Starting phenix.real_space_refine on Mon Nov 18 01:36:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/11_2024/8fww_29521.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/11_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_29521/11_2024/8fww_29521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/11_2024/8fww_29521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/11_2024/8fww_29521.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fww_29521/11_2024/8fww_29521.cif" } 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. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.76, per 1000 atoms: 0.74 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 4.48 Conformation dependent library (CDL) restraints added in 2.0 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... Secondary structure from input PDB file: 58 helices and 20 sheets defined 50.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.787A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.538A pdb=" N ARG A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.615A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.585A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) 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 553 through 557' Processing helix chain 'A' and resid 560 through 585 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 607 through 620 removed outlier: 3.575A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 665 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 671 through 677 Processing helix chain 'A' and resid 688 through 696 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 699 through 712 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 720 through 731 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 749 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 774 through 788 Processing helix chain 'A' and resid 789 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 821 through 850 removed outlier: 3.676A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.623A pdb=" N LEU B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.547A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 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) removed outlier: 3.690A pdb=" N PHE B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 630 through 659 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 671 through 677 removed outlier: 3.705A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 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 699 through 712 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 720 through 730 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 746 Processing helix chain 'B' and resid 774 through 789 removed outlier: 3.545A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 822 through 850 removed outlier: 3.556A pdb=" N LEU B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 473 removed outlier: 3.787A pdb=" N LEU C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.539A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.615A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.585A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) 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 553 through 557' Processing helix chain 'C' and resid 560 through 585 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 607 through 620 removed outlier: 3.575A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET C 620 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 665 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 671 through 677 Processing helix chain 'C' and resid 688 through 696 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 699 through 712 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 720 through 731 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 749 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 774 through 788 Processing helix chain 'C' and resid 789 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 821 through 850 removed outlier: 3.676A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.622A pdb=" N LEU D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.547A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 584 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) removed outlier: 3.690A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 630 through 659 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 671 through 677 removed outlier: 3.705A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 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 699 through 712 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 720 through 730 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 746 Processing helix chain 'D' and resid 774 through 789 removed outlier: 3.545A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 Processing helix chain 'D' and resid 822 through 850 removed outlier: 3.554A