Starting phenix.real_space_refine on Thu Feb 15 09:22:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2024/7lzi_23607.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2024/7lzi_23607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2024/7lzi_23607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2024/7lzi_23607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2024/7lzi_23607.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2024/7lzi_23607.pdb" } resolution = 4.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 7638 2.51 5 N 1934 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 806": "NH1" <-> "NH2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B ARG 789": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 806": "NH1" <-> "NH2" Residue "C ARG 548": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 789": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C ARG 806": "NH1" <-> "NH2" Residue "D ARG 548": "NH1" <-> "NH2" Residue "D ARG 708": "NH1" <-> "NH2" Residue "D ARG 789": "NH1" <-> "NH2" Residue "D ARG 797": "NH1" <-> "NH2" Residue "D PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 806": "NH1" <-> "NH2" Residue "B GLU 1001": "OE1" <-> "OE2" Residue "D GLU 1001": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11782 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2946 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2869 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2946 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2869 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 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: 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: "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: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 6.25, per 1000 atoms: 0.53 Number of scatterers: 11782 At special positions: 0 Unit cell: (107.07, 110.39, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2172 8.00 N 1934 7.00 C 7638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 841 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 841 " distance=2.03 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 841 " distance=2.03 Simple disulfide: pdb=" SG CYS D 786 " - pdb=" SG CYS D 841 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 576 " " NAG F 1 " - " ASN B 576 " " NAG G 1 " - " ASN C 576 " " NAG H 1 " - " ASN D 576 " Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 16 sheets defined 50.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.691A pdb=" N ILE A 529 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.678A pdb=" N ARG A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 613 through 635 removed outlier: 3.782A pdb=" N ALA A 618 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 621 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 630 " --> pdb=" O PHE A 626 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 659 removed outlier: 3.893A pdb=" N SER A 657 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 703 removed outlier: 3.620A pdb=" N ILE A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 728 through 737 removed outlier: 4.454A pdb=" N ASN A 732 " --> pdb=" O THR A 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 736 " --> pdb=" O ASN A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.623A pdb=" N LEU A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 784 removed outlier: 3.694A pdb=" N VAL A 779 " --> pdb=" O PRO A 775 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 825 removed outlier: 3.972A pdb=" N ASP A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 861 through 880 removed outlier: 3.504A pdb=" N VAL A 875 " --> pdb=" O MET A 871 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 530 removed outlier: 3.637A pdb=" N ALA B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 removed outlier: 3.810A pdb=" N VAL B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 581 removed outlier: 3.811A pdb=" N TYR B 580 " --> pdb=" O ASN B 576 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 581 " --> pdb=" O ARG B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 removed outlier: 3.881A pdb=" N PHE B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 604 through 609' Processing helix chain 'B' and resid 614 through 634 removed outlier: 3.953A pdb=" N ALA B 618 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET B 630 " --> pdb=" O PHE B 626 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 631 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.560A pdb=" N PHE B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET B 661 " --> pdb=" O SER B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 701 removed outlier: 3.540A pdb=" N ILE B 679 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 687 " --> pdb=" O PHE B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 705 Processing helix chain 'B' and resid 712 through 717 Processing helix chain 'B' and resid 728 through 737 removed outlier: 4.573A pdb=" N ASN B 732 " --> pdb=" O THR B 728 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 735 " --> pdb=" O ARG B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.749A pdb=" N LEU B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 758 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 784 removed outlier: 3.799A pdb=" N VAL B 779 " --> pdb=" O PRO B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 825 removed outlier: 3.846A pdb=" N ASP B 813 " --> pdb=" O PRO B 809 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 814 " --> pdb=" O LEU B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 835 Processing helix chain 'B' and resid 859 through 880 removed outlier: 3.626A pdb=" N ILE B 864 " --> pdb=" O GLY B 860 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS B 869 " --> pdb=" O CYS B 865 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 870 " --> pdb=" O GLY B 866 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 874 " --> pdb=" O PHE B 870 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 875 " --> pdb=" O MET B 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 532 removed outlier: 3.690A pdb=" N ILE C 529 " --> pdb=" O PHE C 525 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 531 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 561 Processing helix chain 'C' and resid 574 through 581 removed outlier: 3.678A pdb=" N ARG C 579 " --> pdb=" O THR C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 613 through 635 removed outlier: 3.782A pdb=" N ALA C 618 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 621 " --> pdb=" O TRP C 617 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 625 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 627 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET C 630 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 659 removed outlier: 3.893A pdb=" N SER C 657 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 703 removed outlier: 3.621A pdb=" N ILE C 687 " --> pdb=" O PHE C 683 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 699 " --> pdb=" O SER C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 718 Processing helix chain 'C' and resid 728 through 737 removed outlier: 4.455A pdb=" N ASN C 732 " --> pdb=" O THR C 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 736 " --> pdb=" O ASN C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 760 removed outlier: 3.623A pdb=" N LEU C 755 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER C 756 " --> pdb=" O GLU C 752 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 758 " --> pdb=" O TYR C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 784 removed outlier: 3.693A pdb=" N VAL C 779 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 825 removed outlier: 3.972A pdb=" N ASP C 813 " --> pdb=" O PRO C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 834 Processing helix chain 'C' and resid 861 through 880 removed outlier: 3.504A pdb=" N VAL C 875 " --> pdb=" O MET C 871 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 880 " --> pdb=" O PHE C 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 530 removed outlier: 3.637A pdb=" N ALA D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 561 removed outlier: 3.810A pdb=" N VAL D 559 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.811A pdb=" N TYR D 580 " --> pdb=" O ASN D 576 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 581 " --> pdb=" O ARG D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 removed outlier: 3.881A pdb=" N PHE D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 609 " --> pdb=" O PRO D 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 604 through 609' Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.953A pdb=" N ALA D 618 " --> pdb=" O ILE D 614 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET D 630 " --> pdb=" O PHE D 626 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D 631 " --> pdb=" O VAL D 627 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 633 " --> pdb=" O ALA D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 661 removed outlier: 3.560A pdb=" N PHE D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 659 " --> pdb=" O TRP D 655 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 660 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET D 661 " --> pdb=" O SER D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 701 removed outlier: 3.540A pdb=" N ILE D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 687 " --> pdb=" O PHE D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 705 Processing helix chain 'D' and resid 712 through 717 Processing helix chain 'D' and resid 728 through 737 removed outlier: 4.573A pdb=" N ASN D 732 " --> pdb=" O THR D 728 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 735 " --> pdb=" O ARG D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 760 removed outlier: 3.749A pdb=" N LEU D 755 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU D 758 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 784 removed outlier: 3.798A pdb=" N VAL D 779 " --> pdb=" O PRO D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 825 removed outlier: 3.846A pdb=" N ASP D 813 " --> pdb=" O PRO D 809 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET D 814 " --> pdb=" O LEU D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 835 Processing helix chain 'D' and resid 859 through 880 removed outlier: 3.627A pdb=" N ILE D 864 " --> pdb=" O GLY D 860 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS D 869 " --> pdb=" O CYS D 865 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 870 " --> pdb=" O GLY D 866 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR D 874 " --> pdb=" O PHE D 870 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 875 " --> pdb=" O MET D 871 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 539 through 542 removed outlier: 3.510A pdb=" N ILE A 496 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 510 Processing sheet with id=AA3, first strand: chain 'A' and resid 745 through 748 removed outlier: 6.418A pdb=" N ILE A 722 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 748 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 724 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN A 725 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLU A 773 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 596 " --> pdb=" O ARG A 789 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 745 through 748 removed outlier: 6.418A pdb=" N ILE A 722 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 748 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 724 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN A 725 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLU A 773 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR A 796 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.732A pdb=" N ILE B 496 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 509 through 510 Processing sheet with id=AA7, first strand: chain 'B' and resid 745 through 748 removed outlier: 6.255A pdb=" N ILE B 722 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 748 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 724 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 723 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N GLU B 773 " --> pdb=" O GLY B 723 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLN B 725 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 745 through 748 removed outlier: 6.255A pdb=" N ILE B 722 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 748 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 724 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 723 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N GLU B 773 " --> pdb=" O GLY B 723 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLN B 725 " --> pdb=" O GLU B 773 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR B 796 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 539 through 542 removed outlier: 3.510A pdb=" N ILE C 496 " --> pdb=" O THR C 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 508 through 510 Processing sheet with id=AB2, first strand: chain 'C' and resid 745 through 748 removed outlier: 6.418A pdb=" N ILE C 722 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU C 748 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 724 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN C 725 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLU C 773 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 596 " --> pdb=" O ARG C 789 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 745 through 748 removed outlier: 6.418A pdb=" N ILE C 722 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU C 748 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 724 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN C 725 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLU C 773 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR C 796 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 538 through 542 removed outlier: 3.732A pdb=" N ILE D 496 " --> pdb=" O THR D 539 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 509 through 510 Processing sheet with id=AB6, first strand: chain 'D' and resid 745 through 748 removed outlier: 6.255A pdb=" N ILE D 722 " --> pdb=" O VAL D 746 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU D 748 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 724 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY D 723 " --> pdb=" O VAL D 771 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU D 773 " --> pdb=" O GLY D 723 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N GLN D 725 " --> pdb=" O GLU D 773 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 745 through 748 removed outlier: 6.255A pdb=" N ILE D 722 " --> pdb=" O VAL D 746 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU D 748 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 724 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY D 723 " --> pdb=" O VAL D 771 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU D 773 " --> pdb=" O GLY D 723 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N GLN D 725 " --> pdb=" O GLU D 773 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR D 796 " --> pdb=" O LEU D 592 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3706 1.34 - 1.46: 2886 1.46 - 1.58: 5412 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 12060 Sorted by residual: bond pdb=" C LEU B 774 " pdb=" N PRO B 775 " ideal model delta sigma weight residual 1.337 1.376 -0.040 1.06e-02 8.90e+03 1.40e+01 bond pdb=" C LEU D 774 " pdb=" N PRO D 775 " ideal model delta sigma weight residual 1.337 1.376 -0.039 1.06e-02 8.90e+03 1.38e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" N ASN D 719 " pdb=" CA ASN D 719 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.06e+00 ... (remaining 12055 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.06: 303 106.06 - 113.06: 6405 113.06 - 120.06: 4411 120.06 - 127.07: 5150 127.07 - 134.07: 155 Bond angle restraints: 16424 Sorted by residual: angle pdb=" C SER C 718 " pdb=" N ASN C 719 " pdb=" CA ASN C 719 " ideal model delta sigma weight residual 121.54 130.41 -8.87 1.91e+00 2.74e-01 2.16e+01 angle pdb=" C SER A 718 " pdb=" N ASN A 719 " pdb=" CA ASN A 719 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C SER D 603 " pdb=" N SER D 604 " pdb=" CA SER D 604 " ideal model delta sigma weight residual 122.29 128.43 -6.14 1.48e+00 4.57e-01 1.72e+01 angle pdb=" C SER B 603 " pdb=" N SER B 604 " pdb=" CA SER B 604 " ideal model delta sigma weight residual 122.29 128.39 -6.10 1.48e+00 4.57e-01 1.70e+01 angle pdb=" CA LEU B 609 " pdb=" CB LEU B 609 " pdb=" CG LEU B 609 " ideal model delta sigma weight residual 116.30 130.08 -13.78 3.50e+00 8.16e-02 1.55e+01 ... (remaining 16419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.55: 6857 20.55 - 41.10: 271 41.10 - 61.65: 40 61.65 - 82.20: 12 82.20 - 102.75: 16 Dihedral angle restraints: 7196 sinusoidal: 2910 harmonic: 4286 Sorted by residual: dihedral pdb=" CA PHE A 623 " pdb=" C PHE A 623 " pdb=" N PHE A 624 " pdb=" CA PHE A 624 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PHE C 623 " pdb=" C PHE C 623 " pdb=" N PHE C 624 " pdb=" CA PHE C 624 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA THR B 613 " pdb=" C THR B 613 " pdb=" N ILE B 614 " pdb=" CA ILE B 614 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 1892 0.205 - 0.411: 4 0.411 - 0.616: 0 0.616 - 0.821: 1 0.821 - 1.027: 1 Chirality restraints: 1898 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 576 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN C 576 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" CA ASN A 719 " pdb=" N ASN A 719 " pdb=" C ASN A 719 " pdb=" CB ASN A 719 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1895 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 576 " 0.005 2.00e-02 2.50e+03 3.35e-02 1.40e+01 pdb=" CG ASN A 576 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 576 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 576 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 612 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C PHE B 612 " 0.054 2.00e-02 2.50e+03 pdb=" O PHE B 612 " -0.020 2.00e-02 2.50e+03 pdb=" N THR B 613 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 612 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" C PHE D 612 " -0.054 2.00e-02 2.50e+03 pdb=" O PHE D 612 " 0.020 2.00e-02 2.50e+03 pdb=" N THR D 613 " 0.018 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2263 2.77 - 3.30: 11140 3.30 - 3.83: 19136 3.83 - 4.37: 22411 4.37 - 4.90: 36977 Nonbonded interactions: 91927 Sorted by model distance: nonbonded pdb=" OG1 THR A 613 " pdb=" O LYS D 856 " model vdw 2.234 2.440 nonbonded pdb=" O TRP B 485 " pdb=" OH TYR B 534 " model vdw 2.272 2.440 nonbonded pdb=" O TRP D 485 " pdb=" OH TYR D 534 " model vdw 2.273 2.440 nonbonded pdb=" OE2 GLU B 526 " pdb=" OH TYR B 540 " model vdw 2.299 2.440 nonbonded pdb=" OE2 GLU D 526 " pdb=" OH TYR D 540 " model vdw 2.300 2.440 ... (remaining 91922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 483 through 842 or resid 853 through 880 or resid 1001)) selection = chain 'B' selection = (chain 'C' and (resid 483 through 842 or resid 853 through 880 or resid 1001)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 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: 10.240 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.800 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.005 0.057 12060 Z= 0.307 Angle : 0.940 13.778 16424 Z= 0.526 Chirality : 0.063 1.027 1898 Planarity : 0.007 0.060 2072 Dihedral : 13.062 102.751 4416 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.32 % Allowed : 6.35 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.16), residues: 1452 helix: -3.50 (0.12), residues: 700 sheet: -2.84 (0.33), residues: 180 loop : -2.35 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 681 HIS 0.004 0.001 HIS D 831 PHE 0.018 0.002 PHE B 795 TYR 0.024 0.002 TYR C 552 ARG 0.008 0.001 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 516 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 VAL cc_start: 0.9305 (t) cc_final: 0.8994 (t) REVERT: A 570 ASP cc_start: 0.7785 (m-30) cc_final: 0.7170 (m-30) REVERT: A 585 GLN cc_start: 0.9079 (mm110) cc_final: 0.8724 (mm-40) REVERT: A 626 PHE cc_start: 0.7548 (t80) cc_final: 0.7138 (t80) REVERT: A 678 LEU cc_start: 0.8576 (tp) cc_final: 0.8326 (tt) REVERT: A 679 ILE cc_start: 0.8577 (mt) cc_final: 0.8321 (tp) REVERT: A 688 ILE cc_start: 0.9462 (mm) cc_final: 0.9135 (tp) REVERT: A 695 SER cc_start: 0.9191 (m) cc_final: 0.8743 (p) REVERT: A 700 LEU cc_start: 0.9435 (mm) cc_final: 0.9225 (mt) REVERT: A 749 LYS cc_start: 0.7520 (ptmt) cc_final: 0.7155 (ptpp) REVERT: A 750 ASP cc_start: 0.7067 (p0) cc_final: 0.6305 (t70) REVERT: A 790 THR cc_start: 0.8367 (p) cc_final: 0.8122 (p) REVERT: A 814 MET cc_start: 0.9281 (mtp) cc_final: 0.9068 (mtp) REVERT: B 496 ILE cc_start: 0.8632 (mp) cc_final: 0.8259 (mt) REVERT: B 554 ASN cc_start: 0.9125 (m-40) cc_final: 0.8714 (t0) REVERT: B 558 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8278 (mm-30) REVERT: B 564 PHE cc_start: 0.8346 (m-80) cc_final: 0.8049 (m-10) REVERT: B 599 LYS cc_start: 0.6125 (pmmt) cc_final: 0.5677 (mtpt) REVERT: B 610 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8346 (tptt) REVERT: B 611 PRO cc_start: 0.8785 (Cg_exo) cc_final: 0.8273 (Cg_endo) REVERT: B 626 PHE cc_start: 0.8081 (t80) cc_final: 0.7807 (t80) REVERT: B 689 ASN cc_start: 0.8589 (t0) cc_final: 0.8354 (t0) REVERT: B 692 TYR cc_start: 0.8841 (t80) cc_final: 0.8459 (t80) REVERT: B 700 LEU cc_start: 0.9234 (mm) cc_final: 0.8928 (mm) REVERT: B 703 ARG cc_start: 0.8480 (mtp180) cc_final: 0.8269 (mtp85) REVERT: B 746 VAL cc_start: 0.9076 (t) cc_final: 0.8807 (m) REVERT: B 754 TYR cc_start: 0.9155 (m-10) cc_final: 0.8800 (m-80) REVERT: B 767 VAL cc_start: 0.8560 (m) cc_final: 0.8348 (m) REVERT: B 793 GLN cc_start: 0.8334 (mt0) cc_final: 0.8008 (mm110) REVERT: B 818 ILE cc_start: 0.9218 (mt) cc_final: 0.8934 (tp) REVERT: C 513 ASN cc_start: 0.8041 (m-40) cc_final: 0.7106 (p0) REVERT: C 521 CYS cc_start: 0.8709 (m) cc_final: 0.8217 (m) REVERT: C 547 LYS cc_start: 0.8464 (pptt) cc_final: 0.7460 (tppt) REVERT: C 552 TYR cc_start: 0.7501 (m-10) cc_final: 0.6743 (m-10) REVERT: C 554 ASN cc_start: 0.9015 (m-40) cc_final: 0.8777 (m-40) REVERT: C 602 LYS cc_start: 0.7222 (mppt) cc_final: 0.6923 (tppt) REVERT: C 681 TRP cc_start: 0.8094 (t60) cc_final: 0.7851 (t60) REVERT: C 688 ILE cc_start: 0.9168 (mm) cc_final: 0.8858 (tp) REVERT: C 700 LEU cc_start: 0.9056 (mm) cc_final: 0.8854 (mt) REVERT: C 750 ASP cc_start: 0.7135 (p0) cc_final: 0.6077 (t70) REVERT: C 751 GLU cc_start: 0.7761 (pt0) cc_final: 0.7382 (pm20) REVERT: C 754 TYR cc_start: 0.7921 (m-10) cc_final: 0.7368 (m-80) REVERT: C 779 VAL cc_start: 0.9261 (t) cc_final: 0.8889 (t) REVERT: C 794 GLU cc_start: 0.7618 (mp0) cc_final: 0.7221 (mt-10) REVERT: C 826 GLU cc_start: 0.8331 (tp30) cc_final: 0.8127 (tp30) REVERT: D 532 LEU cc_start: 0.8026 (mt) cc_final: 0.7793 (tp) REVERT: D 554 ASN cc_start: 0.9287 (m-40) cc_final: 0.9081 (t0) REVERT: D 572 THR cc_start: 0.9023 (m) cc_final: 0.8430 (p) REVERT: D 599 LYS cc_start: 0.6178 (pmmt) cc_final: 0.5863 (mtpt) REVERT: D 610 LYS cc_start: 0.8456 (ttpt) cc_final: 0.7906 (tptp) REVERT: D 623 PHE cc_start: 0.7437 (m-80) cc_final: 0.7091 (m-80) REVERT: D 676 PHE cc_start: 0.8443 (t80) cc_final: 0.8227 (t80) REVERT: D 691 SER cc_start: 0.8830 (m) cc_final: 0.8525 (p) REVERT: D 703 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7819 (ttt90) REVERT: D 746 VAL cc_start: 0.9077 (t) cc_final: 0.8862 (m) REVERT: D 754 TYR cc_start: 0.9173 (m-10) cc_final: 0.8784 (m-80) REVERT: D 759 GLN cc_start: 0.8936 (mm110) cc_final: 0.8482 (mm110) REVERT: D 767 VAL cc_start: 0.8718 (m) cc_final: 0.8515 (m) REVERT: D 773 GLU cc_start: 0.7780 (mp0) cc_final: 0.7539 (mp0) REVERT: D 833 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8717 (tptp) REVERT: D 856 LYS cc_start: 0.8699 (tppt) cc_final: 0.8347 (tptp) REVERT: D 871 MET cc_start: 0.8158 (tmm) cc_final: 0.7957 (tpt) outliers start: 4 outliers final: 1 residues processed: 520 average time/residue: 0.2524 time to fit residues: 180.4584 Evaluate side-chains 284 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 85 optimal weight: 0.2980 chunk 132 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN A 704 GLN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 HIS B 549 ASN B 554 ASN ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 563 ASN C 725 GLN C 805 GLN D 549 ASN D 554 ASN D 704 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 820 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12060 Z= 0.259 Angle : 0.718 8.829 16424 Z= 0.375 Chirality : 0.049 0.333 1898 Planarity : 0.006 0.056 2072 Dihedral : 10.376 78.225 1766 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.16 % Allowed : 4.21 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.19), residues: 1452 helix: -1.92 (0.15), residues: 732 sheet: -2.48 (0.36), residues: 176 loop : -2.11 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 878 HIS 0.005 0.001 HIS C 831 PHE 0.024 0.002 PHE D 626 TYR 0.015 0.002 TYR C 552 ARG 0.009 0.001 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 353 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 GLN cc_start: 0.9171 (mm110) cc_final: 0.8951 (mm-40) REVERT: A 626 PHE cc_start: 0.7584 (t80) cc_final: 0.6929 (t80) REVERT: A 680 ILE cc_start: 0.9189 (mm) cc_final: 0.8957 (mm) REVERT: A 681 TRP cc_start: 0.8795 (t60) cc_final: 0.8520 (t60) REVERT: A 695 SER cc_start: 0.9155 (m) cc_final: 0.8787 (t) REVERT: A 749 LYS cc_start: 0.7632 (ptmt) cc_final: 0.7317 (ptpt) REVERT: A 754 TYR cc_start: 0.8398 (m-10) cc_final: 0.7912 (m-80) REVERT: A 772 ASP cc_start: 0.8661 (m-30) cc_final: 0.8447 (t70) REVERT: A 829 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8563 (mmmm) REVERT: B 564 PHE cc_start: 0.8350 (m-80) cc_final: 0.8019 (m-10) REVERT: B 599 LYS cc_start: 0.6922 (ptpp) cc_final: 0.6480 (mmmt) REVERT: B 610 LYS cc_start: 0.8765 (ttpt) cc_final: 0.8286 (tptp) REVERT: B 689 ASN cc_start: 0.8870 (t0) cc_final: 0.8652 (t0) REVERT: B 700 LEU cc_start: 0.9227 (mm) cc_final: 0.8895 (mm) REVERT: B 713 ASP cc_start: 0.8611 (t70) cc_final: 0.8393 (t0) REVERT: B 746 VAL cc_start: 0.9060 (t) cc_final: 0.8813 (m) REVERT: B 759 GLN cc_start: 0.8931 (mm110) cc_final: 0.8489 (mm-40) REVERT: B 767 VAL cc_start: 0.8562 (m) cc_final: 0.8297 (m) REVERT: B 772 ASP cc_start: 0.7938 (m-30) cc_final: 0.7529 (m-30) REVERT: B 814 MET cc_start: 0.8945 (mmp) cc_final: 0.8714 (mmm) REVERT: C 513 ASN cc_start: 0.8146 (m-40) cc_final: 0.7213 (p0) REVERT: C 630 MET cc_start: 0.7828 (mpp) cc_final: 0.7366 (mpp) REVERT: C 675 ARG cc_start: 0.5011 (mtt180) cc_final: 0.4421 (mtt180) REVERT: C 688 ILE cc_start: 0.9350 (mm) cc_final: 0.9140 (tp) REVERT: C 750 ASP cc_start: 0.6959 (p0) cc_final: 0.6568 (t70) REVERT: C 751 GLU cc_start: 0.8258 (pt0) cc_final: 0.7915 (pm20) REVERT: C 773 GLU cc_start: 0.8554 (mp0) cc_final: 0.8041 (mp0) REVERT: C 779 VAL cc_start: 0.9227 (t) cc_final: 0.8971 (t) REVERT: C 837 TYR cc_start: 0.6422 (m-10) cc_final: 0.6181 (m-80) REVERT: C 861 LEU cc_start: 0.8769 (tp) cc_final: 0.8567 (tp) REVERT: D 494 LEU cc_start: 0.8952 (tp) cc_final: 0.8729 (tt) REVERT: D 496 ILE cc_start: 0.8336 (mp) cc_final: 0.8094 (mp) REVERT: D 554 ASN cc_start: 0.9030 (m110) cc_final: 0.8829 (t0) REVERT: D 558 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7978 (mm-30) REVERT: D 570 ASP cc_start: 0.7791 (m-30) cc_final: 0.7361 (m-30) REVERT: D 608 PHE cc_start: 0.5932 (t80) cc_final: 0.5369 (t80) REVERT: D 610 LYS cc_start: 0.8524 (ttpt) cc_final: 0.7898 (tptp) REVERT: D 612 PHE cc_start: 0.7487 (m-10) cc_final: 0.7068 (m-80) REVERT: D 676 PHE cc_start: 0.8521 (t80) cc_final: 0.8026 (t80) REVERT: D 703 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7959 (ttt90) REVERT: D 722 ILE cc_start: 0.8776 (mt) cc_final: 0.8544 (mp) REVERT: D 746 VAL cc_start: 0.9081 (t) cc_final: 0.8852 (m) REVERT: D 754 TYR cc_start: 0.9107 (m-10) cc_final: 0.8644 (m-80) REVERT: D 767 VAL cc_start: 0.8691 (m) cc_final: 0.8469 (m) REVERT: D 772 ASP cc_start: 0.7874 (m-30) cc_final: 0.7591 (m-30) REVERT: D 833 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8798 (tptp) REVERT: D 837 TYR cc_start: 0.6154 (m-10) cc_final: 0.5712 (m-80) REVERT: D 856 LYS cc_start: 0.8705 (tppt) cc_final: 0.8043 (tptp) outliers start: 2 outliers final: 0 residues processed: 353 average time/residue: 0.2297 time to fit residues: 115.4865 Evaluate side-chains 247 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 143 optimal weight: 0.0970 chunk 118 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN C 805 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12060 Z= 0.204 Angle : 0.660 9.174 16424 Z= 0.338 Chirality : 0.046 0.179 1898 Planarity : 0.005 0.048 2072 Dihedral : 8.414 54.946 1766 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.34 (0.20), residues: 1452 helix: -1.00 (0.17), residues: 738 sheet: -2.18 (0.38), residues: 176 loop : -1.90 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 485 HIS 0.003 0.001 HIS C 831 PHE 0.021 0.002 PHE D 626 TYR 0.017 0.002 TYR C 520 ARG 0.010 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 GLN cc_start: 0.9160 (mm110) cc_final: 0.8923 (mm-40) REVERT: A 681 TRP cc_start: 0.8744 (t60) cc_final: 0.8508 (t60) REVERT: A 749 LYS cc_start: 0.7647 (ptmt) cc_final: 0.7357 (ptpt) REVERT: A 751 GLU cc_start: 0.8365 (pm20) cc_final: 0.8090 (pm20) REVERT: A 754 TYR cc_start: 0.8383 (m-10) cc_final: 0.7939 (m-80) REVERT: A 814 MET cc_start: 0.9133 (mtp) cc_final: 0.8899 (mtp) REVERT: B 557 ASN cc_start: 0.9354 (t0) cc_final: 0.8862 (t0) REVERT: B 564 PHE cc_start: 0.8321 (m-80) cc_final: 0.8021 (m-10) REVERT: B 599 LYS cc_start: 0.6939 (ptpp) cc_final: 0.6461 (mtpt) REVERT: B 624 PHE cc_start: 0.7675 (t80) cc_final: 0.7448 (t80) REVERT: B 700 LEU cc_start: 0.9209 (mm) cc_final: 0.8901 (mm) REVERT: B 746 VAL cc_start: 0.8997 (t) cc_final: 0.8742 (m) REVERT: B 767 VAL cc_start: 0.8514 (m) cc_final: 0.8219 (m) REVERT: B 772 ASP cc_start: 0.7972 (m-30) cc_final: 0.7521 (m-30) REVERT: B 823 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 828 GLU cc_start: 0.8732 (mp0) cc_final: 0.8484 (mp0) REVERT: C 513 ASN cc_start: 0.8151 (m-40) cc_final: 0.7279 (p0) REVERT: C 554 ASN cc_start: 0.9178 (m110) cc_final: 0.8697 (m-40) REVERT: C 630 MET cc_start: 0.7969 (mpp) cc_final: 0.7453 (mpp) REVERT: C 675 ARG cc_start: 0.4843 (mtt180) cc_final: 0.4216 (mtt180) REVERT: C 688 ILE cc_start: 0.9361 (mm) cc_final: 0.9151 (tp) REVERT: C 754 TYR cc_start: 0.8098 (m-80) cc_final: 0.7506 (m-80) REVERT: C 779 VAL cc_start: 0.9286 (t) cc_final: 0.9080 (t) REVERT: D 494 LEU cc_start: 0.9005 (tp) cc_final: 0.8797 (tt) REVERT: D 496 ILE cc_start: 0.8306 (mp) cc_final: 0.8100 (mp) REVERT: D 554 ASN cc_start: 0.9042 (m110) cc_final: 0.8826 (t0) REVERT: D 558 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7907 (mm-30) REVERT: D 608 PHE cc_start: 0.5749 (t80) cc_final: 0.5166 (t80) REVERT: D 610 LYS cc_start: 0.8475 (ttpt) cc_final: 0.7921 (tptp) REVERT: D 676 PHE cc_start: 0.8590 (t80) cc_final: 0.8350 (t80) REVERT: D 746 VAL cc_start: 0.9058 (t) cc_final: 0.8816 (m) REVERT: D 767 VAL cc_start: 0.8693 (m) cc_final: 0.8448 (m) REVERT: D 814 MET cc_start: 0.8711 (mmp) cc_final: 0.8425 (mmm) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.2049 time to fit residues: 95.9708 Evaluate