERT: D 509 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7640 (mtmt) REVERT: D 620 MET cc_start: 0.8373 (mmt) cc_final: 0.7809 (mmt) REVERT: D 669 ASP cc_start: 0.7803 (t0) cc_final: 0.7419 (t0) REVERT: D 682 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.7038 (m-10) REVERT: D 719 LYS cc_start: 0.8200 (pttp) cc_final: 0.7775 (mttp) REVERT: D 722 GLU cc_start: 0.7172 (tp30) cc_final: 0.6785 (tp30) REVERT: D 797 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7722 (ttpt) outliers start: 45 outliers final: 25 residues processed: 218 average time/residue: 0.2494 time to fit residues: 81.0453 Evaluate side-chains 197 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.3980 chunk 92 optimal weight: 0.0270 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 138 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14768 Z= 0.178 Angle : 0.588 8.660 19864 Z= 0.273 Chirality : 0.042 0.248 2158 Planarity : 0.004 0.041 2398 Dihedral : 18.075 142.746 2924 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.18 % Allowed : 11.95 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1672 helix: 0.66 (0.19), residues: 860 sheet: -2.53 (0.38), residues: 144 loop : -2.69 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 706 HIS 0.001 0.000 HIS C 508 PHE 0.014 0.001 PHE D 584 TYR 0.022 0.001 TYR B 844 ARG 0.006 0.000 ARG A 481 *********************** 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 217 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7831 (mttt) REVERT: A 780 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6285 (mp) REVERT: A 836 PHE cc_start: 0.6375 (m-10) cc_final: 0.6168 (m-10) REVERT: B 499 ASN cc_start: 0.6763 (OUTLIER) cc_final: 0.6270 (p0) REVERT: B 509 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7501 (mtmt) REVERT: B 620 MET cc_start: 0.8329 (mmt) cc_final: 0.7596 (mmt) REVERT: B 719 LYS cc_start: 0.8178 (pttp) cc_final: 0.7787 (mttp) REVERT: B 722 GLU cc_start: 0.7013 (tp30) cc_final: 0.6599 (tp30) REVERT: B 796 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6864 (mm-30) REVERT: B 797 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7477 (ttpp) REVERT: B 798 TRP cc_start: 0.7487 (m100) cc_final: 0.6418 (m100) REVERT: C 487 LYS cc_start: 0.8419 (mtpp) cc_final: 0.7820 (mttt) REVERT: C 695 LYS cc_start: 0.6356 (mttt) cc_final: 0.6109 (mtpt) REVERT: C 780 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6259 (mp) REVERT: D 509 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7549 (mtmt) REVERT: D 620 MET cc_start: 0.8375 (mmt) cc_final: 0.7802 (mmt) REVERT: D 669 ASP cc_start: 0.7881 (t0) cc_final: 0.7475 (t0) REVERT: D 670 SER cc_start: 0.8243 (t) cc_final: 0.7937 (p) REVERT: D 682 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.7112 (m-10) REVERT: D 719 LYS cc_start: 0.8186 (pttp) cc_final: 0.7759 (mttp) REVERT: D 722 GLU cc_start: 0.7227 (tp30) cc_final: 0.6820 (tp30) outliers start: 46 outliers final: 30 residues processed: 207 average time/residue: 0.2513 time to fit residues: 78.2088 Evaluate side-chains 196 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 682 TYR Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14768 Z= 0.252 Angle : 0.613 10.028 19864 Z= 0.287 Chirality : 0.043 0.212 2158 Planarity : 0.004 0.038 2398 Dihedral : 17.553 143.035 2924 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.59 % Allowed : 11.95 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1672 helix: 0.72 (0.19), residues: 860 sheet: -2.30 (0.40), residues: 152 loop : -2.65 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 PHE 0.015 0.002 PHE D 584 TYR 0.022 0.002 TYR B 844 ARG 0.004 0.000 ARG A 468 *********************** 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 222 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 170 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: A 487 LYS cc_start: 0.8438 (mtpp) cc_final: 0.7871 (mttt) REVERT: A 605 ASN cc_start: 0.7644 (m110) cc_final: 0.7309 (m-40) REVERT: A 691 MET cc_start: 0.6994 (ptm) cc_final: 0.6418 (ptt) REVERT: A 695 LYS cc_start: 0.6488 (mttt) cc_final: 0.6224 (mtpp) REVERT: A 723 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6047 (tp30) REVERT: A 780 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6265 (mp) REVERT: A 836 PHE cc_start: 0.6359 (m-10) cc_final: 0.6156 (m-10) REVERT: B 509 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7439 (mtmt) REVERT: B 620 MET cc_start: 0.8365 (mmt) cc_final: 0.7655 (mmt) REVERT: B 669 ASP cc_start: 0.7702 (t0) cc_final: 0.7271 (t0) REVERT: B 719 LYS cc_start: 0.8207 (pttp) cc_final: 0.7816 (mttm) REVERT: B 722 GLU cc_start: 0.7142 (tp30) cc_final: 0.6697 (tp30) REVERT: C 487 LYS cc_start: 0.8437 (mtpp) cc_final: 0.7820 (mttt) REVERT: C 695 LYS cc_start: 0.6419 (mttt) cc_final: 0.6149 (mtpt) REVERT: C 780 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.6248 (mp) REVERT: D 509 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7437 (mttt) REVERT: D 620 MET cc_start: 0.8420 (mmt) cc_final: 0.7813 (mmt) REVERT: D 669 ASP cc_start: 0.7856 (t0) cc_final: 0.7443 (t0) REVERT: D 670 SER cc_start: 0.8350 (t) cc_final: 0.7978 (p) REVERT: D 719 LYS cc_start: 0.8256 (pttp) cc_final: 0.7874 (mttp) REVERT: D 722 GLU cc_start: 0.7262 (tp30) cc_final: 0.6848 (tp30) outliers start: 52 outliers final: 40 residues processed: 210 average time/residue: 0.2494 time to fit residues: 78.7249 Evaluate side-chains 208 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 118 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 101 optimal weight: 0.0270 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 792 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14768 Z= 0.191 Angle : 0.578 9.206 19864 Z= 0.269 Chirality : 0.041 0.172 2158 Planarity : 0.004 0.041 2398 Dihedral : 16.894 142.378 2924 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.38 % Allowed : 12.64 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1672 helix: 0.93 (0.19), residues: 860 sheet: -2.22 (0.40), residues: 142 loop : -2.56 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 PHE 0.013 0.001 PHE D 584 TYR 0.020 0.001 TYR B 844 ARG 0.004 0.000 ARG A 481 *********************** 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 220 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 171 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8419 (mtpp) cc_final: 0.7856 (mttt) REVERT: A 605 ASN cc_start: 0.7628 (m110) cc_final: 0.7299 (m-40) REVERT: A 691 MET cc_start: 0.6992 (ptm) cc_final: 0.6418 (ptt) REVERT: A 695 LYS cc_start: 0.6532 (mttt) cc_final: 0.6262 (mtpp) REVERT: A 723 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6040 (tp30) REVERT: A 780 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6265 (mp) REVERT: A 836 PHE cc_start: 0.6310 (m-10) cc_final: 0.6093 (m-10) REVERT: B 499 ASN cc_start: 0.6609 (OUTLIER) cc_final: 0.6314 (p0) REVERT: B 509 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7425 (mtmt) REVERT: B 620 MET cc_start: 0.8316 (mmt) cc_final: 0.7593 (mmt) REVERT: B 719 LYS cc_start: 0.8151 (pttp) cc_final: 0.7756 (mttm) REVERT: B 722 GLU cc_start: 0.7129 (tp30) cc_final: 0.6690 (tp30) REVERT: B 798 TRP cc_start: 0.7476 (m100) cc_final: 0.6485 (m100) REVERT: C 487 LYS cc_start: 0.8421 (mtpp) cc_final: 0.7857 (mttt) REVERT: C 605 ASN cc_start: 0.7684 (m110) cc_final: 0.7403 (m-40) REVERT: C 664 MET cc_start: 0.7803 (mtp) cc_final: 0.7516 (mtp) REVERT: C 695 LYS cc_start: 0.6374 (mttt) cc_final: 0.6110 (mtpt) REVERT: C 780 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6268 (mp) REVERT: D 509 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7549 (mttt) REVERT: D 620 MET cc_start: 0.8367 (mmt) cc_final: 0.7741 (mmt) REVERT: D 669 ASP cc_start: 0.7813 (t0) cc_final: 0.7373 (t0) REVERT: D 670 SER cc_start: 0.8272 (t) cc_final: 0.7977 (p) REVERT: D 719 LYS cc_start: 0.8217 (pttp) cc_final: 0.7851 (mttp) REVERT: D 722 GLU cc_start: 0.7254 (tp30) cc_final: 0.6821 (tp30) REVERT: D 743 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7070 (mt-10) outliers start: 49 outliers final: 38 residues processed: 209 average time/residue: 0.2412 time to fit residues: 76.7504 Evaluate side-chains 208 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.0060 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 0.0270 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14768 Z= 0.178 Angle : 0.568 9.239 19864 Z= 0.265 Chirality : 0.041 0.162 2158 Planarity : 0.003 0.037 2398 Dihedral : 16.464 142.498 