Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 09:09:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/07_2023/7lzi_23607.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/07_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_23607/07_2023/7lzi_23607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/07_2023/7lzi_23607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/07_2023/7lzi_23607.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzi_23607/07_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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 6.04, per 1000 atoms: 0.51 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: 4.61 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: 0.78 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: 3.45 Time building geometry restraints manager: 5.02 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 - 14.72: 6555 14.72 - 29.44: 352 29.44 - 44.16: 93 44.16 - 58.88: 16 58.88 - 73.60: 12 Dihedral angle restraints: 7028 sinusoidal: 2742 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 7025 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: 2.510 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: 10.230 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.030 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.860 ------------------------------------------------------------------------------- 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 : 10.790 73.597 4248 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 : 1.364 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: 0.2567 time to fit residues: 183.7171 Evaluate side-chains 261 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1066 time to fit residues: 1.9590 ------------------------------------------------------------------------------- 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: 7.9990 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 D 549 ASN D 704 GLN D 725 GLN D 820 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 12060 Z= 0.260 Angle : 0.734 9.140 16424 Z= 0.386 Chirality : 0.048 0.263 1898 Planarity : 0.006 0.056 2072 Dihedral : 5.841 25.037 1598 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % 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: -3.23 (0.19), residues: 1452 helix: -1.88 (0.15), residues: 732 sheet: -2.52 (0.35), residues: 176 loop : -2.10 (0.24), residues: 544 *********************** 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 : 1.339 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 outliers start: 2 outliers final: 0 residues processed: 336 average time/residue: 0.2285 time to fit residues: 110.2456 Evaluate side-chains 242 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8912 ------------------------------------------------------------------------------- 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: 0.9990 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 143 optimal weight: 0.0770 chunk 118 optimal weight: 0.8980 chunk 131 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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 ** B 805 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 D 725 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4730 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= 0.194 Angle : 0.657 11.034 16424 Z= 0.340 Chirality : 0.046 0.224 1898 Planarity : 0.005 0.064 2072 Dihedral : 5.306 24.227 1598 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: -2.20 (0.20), residues: 1452 helix: -0.93 (0.17), residues: 736 sheet: -2.21 (0.38), residues: 176 loop : -1.72 (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 321 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 320 time to evaluate : 1.407 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: 1 outliers final: 0 residues processed: 321 average time/residue: 0.2026 time to fit residues: 96.2748 Evaluate side-chains 217 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7284 ------------------------------------------------------------------------------- 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: 9.9990 chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 805 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 12060 Z= 0.370 Angle : 0.769 8.906 16424 Z= 0.397 Chirality : 0.048 0.211 1898 Planarity : 0.005 0.047 2072 Dihedral : 5.645 23.793 1598 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % 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: -1.86 (0.21), residues: 1452 helix: -0.49 (0.18), residues: 742 sheet: -2.19 (0.39), residues: 172 loop : -1.79 (0.26), residues: 538 *********************** 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 283 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.363 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: 283 average time/residue: 0.2129 time to fit residues: 88.5084 Evaluate side-chains 201 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8313 ------------------------------------------------------------------------------- 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: 0.6980 chunk 2 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 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: 0.7638 moved from start: 0.5786 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= 0.209 Angle : 0.650 9.119 16424 Z= 0.331 Chirality : 0.046 0.206 1898 Planarity : 0.004 0.046 2072 Dihedral : 5.325 22.929 1598 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % 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: -1.48 (0.22), residues: 1452 helix: -0.14 (0.19), residues: 746 sheet: -2.07 (0.41), residues: 172 loop : -1.67 (0.26), residues: 534 *********************** 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 273 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.390 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: 273 average time/residue: 0.2096 time to fit residues: 85.1391 Evaluate side-chains 207 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.411 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8211 ------------------------------------------------------------------------------- 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: 0.5980 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 141 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 12060 Z= 0.183 Angle : 0.613 8.681 16424 Z= 0.312 Chirality : 0.045 0.220 1898 Planarity : 0.004 0.048 2072 Dihedral : 5.123 23.010 1598 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % 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: -1.19 (0.22), residues: 1452 helix: 0.15 (0.19), residues: 742 sheet: -2.02 (0.41), 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 276 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.220 Fit side-chains 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: 0.2127 time to fit residues: 86.5702 Evaluate side-chains 211 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8487 ------------------------------------------------------------------------------- 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: 3.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 88 optimal weight: 0.3980 chunk 85 optimal weight: 0.0030 chunk 64 optimal weight: 3.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 GLN ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7610 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 12060 Z= 0.174 Angle : 0.609 8.567 16424 Z= 0.308 Chirality : 0.046 0.224 1898 Planarity : 0.004 0.048 2072 Dihedral : 4.956 23.691 1598 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: -1.04 (0.22), residues: 1452 helix: 0.25 (0.19), residues: 748 sheet: -1.98 (0.40), residues: 172 loop : -1.48 (0.26), residues: 532 *********************** 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 273 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.427 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: 273 average time/residue: 0.2244 time to fit residues: 89.4520 Evaluate side-chains 208 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8146 ------------------------------------------------------------------------------- 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: 6.9990 chunk 84 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.6473 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= 0.216 Angle : 0.623 7.714 16424 Z= 0.319 Chirality : 0.046 0.242 1898 Planarity : 0.004 0.048 2072 Dihedral : 5.004 23.893 1598 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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: -1.00 (0.22), residues: 1452 helix: 0.28 (0.19), residues: 754 sheet: -2.01 (0.41), residues: 172 loop : -1.45 (0.26), residues: 526 *********************** 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 : 1.318 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: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2217 time to fit residues: 87.5496 Evaluate side-chains 207 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9090 ------------------------------------------------------------------------------- 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: 0.9990 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 0.0000 chunk 102 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 86 optimal weight: 6.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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** ** 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: 0.7634 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12060 Z= 0.193 Angle : 0.623 8.250 16424 Z= 0.313 Chirality : 0.046 0.250 1898 Planarity : 0.004 0.049 2072 Dihedral : 4.943 24.323 1598 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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: -0.90 (0.22), residues: 1452 helix: 0.36 (0.19), residues: 752 sheet: -1.97 (0.41), residues: 172 loop : -1.39 (0.26), residues: 528 *********************** 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 268 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.496 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: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2090 time to fit residues: 83.4180 Evaluate side-chains 208 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7971 ------------------------------------------------------------------------------- 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: 0.4980 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 133 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.6808 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= 0.176 Angle : 0.600 7.957 16424 Z= 0.305 Chirality : 0.046 0.255 1898 Planarity : 0.004 0.048 2072 Dihedral : 4.837 21.649 1598 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: -0.82 (0.22), residues: 1452 helix: 0.43 (0.19), residues: 754 sheet: -1.93 (0.41), residues: 172 loop : -1.37 (0.26), residues: 526 ********************** 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 266 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.438 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: 266 average time/residue: 0.2013 time to fit residues: 80.3155 Evaluate side-chains 208 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6540 ------------------------------------------------------------------------------- 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: 0.7980 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** A 831 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.086795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.068871 restraints weight = 50155.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071018 restraints weight = 32262.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072432 restraints weight = 23732.486| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.6966 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= 0.181 Angle : 0.611 8.612 16424 Z= 0.312 Chirality : 0.046 0.263 1898 Planarity : 0.004 0.047 2072 Dihedral : 4.836 21.762 1598 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % 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: -0.83 (0.22), residues: 1452 helix: 0.39 (0.19), residues: 754 sheet: -1.87 (0.41), residues: 172 loop : -1.33 (0.27), residues: 526 =============================================================================== Job complete usr+sys time: 2539.04 seconds wall clock time: 46 minutes 42.96 seconds (2802.96 seconds total)