side-chains 225 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 133 optimal weight: 0.3980 chunk 141 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 HIS ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12060 Z= 0.197 Angle : 0.634 8.141 16424 Z= 0.327 Chirality : 0.045 0.159 1898 Planarity : 0.004 0.047 2072 Dihedral : 7.108 40.064 1766 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.21), residues: 1452 helix: -0.36 (0.18), residues: 734 sheet: -2.02 (0.39), residues: 176 loop : -1.58 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 681 HIS 0.010 0.001 HIS A 831 PHE 0.020 0.001 PHE A 626 TYR 0.018 0.001 TYR C 520 ARG 0.004 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 GLN cc_start: 0.9172 (mm110) cc_final: 0.8945 (mm-40) REVERT: A 681 TRP cc_start: 0.8712 (t60) cc_final: 0.8485 (t60) REVERT: A 749 LYS cc_start: 0.7709 (ptmt) cc_final: 0.7414 (ptpt) REVERT: A 751 GLU cc_start: 0.8311 (pm20) cc_final: 0.8051 (pm20) REVERT: A 754 TYR cc_start: 0.8413 (m-10) cc_final: 0.7929 (m-80) REVERT: A 814 MET cc_start: 0.9148 (mtp) cc_final: 0.8898 (mtp) REVERT: B 557 ASN cc_start: 0.9358 (t0) cc_final: 0.8907 (t0) REVERT: B 564 PHE cc_start: 0.8272 (m-80) cc_final: 0.7989 (m-10) REVERT: B 599 LYS cc_start: 0.6964 (ptpp) cc_final: 0.6476 (mmmt) REVERT: B 685 VAL cc_start: 0.8877 (t) cc_final: 0.8665 (t) REVERT: B 700 LEU cc_start: 0.9228 (mm) cc_final: 0.8970 (mm) REVERT: B 772 ASP cc_start: 0.7905 (m-30) cc_final: 0.7462 (m-30) REVERT: B 828 GLU cc_start: 0.8731 (mp0) cc_final: 0.8498 (mp0) REVERT: C 513 ASN cc_start: 0.8246 (m-40) cc_final: 0.7394 (p0) REVERT: C 562 ASP cc_start: 0.8291 (t70) cc_final: 0.7984 (t70) REVERT: C 630 MET cc_start: 0.8003 (mpp) cc_final: 0.7479 (mpp) REVERT: C 675 ARG cc_start: 0.4807 (mtt180) cc_final: 0.4281 (mtt180) REVERT: C 691 SER cc_start: 0.9011 (m) cc_final: 0.8659 (p) REVERT: D 570 ASP cc_start: 0.7817 (m-30) cc_final: 0.7548 (m-30) REVERT: D 608 PHE cc_start: 0.5603 (t80) cc_final: 0.5183 (t80) REVERT: D 610 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7852 (tptp) REVERT: D 746 VAL cc_start: 0.9042 (t) cc_final: 0.8781 (m) REVERT: D 767 VAL cc_start: 0.8660 (m) cc_final: 0.8389 (m) REVERT: D 772 ASP cc_start: 0.7719 (m-30) cc_final: 0.7513 (m-30) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2088 time to fit residues: 92.3607 Evaluate side-chains 221 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN C 554 ASN D 725 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12060 Z= 0.276 Angle : 0.694 11.219 16424 Z= 0.358 Chirality : 0.047 0.278 1898 Planarity : 0.005 0.047 2072 Dihedral : 6.885 39.975 1766 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.22), residues: 1452 helix: -0.17 (0.18), residues: 742 sheet: -1.97 (0.41), residues: 176 loop : -1.64 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 859 HIS 0.007 0.001 HIS A 831 PHE 0.021 0.002 PHE A 623 TYR 0.017 0.002 TYR C 552 ARG 0.005 0.001 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 GLN cc_start: 0.9273 (mm110) cc_final: 0.9011 (mm-40) REVERT: A 626 PHE cc_start: 0.7774 (t80) cc_final: 0.7385 (t80) REVERT: A 675 ARG cc_start: 0.5878 (mtt180) cc_final: 0.5573 (mtt180) REVERT: A 681 TRP cc_start: 0.8721 (t60) cc_final: 0.8495 (t60) REVERT: A 749 LYS cc_start: 0.7930 (ptmt) cc_final: 0.7610 (ptpt) REVERT: A 751 GLU cc_start: 0.8261 (pm20) cc_final: 0.7901 (pm20) REVERT: A 754 TYR cc_start: 0.8343 (m-10) cc_final: 0.7841 (m-80) REVERT: A 814 MET cc_start: 0.9191 (mtp) cc_final: 0.8952 (mtp) REVERT: A 855 LEU cc_start: 0.7752 (mm) cc_final: 0.7429 (tp) REVERT: B 557 ASN cc_start: 0.9382 (t0) cc_final: 0.8974 (t0) REVERT: B 599 LYS cc_start: 0.7285 (ptpp) cc_final: 0.6559 (mmmt) REVERT: B 610 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8314 (tptp) REVERT: B 700 LEU cc_start: 0.9317 (mm) cc_final: 0.9089 (mm) REVERT: B 746 VAL cc_start: 0.8901 (t) cc_final: 0.8613 (m) REVERT: B 767 VAL cc_start: 0.8457 (m) cc_final: 0.8109 (m) REVERT: B 828 GLU cc_start: 0.8723 (mp0) cc_final: 0.8522 (mp0) REVERT: C 562 ASP cc_start: 0.8600 (t70) cc_final: 0.8214 (t0) REVERT: C 599 LYS cc_start: 0.5933 (mmtm) cc_final: 0.5306 (pptt) REVERT: C 630 MET cc_start: 0.8107 (mpp) cc_final: 0.7467 (mpp) REVERT: C 632 TRP cc_start: 0.6922 (t60) cc_final: 0.6680 (t60) REVERT: C 675 ARG cc_start: 0.5146 (mtt180) cc_final: 0.4856 (mtt180) REVERT: C 695 SER cc_start: 0.8855 (m) cc_final: 0.8549 (t) REVERT: C 754 TYR cc_start: 0.8091 (m-80) cc_final: 0.7878 (m-80) REVERT: C 814 MET cc_start: 0.9374 (mmp) cc_final: 0.9129 (mmp) REVERT: C 861 LEU cc_start: 0.9056 (tp) cc_final: 0.8794 (tt) REVERT: D 570 ASP cc_start: 0.7921 (m-30) cc_final: 0.7584 (m-30) REVERT: D 610 LYS cc_start: 0.8493 (ttpt) cc_final: 0.7932 (tptp) REVERT: D 746 VAL cc_start: 0.9016 (t) cc_final: 0.8743 (m) REVERT: D 767 VAL cc_start: 0.8690 (m) cc_final: 0.8396 (m) REVERT: D 772 ASP cc_start: 0.7774 (m-30) cc_final: 0.7556 (m-30) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2117 time to fit residues: 89.2857 Evaluate side-chains 212 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 820 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12060 Z= 0.232 Angle : 0.651 7.806 16424 Z= 0.332 Chirality : 0.047 0.287 1898 Planarity : 0.004 0.045 2072 Dihedral : 6.633 41.125 1766 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1452 helix: 0.11 (0.19), residues: 740 sheet: -1.88 (0.42), residues: 176 loop : -1.59 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 859 HIS 0.005 0.001 HIS A 831 PHE 0.020 0.002 PHE D 626 TYR 0.014 0.002 TYR C 552 ARG 0.007 0.001 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 GLN cc_start: 0.9258 (mm110) cc_final: 0.9035 (mm-40) REVERT: A 626 PHE cc_start: 0.7700 (t80) cc_final: 0.7257 (t80) REVERT: A 675 ARG cc_start: 0.5955 (mtt180) cc_final: 0.5637 (mtt180) REVERT: A 681 TRP cc_start: 0.8776 (t60) cc_final: 0.8298 (t60) REVERT: A 749 LYS cc_start: 0.7792 (ptmt) cc_final: 0.7571 (ptpt) REVERT: A 751 GLU cc_start: 0.8299 (pm20) cc_final: 0.7915 (pm20) REVERT: A 754 TYR cc_start: 0.8309 (m-10) cc_final: 0.7830 (m-80) REVERT: A 814 MET cc_start: 0.9270 (mtp) cc_final: 0.9019 (mtp) REVERT: A 855 LEU cc_start: 0.7513 (mm) cc_final: 0.7311 (tp) REVERT: A 858 PHE cc_start: 0.8367 (m-10) cc_final: 0.8157 (m-10) REVERT: B 557 ASN cc_start: 0.9379 (t0) cc_final: 0.8981 (t0) REVERT: B 570 ASP cc_start: 0.7744 (m-30) cc_final: 0.6983 (m-30) REVERT: B 599 LYS cc_start: 0.7431 (ptpp) cc_final: 0.6644 (mmtt) REVERT: B 610 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8465 (mtpp) REVERT: B 630 MET cc_start: 0.7631 (ppp) cc_final: 0.7258 (ppp) REVERT: B 681 TRP cc_start: 0.7967 (t60) cc_final: 0.7691 (t60) REVERT: B 828 GLU cc_start: 0.8680 (mp0) cc_final: 0.8443 (mp0) REVERT: C 562 ASP cc_start: 0.8665 (t70) cc_final: 0.8281 (t0) REVERT: C 630 MET cc_start: 0.8154 (mpp) cc_final: 0.7527 (mpp) REVERT: C 675 ARG cc_start: 0.5567 (mtt180) cc_final: 0.5280 (mtt180) REVERT: C 695 SER cc_start: 0.8914 (m) cc_final: 0.8631 (t) REVERT: C 754 TYR cc_start: 0.8126 (m-80) cc_final: 0.7840 (m-10) REVERT: C 814 MET cc_start: 0.9400 (mmp) cc_final: 0.9188 (mmm) REVERT: C 861 LEU cc_start: 0.9059 (tp) cc_final: 0.8835 (tt) REVERT: D 570 ASP cc_start: 0.8027 (m-30) cc_final: 0.7621 (m-30) REVERT: D 610 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7909 (tptp) REVERT: D 676 PHE cc_start: 0.8300 (t80) cc_final: 0.8065 (t80) REVERT: D 746 VAL cc_start: 0.9009 (t) cc_final: 0.8746 (m) REVERT: D 767 VAL cc_start: 0.8693 (m) cc_final: 0.8355 (m) REVERT: D 772 ASP cc_start: 0.7822 (m-30) cc_final: 0.7563 (m-30) REVERT: D 828 GLU cc_start: 0.8383 (pm20) cc_final: 0.8150 (pm20) REVERT: D 832 ARG cc_start: 0.8076 (mpp80) cc_final: 0.7860 (mtm110) REVERT: C 1001 GLU cc_start: 0.5696 (tt0) cc_final: 0.5230 (tt0) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2158 time to fit residues: 88.8521 Evaluate side-chains 215 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN A 725 GLN ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12060 Z= 0.198 Angle : 0.621 7.575 16424 Z= 0.316 Chirality : 0.046 0.291 1898 Planarity : 0.004 0.045 2072 Dihedral : 6.418 40.581 1766 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.08 % Allowed : 1.35 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1452 helix: 0.31 (0.19), residues: 736 sheet: -1.89 (0.42), residues: 176 loop : -1.46 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 681 HIS 0.003 0.000 HIS A 831 PHE 0.027 0.002 PHE C 877 TYR 0.017 0.001 TYR A 504 ARG 0.011 0.000 ARG A 708 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 ARG cc_start: 0.8403 (tmt170) cc_final: 0.8087 (tpt90) REVERT: A 585 GLN cc_start: 0.9254 (mm110) cc_final: 0.9045 (mm-40) REVERT: A 599 LYS cc_start: 0.5810 (mptt) cc_final: 0.5387 (mmtm) REVERT: A 626 PHE cc_start: 0.7710 (t80) cc_final: 0.7415 (m-80) REVERT: A 680 ILE cc_start: 0.9211 (mm) cc_final: 0.8983 (mm) REVERT: A 751 GLU cc_start: 0.8269 (pm20) cc_final: 0.7836 (pm20) REVERT: A 754 TYR cc_start: 0.8273 (m-10) cc_final: 0.7782 (m-80) REVERT: A 855 LEU cc_start: 0.7523 (mm) cc_final: 0.7311 (tp) REVERT: B 570 ASP cc_start: 0.7708 (m-30) cc_final: 0.7076 (m-30) REVERT: B 599 LYS cc_start: 0.7458 (ptpp) cc_final: 0.6622 (mmtt) REVERT: B 610 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8330 (tptp) REVERT: B 630 MET cc_start: 0.7619 (ppp) cc_final: 0.7285 (ppp) REVERT: B 681 TRP cc_start: 0.7976 (t60) cc_final: 0.7625 (t60) REVERT: B 754 TYR cc_start: 0.9129 (m-10) cc_final: 0.8881 (m-10) REVERT: B 828 GLU cc_start: 0.8703 (mp0) cc_final: 0.8464 (mp0) REVERT: C 562 ASP cc_start: 0.8707 (t70) cc_final: 0.8382 (t0) REVERT: C 592 LEU cc_start: 0.9299 (mt) cc_final: 0.8985 (mt) REVERT: C 630 MET cc_start: 0.8157 (mpp) cc_final: 0.7511 (mpp) REVERT: C 675 ARG cc_start: 0.5690 (mtt180) cc_final: 0.5390 (mtt180) REVERT: C 695 SER cc_start: 0.8935 (m) cc_final: 0.8672 (t) REVERT: C 754 TYR cc_start: 0.8169 (m-80) cc_final: 0.7942 (m-10) REVERT: C 814 MET cc_start: 0.9389 (mmp) cc_final: 0.9166 (mmp) REVERT: C 877 PHE cc_start: 0.7494 (m-80) cc_final: 0.7144 (m-80) REVERT: D 570 ASP cc_start: 0.7982 (m-30) cc_final: 0.7559 (m-30) REVERT: D 610 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7890 (tptp) REVERT: D 676 PHE cc_start: 0.8249 (t80) cc_final: 0.8026 (t80) REVERT: D 746 VAL cc_start: 0.9003 (t) cc_final: 0.8758 (m) REVERT: D 767 VAL cc_start: 0.8705 (m) cc_final: 0.8356 (m) REVERT: D 772 ASP cc_start: 0.7815 (m-30) cc_final: 0.7564 (m-30) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.2195 time to fit residues: 90.6747 Evaluate side-chains 218 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12060 Z= 0.257 Angle : 0.663 7.781 16424 Z= 0.339 Chirality : 0.047 0.305 1898 Planarity : 0.004 0.044 2072 Dihedral : 6.499 40.853 1766 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1452 helix: 0.24 (0.19), residues: 738 sheet: -1.83 (0.43), residues: 172 loop : -1.57 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 681 HIS 0.004 0.001 HIS A 831 PHE 0.024 0.002 PHE C 877 TYR 0.014 0.002 TYR C 552 ARG 0.006 0.001 ARG D 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 GLN cc_start: 0.9251 (mm110) cc_final: 0.8878 (mm-40) REVERT: A 626 PHE cc_start: 0.7680 (t80) cc_final: 0.7463 (m-80) REVERT: A 751 GLU cc_start: 0.8246 (pm20) cc_final: 0.7841 (pm20) REVERT: A 754 TYR cc_start: 0.8253 (m-10) cc_final: 0.7778 (m-80) REVERT: A 855 LEU cc_start: 0.7549 (mm) cc_final: 0.7220 (tp) REVERT: B 557 ASN cc_start: 0.9361 (t0) cc_final: 0.8983 (t0) REVERT: B 570 ASP cc_start: 0.8257 (m-30) cc_final: 0.8035 (m-30) REVERT: B 610 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8582 (mtpp) REVERT: B 630 MET cc_start: 0.7603 (ppp) cc_final: 0.7218 (ppp) REVERT: B 681 TRP cc_start: 0.7952 (t60) cc_final: 0.7220 (t-100) REVERT: B 754 TYR cc_start: 0.9142 (m-10) cc_final: 0.8878 (m-10) REVERT: B 828 GLU cc_start: 0.8684 (mp0) cc_final: 0.8451 (mp0) REVERT: C 562 ASP cc_start: 0.8660 (t70) cc_final: 0.8385 (t0) REVERT: C 630 MET cc_start: 0.8202 (mpp) cc_final: 0.7472 (mpp) REVERT: C 675 ARG cc_start: 0.5834 (mtt180) cc_final: 0.5413 (mtt180) REVERT: C 695 SER cc_start: 0.8957 (m) cc_final: 0.8721 (t) REVERT: C 754 TYR cc_start: 0.8223 (m-80) cc_final: 0.8002 (m-10) REVERT: C 814 MET cc_start: 0.9422 (mmp) cc_final: 0.9169 (mmm) REVERT: C 839 HIS cc_start: 0.6722 (m90) cc_final: 0.6509 (m90) REVERT: D 570 ASP cc_start: 0.8010 (m-30) cc_final: 0.7600 (m-30) REVERT: D 610 LYS cc_start: 0.8456 (ttpt) cc_final: 0.7915 (tptp) REVERT: D 676 PHE cc_start: 0.8253 (t80) cc_final: 0.8038 (t80) REVERT: D 746 VAL cc_start: 0.8983 (t) cc_final: 0.8718 (m) REVERT: D 767 VAL cc_start: 0.8665 (m) cc_final: 0.8296 (m) REVERT: D 