2924 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.90 % Allowed : 12.98 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1672 helix: 0.98 (0.19), residues: 872 sheet: -2.34 (0.41), residues: 134 loop : -2.60 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 798 HIS 0.004 0.000 HIS C 792 PHE 0.014 0.001 PHE D 584 TYR 0.020 0.001 TYR B 844 ARG 0.005 0.000 ARG A 481 *********************** 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 209 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 1.586 Fit side-chains REVERT: A 487 LYS cc_start: 0.8425 (mtpp) cc_final: 0.7883 (mttt) REVERT: A 605 ASN cc_start: 0.7658 (m110) cc_final: 0.7338 (m-40) REVERT: A 691 MET cc_start: 0.7055 (ptm) cc_final: 0.6515 (ptt) REVERT: A 695 LYS cc_start: 0.6536 (mttt) cc_final: 0.6282 (mtpp) REVERT: A 723 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6009 (tp30) REVERT: A 780 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6269 (mp) REVERT: A 836 PHE cc_start: 0.6305 (m-10) cc_final: 0.6086 (m-10) REVERT: B 509 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7410 (mtmt) REVERT: B 620 MET cc_start: 0.8311 (mmt) cc_final: 0.7639 (mmt) REVERT: B 719 LYS cc_start: 0.8170 (pttp) cc_final: 0.7753 (mttm) REVERT: B 722 GLU cc_start: 0.7128 (tp30) cc_final: 0.6684 (tp30) REVERT: B 798 TRP cc_start: 0.7487 (m100) cc_final: 0.6516 (m100) REVERT: C 487 LYS cc_start: 0.8408 (mtpp) cc_final: 0.7833 (mttt) REVERT: C 605 ASN cc_start: 0.7674 (m110) cc_final: 0.7429 (m-40) REVERT: C 695 LYS cc_start: 0.6386 (mttt) cc_final: 0.6131 (mtpt) REVERT: C 780 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6246 (mp) REVERT: D 509 LYS cc_start: 0.8123 (mtpp) cc_final: 0.7568 (mttt) REVERT: D 620 MET cc_start: 0.8352 (mmt) cc_final: 0.7791 (mmt) REVERT: D 669 ASP cc_start: 0.7629 (t0) cc_final: 0.7115 (t0) REVERT: D 719 LYS cc_start: 0.8201 (pttp) cc_final: 0.7857 (mttp) REVERT: D 722 GLU cc_start: 0.7244 (tp30) cc_final: 0.6803 (tp30) REVERT: D 743 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7034 (mt-10) outliers start: 42 outliers final: 35 residues processed: 200 average time/residue: 0.2416 time to fit residues: 73.1358 Evaluate side-chains 205 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 772 SER 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: 0.3980 chunk 150 optimal weight: 0.2980 chunk 90 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 46 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 142 optimal weight: 0.0050 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 786 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14768 Z= 0.143 Angle : 0.549 8.570 19864 Z= 0.256 Chirality : 0.040 0.159 2158 Planarity : 0.003 0.039 2398 Dihedral : 16.026 142.154 2924 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.42 % Allowed : 13.54 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1672 helix: 1.19 (0.19), residues: 872 sheet: -2.33 (0.42), residues: 132 loop : -2.48 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 798 HIS 0.000 0.000 HIS C 792 PHE 0.012 0.001 PHE D 584 TYR 0.019 0.001 TYR B 844 ARG 0.007 0.000 ARG A 481 *********************** 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 216 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8395 (mtpp) cc_final: 0.7870 (mttt) REVERT: A 605 ASN cc_start: 0.7592 (m110) cc_final: 0.7362 (m110) REVERT: A 682 TYR cc_start: 0.6553 (m-10) cc_final: 0.6171 (m-10) REVERT: A 695 LYS cc_start: 0.6514 (mttt) cc_final: 0.6267 (mtpp) REVERT: A 723 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5970 (tp30) REVERT: A 780 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6224 (mp) REVERT: A 836 PHE cc_start: 0.6293 (m-10) cc_final: 0.6069 (m-10) REVERT: B 509 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7433 (mtmt) REVERT: B 620 MET cc_start: 0.8259 (mmt) cc_final: 0.7626 (mmt) REVERT: B 719 LYS cc_start: 0.8104 (pttp) cc_final: 0.7764 (mttm) REVERT: B 722 GLU cc_start: 0.7117 (tp30) cc_final: 0.6669 (tp30) REVERT: C 484 GLU cc_start: 0.6038 (mp0) cc_final: 0.5699 (mp0) REVERT: C 487 LYS cc_start: 0.8449 (mtpp) cc_final: 0.7871 (mttt) REVERT: C 605 ASN cc_start: 0.7659 (m110) cc_final: 0.7395 (m-40) REVERT: C 695 LYS cc_start: 0.6321 (mttt) cc_final: 