pdb=" N LEU D 833 " --> pdb=" O ALA D 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 437 removed outlier: 6.641A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA3, 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=AA4, 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=AA5, first strand: chain 'B' and resid 432 through 435 removed outlier: 6.435A pdb=" N LEU B 433 " --> pdb=" O GLU B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA7, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AA8, 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=AA9, first strand: chain 'B' and resid 735 through 738 Processing sheet with id=AB1, first strand: chain 'B' and resid 684 through 685 removed outlier: 5.593A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 433 through 437 removed outlier: 6.641A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AB4, 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=AB5, 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=AB6, first strand: chain 'D' and resid 432 through 435 removed outlier: 6.434A pdb=" N LEU D 433 " --> pdb=" O GLU D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AB9, 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=AC1, first strand: chain 'D' and resid 735 through 738 Processing sheet with id=AC2, first strand: chain 'D' and resid 684 through 685 removed outlier: 5.594A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 572 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 4.99 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: 0.00 - 6.56: 19676 6.56 - 13.12: 177 13.12 - 19.68: 3 19.68 - 26.24: 0 26.24 - 32.80: 8 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: 1802 2.74 - 3.28: 12806 3.28 - 3.82: 22623 3.82 - 4.36: 28730 4.36 - 4.90: 48980 Nonbonded interactions: 114941 Sorted by model distance: nonbonded pdb=" OG SER A 834 " pdb=" O SER D 632 " model vdw 2.206 3.040 nonbonded pdb=" NH2 ARG D 543 " pdb=" O LEU D 729 " model vdw 2.249 3.120 nonbonded pdb=" NH2 ARG B 543 " pdb=" O LEU B 729 " model vdw 2.250 3.120 nonbonded pdb=" OG SER A 585 " pdb=" OE1 GLU B 841 " model vdw 2.263 3.040 nonbonded pdb=" NH2 ARG B 634 " pdb=" OE2 GLU C 625 " model vdw 2.278 3.120 ... (remaining 114936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.660 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.910 ------------------------------------------------------------------------------- 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= 0.789 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 to be fit. rotamer outliers: 17 poor density : 281 time to evaluate : 1.475 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: 0.3009 time to fit residues: 126.3324 Evaluate side-chains 201 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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: 1.9990 chunk 70 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 849 ASN B 456 ASN B 621 GLN ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN C 557 ASN C 621 GLN C 792 HIS C 849 ASN D 456 ASN D 604 ASN D 621 GLN D 849 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14768 Z= 0.241 Angle : 0.747 10.221 19864 Z= 0.356 Chirality : 0.046 0.218 2158 Planarity : 0.005 0.049 2398 Dihedral : 22.578 148.741 2945 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.07 % Allowed : 8.08 % Favored : 89.85 % 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: -3.83 (0.17), residues: 1672 helix: -1.86 (0.14), residues: 852 sheet: -2.70 (0.39), residues: 150 loop : -3.31 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 706 HIS 0.002 0.000 HIS A 792 PHE 0.020 0.002 PHE C 579 TYR 0.024 0.002 TYR D 590 ARG 0.006 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 234 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8367 (mtpp) cc_final: 0.7973 (mttt) REVERT: A 531 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7747 (mmtp) REVERT: A 629 LYS cc_start: 0.7911 (ttmp) cc_final: 0.6804 (tptp) REVERT: A 691 MET cc_start: 0.6790 (ptm) cc_final: 0.6227 (ptt) REVERT: B 499 ASN cc_start: 0.7147 (m-40) cc_final: 0.6863 (m-40) REVERT: B 509 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7437 (mttt) REVERT: B 590 TYR cc_start: 0.8071 (p90) cc_final: 0.7862 (p90) REVERT: B 669 ASP cc_start: 0.7793 (t0) cc_final: 0.7316 (t0) REVERT: B 719 LYS cc_start: 0.8293 (pttp) cc_final: 0.7831 (mttp) REVERT: B 722 GLU cc_start: 0.6963 (tp30) cc_final: 0.6408 (mt-10) REVERT: B 762 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7471 (mttt) REVERT: B 793 MET cc_start: 0.6916 (mtm) cc_final: 0.6365 (mmm) REVERT: B 796 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7103 (mm-30) REVERT: B 798 TRP cc_start: 0.7658 (m100) cc_final: 0.7237 (m100) REVERT: C 481 ARG cc_start: 0.6785 (mmt90) cc_final: 0.6533 (mmt90) REVERT: C 487 LYS cc_start: 0.8475 (mtpp) cc_final: 0.7843 (mttt) REVERT: C 531 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7503 (mmtp) REVERT: C 665 GLU cc_start: 0.6122 (pt0) cc_final: 0.5828 (mt-10) REVERT: C 712 ARG cc_start: 0.6409 (ttp-110) cc_final: 0.6011 (ttm170) REVERT: D 465 ASP cc_start: 0.7366 (m-30) cc_final: 0.7139 (m-30) REVERT: D 509 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7788 (mttt) REVERT: D 566 TYR cc_start: 0.7534 (m-10) cc_final: 0.7265 (m-80) REVERT: D 669 ASP cc_start: 0.7788 (t0) cc_final: 0.7474 (t0) REVERT: D 719 LYS cc_start: 0.8187 (pttp) cc_final: 0.7719 (mttp) REVERT: D 722 GLU cc_start: 0.7261 (tp30) cc_final: 0.6946 (tp30) REVERT: D 796 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7097 (mm-30) REVERT: D 797 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7800 (ttpt) REVERT: D 798 TRP cc_start: 0.7719 (m100) cc_final: 0.6519 (m100) outliers start: 30 outliers final: 13 residues processed: 230 average time/residue: 0.2832 time to fit residues: 95.2984 Evaluate side-chains 199 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 536 LEU 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 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 531 LYS Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 666 SER 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: 2.9990 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN D 786 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14768 Z= 0.317 Angle : 0.722 11.182 19864 Z= 0.344 Chirality : 0.046 0.246 2158 Planarity : 0.005 0.045 2398 Dihedral : 21.087 144.696 2936 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.18 % Allowed : 10.22 % Favored : 86.60 % 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: -2.55 (0.19), residues: 1672 helix: -0.52 (0.17), residues: 874 sheet: -2.44 (0.41), residues: 140 loop : -3.15 (0.20), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 706 HIS 0.002 0.001 HIS A 792 PHE 0.023 0.002 PHE A 735 TYR 0.022 0.002 TYR B 844 ARG 0.005 0.000 ARG A 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 234 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 1.686 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8467 (mtpp) cc_final: 0.7941 (mttt) REVERT: A 691 MET cc_start: 0.6867 (ptm) cc_final: 0.6249 (ptt) REVERT: A 780 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6312 (mp) REVERT: B 499 ASN cc_start: 0.7067 (m-40) cc_final: 0.6837 (m-40) REVERT: B 509 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7460 (mttt) REVERT: B 620 MET cc_start: 0.8461 (mmt) cc_final: 0.7640 (mmt) REVERT: B 669 ASP cc_start: 0.7864 (t0) cc_final: 0.7476 (t0) REVERT: B 719 LYS cc_start: 0.8276 (pttp) cc_final: 0.7831 (mttp) REVERT: B 722 GLU cc_start: 0.7025 (tp30) cc_final: 0.6497 (mt-10) REVERT: B 778 ILE cc_start: 0.7572 (mm) cc_final: 0.7366 (mt) REVERT: B 796 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7105 (mm-30) REVERT: B 798 TRP cc_start: 0.7694 (m100) cc_final: 0.6806 (m100) REVERT: C 487 LYS cc_start: 0.8508 (mtpp) cc_final: 0.7842 (mttt) REVERT: C 665 GLU cc_start: 0.6192 (pt0) cc_final: 0.5854 (mt-10) REVERT: C 780 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6271 (mp) REVERT: D 509 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7704 (mtmt) REVERT: D 669 ASP cc_start: 0.7949 (t0) cc_final: 0.7584 (t0) REVERT: D 719 LYS cc_start: 0.8268 (pttp) cc_final: 0.7890 (mttp) REVERT: D 722 GLU cc_start: 0.7338 (tp30) cc_final: 0.6936 (tp30) REVERT: D 796 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7073 (mm-30) outliers start: 46 outliers final: 27 residues processed: 227 average time/residue: 0.2785 time to fit residues: 93.6134 Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 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 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 568 LEU 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 698 LYS 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: 2.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 80 optimal weight: 0.0670 chunk 145 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 HIS C 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14768 Z= 0.237 Angle : 0.655 10.055 19864 Z= 0.308 Chirality : 0.044 0.254 2158 Planarity : 0.004 0.044 2398 Dihedral : 19.908 142.696 2926 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.59 % Allowed : 11.53 % Favored : 84.88 % 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: -1.81 (0.20), residues: 1672 helix: 0.27 (0.18), residues: 872 sheet: -2.41 (0.41), residues: 140 loop : -3.00 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 798 HIS 0.002 0.000 HIS A 792 PHE 0.022 0.002 PHE C 584 TYR 0.020 0.002 TYR B 590 ARG 0.008 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8435 (mtpp) cc_final: 0.7886 (mttt) REVERT: A 691 MET cc_start: 0.6796 (ptm) cc_final: 0.6169 (ptt) REVERT: A 780 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6271 (mp) REVERT: B 509 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7490 (mttt) REVERT: B 565 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7605 (ttm) REVERT: B 669 ASP cc_start: 0.7818 (t0) cc_final: 0.7592 (t0) REVERT: B 719 LYS cc_start: 0.8227 (pttp) cc_final: 0.7823 (mttp) REVERT: B 722 GLU cc_start: 0.7092 (tp30) cc_final: 0.6496 (mt-10) REVERT: B 796 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 798 TRP cc_start: 0.7676 (m100) cc_final: 0.6822 (m100) REVERT: C 487 LYS cc_start: 0.8435 (mtpp) cc_final: 0.7886 (mttt) REVERT: C 665 GLU cc_start: 0.6078 (pt0) cc_final: 0.5811 (mt-10) REVERT: C 749 ASN cc_start: 0.7403 (t0) cc_final: 0.7189 (t0) REVERT: C 780 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.6248 (mp) REVERT: D 509 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7655 (mtmt) REVERT: D 669 ASP cc_start: 0.7846 (t0) cc_final: 0.7471 (t0) REVERT: D 674 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7517 (tp) REVERT: D 712 ARG cc_start: 0.6173 (mtp180) cc_final: 0.5848 (mtt90) REVERT: D 719 LYS cc_start: 0.8285 (pttp) cc_final: 0.7849 (mttp) REVERT: D 722 GLU cc_start: 0.7248 (tp30) cc_final: 0.6812 (tp30) REVERT: D 796 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7097 (mm-30) outliers start: 52 outliers final: 38 residues processed: 212 average time/residue: 0.2660 time to fit residues: 83.5320 Evaluate side-chains 204 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 603 GLU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 717 LEU 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 536 LEU Chi-restraints excluded: chain B residue 565 MET 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 B residue 791 LEU 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 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 783 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 536 LEU 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 698 LYS Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.0060 chunk 138 optimal weight: 0.0980 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14768 Z= 0.178 Angle : 0.613 9.494 19864 Z= 0.286 Chirality : 0.043 0.250 2158 Planarity : 0.004 0.042 2398 Dihedral : 18.413 142.266 2926 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.83 % Allowed : 12.15 % Favored : 85.01 % 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: -1.25 (0.21), residues: 1672 helix: 0.80 (0.19), residues: 872 sheet: -2.28 (0.41), residues: 140 loop : -2.83 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 798 HIS 0.001 0.000 HIS A 792 PHE 0.014 0.001 PHE D 584 TYR 0.020 0.001 TYR B 844 ARG 0.009 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.568 Fit side-chains REVERT: A 487 LYS cc_start: 0.8426 (mtpp) cc_final: 0.7898 (mttt) REVERT: A 691 MET cc_start: 0.6791 (ptm) cc_final: 0.6176 (ptt) REVERT: A 780 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.6271 (mp) REVERT: B 509 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7521 (mttt) REVERT: B 620 MET cc_start: 0.8375 (mmt) cc_final: 0.7590 (mmt) REVERT: B 625 GLU cc_start: 0.7079 (pm20) cc_final: 0.6443 (pm20) REVERT: B 669 ASP cc_start: 0.7776 (t0) cc_final: 0.7520 (t0) REVERT: B 719 LYS cc_start: 0.8178 (pttp) cc_final: 0.7776 (mttp) REVERT: B 722 GLU cc_start: 0.7071 (tp30) cc_final: 0.6434 (mt-10) REVERT: B 796 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7150 (mm-30) REVERT: B 797 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7561 (ttpp) REVERT: B 798 TRP cc_start: 0.7636 (m100) cc_final: 0.6703 (m100) REVERT: C 487 LYS cc_start: 0.8444 (mtpp) cc_final: 0.7849 (mttt) REVERT: C 749 ASN cc_start: 0.7134 (t0) cc_final: 0.6901 (t0) REVERT: C 780 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6230 (mp) REVERT: D 509 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7697 (mtmt) REVERT: D 620 MET cc_start: 0.8413 (mmt) cc_final: 0.7725 (mmt) REVERT: D 669 ASP cc_start: 0.7786 (t0) cc_final: 0.7378 (t0) REVERT: D 719 LYS cc_start: 0.8205 (pttp) cc_final: 0.7817 (mttp) REVERT: D 722 GLU cc_start: 0.7207 (tp30) cc_final: 0.6812 (tp30) REVERT: D 796 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7069 (mm-30) outliers start: 41 outliers final: 29 residues processed: 204 average time/residue: 0.2742 time to fit residues: 83.2121 Evaluate side-chains 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 624 SER Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 ILE 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 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 701 THR 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 536 LEU 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 698 LYS Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.0050 chunk 146 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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: 0.7172 moved from start: 0.3330 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= 0.172 Angle : 0.597 9.486 19864 Z= 0.280 Chirality : 0.042 0.222 2158 Planarity : 0.004 0.042 2398 Dihedral : 17.389 142.491 2926 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.97 % Allowed : 12.64 % Favored : 84.39 % 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: -0.96 (0.21), residues: 1672 helix: 1.07 (0.19), residues: 870 sheet: -2.15 (0.42), residues: 140 loop : -2.71 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 798 HIS 0.001 0.000 HIS A 792 PHE 0.015 0.001 PHE D 584 TYR 0.019 0.001 TYR B 844 ARG 0.009 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 1.522 Fit side-chains REVERT: A 487 LYS cc_start: 0.8469 (mtpp) cc_final: 0.7918 (mttt) REVERT: A 691 MET cc_start: 0.6852 (ptm) cc_final: 0.6211 (ptt) REVERT: A 780 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6249 (mp) REVERT: B 509 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7476 (mttt) REVERT: B 620 MET cc_start: 0.8346 (mmt) cc_final: 0.7527 (mmt) REVERT: B 625 GLU cc_start: 0.7048 (pm20) cc_final: 0.6418 (pm20) REVERT: B 669 ASP cc_start: 0.7681 (t0) cc_final: 0.7417 (t0) REVERT: B 719 LYS cc_start: 0.8158 (pttp) cc_final: 0.7762 (mttp) REVERT: B 722 GLU cc_start: 0.7161 (tp30) cc_final: 0.6688 (tp30) REVERT: B 796 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7114 (mm-30) REVERT: B 797 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7568 (ttpp) REVERT: B 798 TRP cc_start: 0.7564 (m100) cc_final: 0.6746 (m100) REVERT: C 487 LYS cc_start: 0.8447 (mtpp) cc_final: 0.7880 (mttt) REVERT: C 780 ILE cc_start: 0.6661 (OUTLIER) cc_final: 0.6198 (mp) REVERT: D 509 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7666 (mtmt) REVERT: D 669 ASP cc_start: 0.7740 (t0) cc_final: 0.7307 (t0) REVERT: D 719 LYS cc_start: 0.8207 (pttp) cc_final: 0.7841 (mttp) REVERT: D 722 GLU cc_start: 0.7228 (tp30) cc_final: 0.6816 (tp30) REVERT: D 796 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7059 (mm-30) outliers start: 43 outliers final: 34 residues processed: 212 average time/residue: 0.2483 time to fit residues: 79.4710 Evaluate side-chains 203 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 603 GLU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 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 B residue 791 LEU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 444 VAL 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 701 THR 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 536 LEU 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 698 LYS Chi-restraints excluded: chain D residue 772 SER Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 0.0010 chunk 136 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3425 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= 0.302 Angle : 0.649 10.618 19864 Z= 0.308 Chirality : 0.045 0.188 2158 Planarity : 0.004 0.042 2398 Dihedral : 17.283 143.214 2926 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.52 % Allowed : 12.36 % 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: -1.06 (0.21), residues: 1672 helix: 0.94 (0.18), residues: 870 sheet: -2.22 (0.43), residues: 140 loop : -2.69 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 798 HIS 0.001 0.000 HIS A 508 PHE 0.016 0.002 PHE D 584 TYR 0.020 0.002 TYR B 844 ARG 0.005 0.000 ARG C 543 *********************** 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 221 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8481 (mtpp) cc_final: 0.7921 (mttt) REVERT: A 691 MET cc_start: 0.6793 (ptm) cc_final: 0.6124 (ptt) REVERT: A 780 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6267 (mp) REVERT: B 509 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7598 (mttt) REVERT: B 620 MET cc_start: 0.8444 (mmt) cc_final: 0.7732 (mmt) REVERT: B 625 GLU cc_start: 0.7128 (pm20) cc_final: 0.6344 (pm20) REVERT: B 719 LYS cc_start: 0.8154 (pttp) cc_final: 0.7778 (mttp) REVERT: B 722 GLU cc_start: 0.7277 (tp30) cc_final: 0.6812 (tp30) REVERT: B 796 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 798 TRP cc_start: 0.7615 (m100) cc_final: 0.6695 (m100) REVERT: C 487 LYS cc_start: 0.8476 (mtpp) cc_final: 0.7819 (mttt) REVERT: C 780 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6254 (mp) REVERT: D 509 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7631 (mtmt) REVERT: D 620 MET cc_start: 0.8488 (mmt) cc_final: 0.7766 (mmt) REVERT: D 669 ASP cc_start: 0.7774 (t0) cc_final: 0.7259 (t0) REVERT: D 719 LYS cc_start: 0.8227 (pttp) cc_final: 0.7862 (mttp) REVERT: D 722 GLU cc_start: 0.7299 (tp30) cc_final: 0.6534 (mm-30) REVERT: D 796 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7047 (mm-30) outliers start: 51 outliers final: 37 residues processed: 212 average time/residue: 0.2633 time to fit residues: 82.7180 Evaluate side-chains 200 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 603 GLU 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 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 666 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 TYR 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 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 701 THR 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 438 ILE Chi-restraints excluded: chain D residue 536 LEU 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 698 LYS 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: 0.0370 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 792 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14768 Z= 0.200 Angle : 0.605 10.045 19864 Z= 0.286 Chirality : 0.042 0.223 2158 Planarity : 0.004 0.042 2398 Dihedral : 16.728 142.353 2926 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.83 % Allowed : 13.33 % Favored : 83.84 % 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: -0.81 (0.21), residues: 1672 helix: 1.17 (0.18), residues: 870 sheet: -2.09 (0.43), residues: 140 loop : -2.61 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 PHE 0.014 0.001 PHE D 584 TYR 0.020 0.001 TYR B 590 ARG 0.005 0.000 ARG C 543 *********************** 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 213 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8452 (mtpp) cc_final: 0.7907 (mttt) REVERT: A 691 MET cc_start: 0.6792 (ptm) cc_final: 0.6132 (ptt) REVERT: A 780 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6263 (mp) REVERT: B 468 ARG cc_start: 0.6247 (OUTLIER) cc_final: 0.5980 (ttp-110) REVERT: B 509 LYS cc_start: 0.8194 (mtpp) cc_final: 0.7596 (mtmt) REVERT: B 620 MET cc_start: 0.8382 (mmt) cc_final: 0.7674 (mmt) REVERT: B 625 GLU cc_start: 0.7103 (pm20) cc_final: 0.6287 (pm20) REVERT: B 719 LYS cc_start: 0.8171 (pttp) cc_final: 0.7811 (mttp) REVERT: B 722 GLU cc_start: 0.7233 (tp30) cc_final: 0.6783 (tp30) REVERT: B 796 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7050 (mm-30) REVERT: B 797 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7588 (ttpp) REVERT: B 798 TRP cc_start: 0.7557 (m100) cc_final: 0.6620 (m100) REVERT: C 487 LYS cc_start: 0.8468 (mtpp) cc_final: 0.7805 (mttt) REVERT: C 780 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6245 (mp) REVERT: D 509 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7616 (mtmt) REVERT: D 669 ASP cc_start: 0.7721 (t0) cc_final: 0.7237 (t0) REVERT: D 670 SER cc_start: 0.8091 (t) cc_final: 0.7626 (p) REVERT: D 719 LYS cc_start: 0.8197 (pttp) cc_final: 0.7828 (mttp) REVERT: D 722 GLU cc_start: 0.7253 (tp30) cc_final: 0.6500 (mm-30) REVERT: D 796 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7017 (mm-30) outliers start: 41 outliers final: 32 residues processed: 206 average time/residue: 0.2732 time to fit residues: 83.4918 Evaluate side-chains 202 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 468 ARG 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 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 624 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 701 THR 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 536 LEU 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 698 LYS Chi-restraints excluded: chain D residue 772 SER 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: 3.9990 chunk 150 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 chunk 142 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.7217 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14768 Z= 0.247 Angle : 0.621 10.413 19864 Z= 0.296 Chirality : 0.043 0.166 2158 Planarity : 0.004 0.041 2398 Dihedral : 16.597 142.866 2926 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.69 % Allowed : 13.60 % Favored : 83.70 % 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: -0.79 (0.21), residues: 1672 helix: 1.16 (0.18), residues: 870 sheet: -2.05 (0.43), residues: 140 loop : -2.57 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 798 HIS 0.002 0.000 HIS A 792 PHE 0.015 0.002 PHE D 584 TYR 0.020 0.001 TYR B 590 ARG 0.005 0.000 ARG C 543 *********************** 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 208 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 1.637 Fit side-chains REVERT: A 487 LYS cc_start: 0.8459 (mtpp) cc_final: 0.7967 (mttt) REVERT: A 691 MET cc_start: 0.6833 (ptm) cc_final: 0.6152 (ptt) REVERT: A 780 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6247 (mp) REVERT: B 468 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.5905 (ttp-110) REVERT: B 509 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7627 (mtmt) REVERT: B 620 MET cc_start: 0.8392 (mmt) cc_final: 0.7702 (mmt) REVERT: B 625 GLU cc_start: 0.7117 (pm20) cc_final: 0.6312 (pm20) REVERT: B 719 LYS cc_start: 0.8186 (pttp) cc_final: 0.7831 (mttp) REVERT: B 722 GLU cc_start: 0.7257 (tp30) cc_final: 0.6790 (tp30) REVERT: B 796 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7046 (mm-30) REVERT: B 797 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7572 (ttpp) REVERT: B 798 TRP cc_start: 0.7562 (m100) cc_final: 0.6621 (m100) REVERT: C 487 LYS cc_start: 0.8476 (mtpp) cc_final: 0.7828 (mttt) REVERT: C 749 ASN cc_start: 0.7027 (t0) cc_final: 0.6826 (t0) REVERT: C 780 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6259 (mp) REVERT: D 468 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5947 (ttp-110) REVERT: D 509 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7619 (mtmt) REVERT: D 620 MET cc_start: 0.8454 (mmt) cc_final: 0.7708 (mmt) REVERT: D 669 ASP cc_start: 0.7653 (t0) cc_final: 0.7138 (t0) REVERT: D 719 LYS cc_start: 0.8214 (pttp) cc_final: 0.7847 (mttp) REVERT: D 722 GLU cc_start: 0.7259 (tp30) cc_final: 0.6500 (mm-30) REVERT: D 796 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7005 (mm-30) outliers start: 39 outliers final: 33 residues processed: 200 average time/residue: 0.2761 time to fit residues: 81.5044 Evaluate side-chains 204 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 468 ARG 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 B residue 791 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 444 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 701 THR 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 468 ARG Chi-restraints excluded: chain D residue 536 LEU 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 698 LYS Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.0770 chunk 75 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 154 optimal weight: 0.2980 chunk 133 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14768 Z= 0.184 Angle : 0.597 9.911 19864 Z= 0.282 Chirality : 0.042 0.250 2158 Planarity : 0.004 0.042 2398 Dihedral : 16.201 142.205 2926 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.62 % Allowed : 13.67 % Favored : 83.70 % 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: -0.60 (0.21), residues: 1672 helix: 1.32 (0.18), residues: 870 sheet: -1.95 (0.42), residues: 140 loop : -2.49 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 798 HIS 0.001 0.000 HIS C 792 PHE 0.019 0.001 PHE D 579 TYR 0.020 0.001 TYR B 844 ARG 0.005 0.000 ARG C 543 ********************** 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 216 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8449 (mtpp) cc_final: 0.7946 (mttt) REVERT: A 780 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6214 (mp) REVERT: B 468 ARG cc_start: 0.6239 (OUTLIER) cc_final: 0.5825 (ttp-110) REVERT: B 509 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7614 (mtmt) REVERT: B 620 MET cc_start: 0.8343 (mmt) cc_final: 0.7638 (mmt) REVERT: B 625 GLU cc_start: 0.7116 (pm20) cc_final: 0.6541 (pm20) REVERT: B 719 LYS cc_start: 0.8184 (pttp) cc_final: 0.7819 (mttp) REVERT: B 722 GLU cc_start: 0.7217 (tp30) cc_final: 0.6385 (mm-30) REVERT: B 796 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7049 (mm-30) REVERT: B 797 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7588 (ttpp) REVERT: B 798 TRP cc_start: 0.7524 (m100) cc_final: 0.6596 (m100) REVERT: C 487 LYS cc_start: 0.8468 (mtpp) cc_final: 0.7812 (mttt) REVERT: C 749 ASN cc_start: 0.6896 (t0) cc_final: 0.6691 (t0) REVERT: C 780 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6203 (mp) REVERT: D 468 ARG cc_start: 0.6266 (OUTLIER) cc_final: 0.5926 (ttp-110) REVERT: D 509 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7646 (mtmt) REVERT: D 669 ASP cc_start: 0.7666 (t0) cc_final: 0.7171 (t0) REVERT: D 719 LYS cc_start: 0.8179 (pttp) cc_final: 0.7832 (mttp) REVERT: D 722 GLU cc_start: 0.7264 (tp30) cc_final: 0.6477 (mm-30) REVERT: D 796 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7043 (mm-30) outliers start: 38 outliers final: 32 residues processed: 207 average time/residue: 0.2620 time to fit residues: 80.5566 Evaluate side-chains 204 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 685 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 468 ARG 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 823 ILE 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 701 THR 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 468 ARG Chi-restraints excluded: chain D residue 536 LEU 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 698 LYS Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.181784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141246 restraints weight = 14486.006| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.04 r_work: 0.3289 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14768 Z= 0.270 Angle : 0.633 10.956 19864 Z= 0.302 Chirality : 0.044 0.266 2158 Planarity : 0.004 0.042 2398 Dihedral : 16.251 143.101 2924 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.76 % Allowed : 14.09 % Favored : 83.15 % 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: 1.21 (0.18), residues: 870 sheet: -1.96 (0.43), residues: 140 loop : -2.51 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 798 HIS 0.001 0.000 HIS B 792 PHE 0.016 0.002 PHE D 584 TYR 0.021 0.002 TYR B 844 ARG 0.005 0.000 ARG C 543 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.46 seconds wall clock time: 64 minutes 12.88 seconds (3852.88 seconds total)