772 ASP cc_start: 0.7888 (m-30) cc_final: 0.7622 (m-30) REVERT: D 814 MET cc_start: 0.9042 (mmp) cc_final: 0.8806 (mmp) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2069 time to fit residues: 82.4516 Evaluate side-chains 209 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 5.9990 chunk 122 optimal weight: 0.0870 chunk 131 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN A 725 GLN ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12060 Z= 0.178 Angle : 0.616 8.315 16424 Z= 0.310 Chirality : 0.046 0.300 1898 Planarity : 0.004 0.044 2072 Dihedral : 6.253 41.373 1766 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1452 helix: 0.45 (0.19), residues: 740 sheet: -1.72 (0.43), residues: 172 loop : -1.55 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 681 HIS 0.002 0.000 HIS C 831 PHE 0.017 0.002 PHE B 858 TYR 0.013 0.001 TYR C 552 ARG 0.004 0.000 ARG D 832 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 ARG cc_start: 0.8474 (tmt170) cc_final: 0.8115 (tpt90) REVERT: A 585 GLN cc_start: 0.9248 (mm110) cc_final: 0.8988 (mm-40) REVERT: A 626 PHE cc_start: 0.7725 (t80) cc_final: 0.7059 (t80) REVERT: A 630 MET cc_start: 0.7958 (mtp) cc_final: 0.7692 (mtt) REVERT: A 751 GLU cc_start: 0.8231 (pm20) cc_final: 0.7795 (pm20) REVERT: A 754 TYR cc_start: 0.8276 (m-10) cc_final: 0.7793 (m-80) REVERT: A 855 LEU cc_start: 0.7470 (mm) cc_final: 0.7177 (tp) REVERT: B 570 ASP cc_start: 0.8140 (m-30) cc_final: 0.7876 (m-30) REVERT: B 630 MET cc_start: 0.7579 (ppp) cc_final: 0.7251 (ppp) REVERT: B 681 TRP cc_start: 0.7885 (t60) cc_final: 0.7161 (t-100) REVERT: B 754 TYR cc_start: 0.9100 (m-10) cc_final: 0.8821 (m-10) REVERT: B 828 GLU cc_start: 0.8733 (mp0) cc_final: 0.8436 (mp0) REVERT: C 562 ASP cc_start: 0.8598 (t70) cc_final: 0.8375 (t0) REVERT: C 630 MET cc_start: 0.8212 (mpp) cc_final: 0.7549 (mpp) REVERT: C 675 ARG cc_start: 0.5836 (mtt180) cc_final: 0.5333 (mtt180) REVERT: C 695 SER cc_start: 0.8923 (m) cc_final: 0.8707 (t) REVERT: C 754 TYR cc_start: 0.8241 (m-80) cc_final: 0.8034 (m-80) REVERT: C 779 VAL cc_start: 0.9237 (t) cc_final: 0.9031 (t) REVERT: C 814 MET cc_start: 0.9403 (mmp) cc_final: 0.9128 (mmp) REVERT: D 570 ASP cc_start: 0.8038 (m-30) cc_final: 0.7559 (m-30) REVERT: D 610 LYS cc_start: 0.8578 (ttpt) cc_final: 0.7840 (tptp) REVERT: D 676 PHE cc_start: 0.8213 (t80) cc_final: 0.7993 (t80) REVERT: D 703 ARG cc_start: 0.7840 (ttm110) cc_final: 0.7574 (ttp-110) REVERT: D 725 GLN cc_start: 0.6782 (tt0) cc_final: 0.6175 (tt0) REVERT: D 746 VAL cc_start: 0.8928 (t) cc_final: 0.8721 (m) REVERT: D 767 VAL cc_start: 0.8653 (m) cc_final: 0.8309 (m) REVERT: D 772 ASP cc_start: 0.7839 (m-30) cc_final: 0.7582 (m-30) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2167 time to fit residues: 85.8749 Evaluate side-chains 229 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 133 optimal weight: 0.0770 chunk 115 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.6669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12060 Z= 0.219 Angle : 0.626 7.500 16424 Z= 0.321 Chirality : 0.046 0.304 1898 Planarity : 0.004 0.044 2072 Dihedral : 6.264 41.568 1766 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1452 helix: 0.47 (0.19), residues: 734 sheet: -1.78 (0.43), residues: 172 loop : -1.43 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 617 HIS 0.002 0.000 HIS A 831 PHE 0.042 0.002 PHE C 564 TYR 0.014 0.002 TYR A 504 ARG 0.009 0.001 ARG C 483 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 ARG cc_start: 0.8497 (tmt170) cc_final: 0.8141 (tpt90) REVERT: A 585 GLN cc_start: 0.9236 (mm110) cc_final: 0.9035 (mm-40) REVERT: A 626 PHE cc_start: 0.7615 (t80) cc_final: 0.7079 (t80) REVERT: A 630 MET cc_start: 0.7998 (mtp) cc_final: 0.7724 (mtt) REVERT: A 754 TYR cc_start: 0.8130 (m-10) cc_final: 0.7624 (m-80) REVERT: A 855 LEU cc_start: 0.7474 (mm) cc_final: 0.7223 (tp) REVERT: B 570 ASP cc_start: 0.8178 (m-30) cc_final: 0.7903 (m-30) REVERT: B 630 MET cc_start: 0.7603 (ppp) cc_final: 0.7270 (ppp) REVERT: B 681 TRP cc_start: 0.7939 (t60) cc_final: 0.7230 (t-100) REVERT: B 746 VAL cc_start: 0.8789 (t) cc_final: 0.8541 (m) REVERT: B 754 TYR cc_start: 0.9127 (m-10) cc_final: 0.8883 (m-10) REVERT: B 767 VAL cc_start: 0.8489 (m) cc_final: 0.8119 (m) REVERT: B 828 GLU cc_start: 0.8766 (mp0) cc_final: 0.8494 (mp0) REVERT: C 630 MET cc_start: 0.8190 (mpp) cc_final: 0.7474 (mpp) REVERT: C 675 ARG cc_start: 0.6015 (mtt180) cc_final: 0.5707 (mtt180) REVERT: C 695 SER cc_start: 0.8947 (m) cc_final: 0.8741 (t) REVERT: C 779 VAL cc_start: 0.9233 (t) cc_final: 0.9016 (t) REVERT: C 814 MET cc_start: 0.9449 (mmp) cc_final: 0.9189 (mmm) REVERT: D 570 ASP cc_start: 0.8017 (m-30) cc_final: 0.7551 (m-30) REVERT: D 610 LYS cc_start: 0.8562 (ttpt) cc_final: 0.7923 (tptp) REVERT: D 676 PHE cc_start: 0.8192 (t80) cc_final: 0.7987 (t80) REVERT: D 725 GLN cc_start: 0.6737 (tt0) cc_final: 0.6162 (tt0) REVERT: D 746 VAL cc_start: 0.8960 (t) cc_final: 0.8740 (m) REVERT: D 754 TYR cc_start: 0.9087 (m-10) cc_final: 0.8872 (m-10) REVERT: D 767 VAL cc_start: 0.8615 (m) cc_final: 0.8256 (m) REVERT: D 772 ASP cc_start: 0.7849 (m-30) cc_final: 0.7595 (m-30) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2091 time to fit residues: 82.4932 Evaluate side-chains 216 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 17 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN A 725 GLN ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.085016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067468 restraints weight = 50770.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.069678 restraints weight = 32150.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.071183 restraints weight = 23332.634| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12060 Z= 0.206 Angle : 0.625 8.550 16424 Z= 0.318 Chirality : 0.046 0.302 1898 Planarity : 0.004 0.043 2072 Dihedral : 6.190 41.583 1766 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.22), residues: 1452 helix: 0.50 (0.19), residues: 740 sheet: -1.73 (0.43), residues: 172 loop : -1.44 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 681 HIS 0.002 0.000 HIS A 831 PHE 0.025 0.002 PHE C 564 TYR 0.013 0.002 TYR B 692 ARG 0.006 0.000 ARG B 832 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.18 seconds wall clock time: 48 minutes 40.83 seconds (2920.83 seconds total)