Starting phenix.real_space_refine (version: dev) on Mon Feb 20 09:19:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2023/7lzi_23607.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2023/7lzi_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_2023/7lzi_23607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2023/7lzi_23607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2023/7lzi_23607.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/02_2023/7lzi_23607.pdb" } resolution = 4.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 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 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 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 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: 6.73, per 1000 atoms: 0.57 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: 4.70 Conformation dependent library (CDL) restraints added in 1.9 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: 0.73 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: 3.97 Time building geometry restraints manager: 5.08 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=" 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 bond pdb=" N ASN B 719 " pdb=" CA ASN B 719 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.89e+00 bond pdb=" C TYR B 534 " pdb=" N PRO B 535 " ideal model delta sigma weight residual 1.335 1.317 0.018 8.70e-03 1.32e+04 4.07e+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=" C3 NAG G 1 " pdb=" C4 NAG G 1 " pdb=" C5 NAG G 1 " ideal model delta sigma weight residual 110.18 117.49 -7.31 1.42e+00 4.96e-01 2.65e+01 angle pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" C5 NAG E 1 " ideal model delta sigma weight residual 110.18 116.86 -6.68 1.42e+00 4.96e-01 2.22e+01 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=" C4 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 109.74 115.70 -5.96 1.35e+00 5.51e-01 1.96e+01 ... (remaining 16419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.87: 6782 19.87 - 39.74: 256 39.74 - 59.60: 22 59.60 - 79.47: 12 79.47 - 99.34: 4 Dihedral angle restraints: 7076 sinusoidal: 2790 harmonic: 4286 Sorted by residual: dihedral pdb=" C1 NAG F 2 " pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " ideal model delta sinusoidal sigma weight residual -50.00 49.34 -99.34 1 2.00e+01 2.50e-03 2.79e+01 dihedral pdb=" C2 NAG H 2 " pdb=" C3 NAG H 2 " pdb=" C4 NAG H 2 " pdb=" C5 NAG H 2 " ideal model delta sinusoidal sigma weight residual 50.00 -48.02 98.02 1 2.00e+01 2.50e-03 2.73e+01 dihedral pdb=" C1 NAG H 2 " pdb=" C2 NAG H 2 " pdb=" C3 NAG H 2 " pdb=" C4 NAG H 2 " ideal model delta sinusoidal sigma weight residual -50.00 46.75 -96.75 1 2.00e+01 2.50e-03 2.68e+01 ... (remaining 7073 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 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: 10.290 Check model and map are aligned: 0.160 Process input model: 31.710 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 0.054 12060 Z= 0.300 Angle : 0.930 13.778 16424 Z= 0.531 Chirality : 0.063 1.027 1898 Planarity : 0.007 0.060 2072 Dihedral : 11.347 99.338 4296 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 % 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 *********************** 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 : 1.493 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 outliers start: 4 outliers final: 1 residues processed: 520 average time/residue: 0.2604 time to fit residues: 185.8384 Evaluate side-chains 261 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1041 time to fit residues: 2.0629 ------------------------------------------------------------------------------- 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: 4.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 0.0770 chunk 132 optimal weight: 8.9990 overall best weight: 1.4944 ------------------------------------------------------------------------------- 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 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 554 ASN C 563 ASN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 549 ASN D 704 GLN D 725 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 820 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 12060 Z= 0.287 Angle : 0.736 9.151 16424 Z= 0.399 Chirality : 0.051 0.640 1898 Planarity : 0.006 0.048 2072 Dihedral : 8.351 100.448 1646 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.16 % 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: -3.35 (0.19), residues: 1452 helix: -2.01 (0.15), residues: 734 sheet: -2.55 (0.35), residues: 176 loop : -2.12 (0.24), residues: 542 *********************** 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 338 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 336 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 336 average time/residue: 0.2358 time to fit residues: 113.5332 Evaluate side-chains 234 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9891 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 736 ASN ** C 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 12060 Z= 0.210 Angle : 0.670 9.315 16424 Z= 0.357 Chirality : 0.047 0.190 1898 Planarity : 0.005 0.047 2072 Dihedral : 8.082 100.343 1646 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.08 % 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: -2.40 (0.20), residues: 1452 helix: -1.13 (0.17), residues: 736 sheet: -2.18 (0.38), residues: 176 loop : -1.80 (0.25), residues: 540 *********************** 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 307 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 307 average time/residue: 0.2064 time to fit residues: 94.5568 Evaluate side-chains 214 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8111 ------------------------------------------------------------------------------- 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: 6.9990 chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 GLN D 831 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 12060 Z= 0.334 Angle : 0.729 8.499 16424 Z= 0.390 Chirality : 0.052 0.599 1898 Planarity : 0.005 0.050 2072 Dihedral : 7.992 100.266 1646 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 0.00 % 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: -1.97 (0.21), residues: 1452 helix: -0.61 (0.18), residues: 740 sheet: -2.23 (0.39), residues: 172 loop : -1.79 (0.26), residues: 540 *********************** 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 