0.6089 (mtpt) REVERT: C 780 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6251 (mp) REVERT: D 509 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7572 (mtmt) REVERT: D 620 MET cc_start: 0.8336 (mmt) cc_final: 0.7771 (mmt) REVERT: D 669 ASP cc_start: 0.7656 (t0) cc_final: 0.7131 (t0) REVERT: D 719 LYS cc_start: 0.8109 (pttp) cc_final: 0.7760 (mttp) REVERT: D 722 GLU cc_start: 0.7208 (tp30) cc_final: 0.6763 (tp30) outliers start: 35 outliers final: 28 residues processed: 209 average time/residue: 0.2443 time to fit residues: 76.9318 Evaluate side-chains 195 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 772 SER 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: 0.7980 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 0.0870 chunk 13 optimal weight: 0.0980 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14768 Z= 0.194 Angle : 0.570 9.429 19864 Z= 0.267 Chirality : 0.041 0.198 2158 Planarity : 0.004 0.040 2398 Dihedral : 15.960 142.758 2924 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.49 % Allowed : 13.40 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1672 helix: 1.16 (0.19), residues: 872 sheet: -2.15 (0.43), residues: 132 loop : -2.47 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 798 HIS 0.001 0.000 HIS C 792 PHE 0.014 0.001 PHE D 584 TYR 0.022 0.001 TYR B 844 ARG 0.007 0.000 ARG A 481 ********************** 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 205 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8429 (mtpp) cc_final: 0.7919 (mttt) REVERT: A 605 ASN cc_start: 0.7606 (m110) cc_final: 0.7333 (m-40) REVERT: A 695 LYS cc_start: 0.6532 (mttt) cc_final: 0.6293 (mtpp) REVERT: A 723 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.5993 (tp30) REVERT: A 780 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6261 (mp) REVERT: A 836 PHE cc_start: 0.6308 (m-10) cc_final: 0.6086 (m-10) REVERT: B 509 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7421 (mtmt) REVERT: B 620 MET cc_start: 0.8306 (mmt) cc_final: 0.7545 (mmt) REVERT: B 622 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.6287 (mp10) REVERT: B 669 ASP cc_start: 0.7521 (t0) cc_final: 0.7113 (t0) REVERT: B 719 LYS cc_start: 0.8172 (pttp) cc_final: 0.7823 (mttp) REVERT: B 722 GLU cc_start: 0.7155 (tp30) cc_final: 0.6690 (tp30) REVERT: C 484 GLU cc_start: 0.6046 (mp0) cc_final: 0.5700 (mp0) REVERT: C 487 LYS cc_start: 0.8438 (mtpp) cc_final: 0.7890 (mttt) REVERT: C 605 ASN cc_start: 0.7655 (m110) cc_final: 0.7406 (m-40) REVERT: C 695 LYS cc_start: 0.6371 (mttt) cc_final: 0.6130 (mtpt) REVERT: C 780 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.6288 (mp) REVERT: D 499 ASN cc_start: 0.6793 (OUTLIER) cc_final: 0.6166 (p0) REVERT: D 509 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7558 (mtmt) REVERT: D 620 MET cc_start: 0.8371 (mmt) cc_final: 0.7734 (mmt) REVERT: D 669 ASP cc_start: 0.7728 (t0) cc_final: 0.7191 (t0) REVERT: D 719 LYS cc_start: 0.8196 (pttp) cc_final: 0.7874 (mttp) REVERT: D 722 GLU cc_start: 0.7252 (tp30) cc_final: 0.6799 (tp30) REVERT: D 778 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7100 (pt) outliers start: 36 outliers final: 27 residues processed: 197 average time/residue: 0.2429 time to fit residues: 72.4390 Evaluate side-chains 201 residues out of total 1448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 778 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.187317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144472 restraints weight = 14470.349| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.13 r_work: 0.3350 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14768 Z= 0.194 Angle : 0.565 9.521 19864 Z= 0.265 Chirality : 0.041 0.163 2158 Planarity : 0.004 0.042 2398 Dihedral : 15.730 142.493 2924 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.35 % Allowed : 13.67 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1672 helix: 1.19 (0.19), residues: 874 sheet: -2.14 (0.42), residues: 134 loop : -2.45 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 PHE 0.019 0.001 PHE D 579 TYR 0.022 0.001 TYR B 590 ARG 0.007 0.000 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3535.62 seconds wall clock time: 64 minutes 35.28 seconds (3875.28 seconds total)