282 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.538 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 outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2192 time to fit residues: 91.0053 Evaluate side-chains 207 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7864 ------------------------------------------------------------------------------- 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: 0.5980 chunk 80 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 704 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: 0.7546 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 12060 Z= 0.215 Angle : 0.654 8.543 16424 Z= 0.345 Chirality : 0.049 0.578 1898 Planarity : 0.004 0.045 2072 Dihedral : 7.764 99.127 1646 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 0.00 % 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: -1.60 (0.21), residues: 1452 helix: -0.27 (0.19), residues: 738 sheet: -2.16 (0.40), residues: 172 loop : -1.64 (0.26), residues: 542 *********************** 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 271 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.434 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 outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2517 time to fit residues: 101.7062 Evaluate side-chains 205 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9502 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.0870 chunk 141 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.0370 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN A 831 HIS B 725 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 12060 Z= 0.193 Angle : 0.618 8.502 16424 Z= 0.325 Chirality : 0.049 0.596 1898 Planarity : 0.004 0.047 2072 Dihedral : 7.631 99.490 1646 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.00 % 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: -1.31 (0.22), residues: 1452 helix: 0.03 (0.19), residues: 742 sheet: -2.12 (0.39), residues: 172 loop : -1.57 (0.26), residues: 538 *********************** 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 281 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.308 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 outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2291 time to fit residues: 95.0087 Evaluate side-chains 214 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9568 ------------------------------------------------------------------------------- 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: 0.9980 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN A 831 HIS B 725 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 12060 Z= 0.199 Angle : 0.613 7.442 16424 Z= 0.323 Chirality : 0.049 0.603 1898 Planarity : 0.004 0.048 2072 Dihedral : 7.529 99.928 1646 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 0.00 % 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: -1.16 (0.22), residues: 1452 helix: 0.16 (0.19), residues: 742 sheet: -2.11 (0.39), residues: 172 loop : -1.51 (0.26), residues: 538 *********************** 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 276 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.429 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 outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2355 time to fit residues: 93.7443 Evaluate side-chains 201 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9085 ------------------------------------------------------------------------------- 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: 0.9980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN A 759 GLN B 725 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 12060 Z= 0.230 Angle : 0.637 9.498 16424 Z= 0.334 Chirality : 0.050 0.633 1898 Planarity : 0.004 0.049 2072 Dihedral : 7.547 100.286 1646 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.00 % 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: -1.18 (0.22), residues: 1452 helix: 0.16 (0.19), residues: 746 sheet: -2.11 (0.39), residues: 172 loop : -1.54 (0.26), residues: 534 *********************** 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 264 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.443 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 outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2352 time to fit residues: 90.7176 Evaluate side-chains 206 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7588 ------------------------------------------------------------------------------- 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: 0.0070 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 124 optimal weight: 0.2980 chunk 130 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN B 725 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 12060 Z= 0.179 Angle : 0.630 9.364 16424 Z= 0.324 Chirality : 0.049 0.612 1898 Planarity : 0.004 0.049 2072 Dihedral : 7.453 100.570 1646 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.00 % 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: -1.07 (0.22), residues: 1452 helix: 0.23 (0.19), residues: 744 sheet: -2.00 (0.40), residues: 172 loop : -1.47 (0.26), residues: 536 *********************** 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 274 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.530 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 outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2371 time to fit residues: 93.4904 Evaluate side-chains 208 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9726 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN B 725 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 12060 Z= 0.219 Angle : 0.642 8.695 16424 Z= 0.333 Chirality : 0.050 0.649 1898 Planarity : 0.004 0.049 2072 Dihedral : 7.462 100.931 1646 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 0.00 % 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: -1.01 (0.22), residues: 1452 helix: 0.30 (0.19), residues: 742 sheet: -1.98 (0.39), residues: 182 loop : -1.45 (0.26), residues: 528 ********************** 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 267 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.062 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 outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1853 time to fit residues: 71.9818 Evaluate side-chains 205 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3497 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 0.1980 chunk 106 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: