Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 12:45:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/07_2023/6kz4_0785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/07_2023/6kz4_0785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/07_2023/6kz4_0785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/07_2023/6kz4_0785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/07_2023/6kz4_0785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/07_2023/6kz4_0785.pdb" } resolution = 3.0 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= 0.002 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 24 5.16 5 C 10614 2.51 5 N 2922 2.21 5 O 3138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 597": "NH1" <-> "NH2" Residue "E ARG 616": "NH1" <-> "NH2" Residue "E ASP 667": "OD1" <-> "OD2" Residue "E GLU 709": "OE1" <-> "OE2" Residue "E GLU 722": "OE1" <-> "OE2" Residue "E ARG 729": "NH1" <-> "NH2" Residue "E GLU 736": "OE1" <-> "OE2" Residue "E ASP 741": "OD1" <-> "OD2" Residue "E ASP 746": "OD1" <-> "OD2" Residue "E GLU 756": "OE1" <-> "OE2" Residue "E GLU 772": "OE1" <-> "OE2" Residue "E ARG 803": "NH1" <-> "NH2" Residue "E PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 522": "OE1" <-> "OE2" Residue "F ASP 526": "OD1" <-> "OD2" Residue "F PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 616": "NH1" <-> "NH2" Residue "F GLU 709": "OE1" <-> "OE2" Residue "F GLU 722": "OE1" <-> "OE2" Residue "F ARG 729": "NH1" <-> "NH2" Residue "F ASP 731": "OD1" <-> "OD2" Residue "F GLU 733": "OE1" <-> "OE2" Residue "F GLU 736": "OE1" <-> "OE2" Residue "F ASP 741": "OD1" <-> "OD2" Residue "F ASP 746": "OD1" <-> "OD2" Residue "F GLU 756": "OE1" <-> "OE2" Residue "F ARG 803": "NH1" <-> "NH2" Residue "C ARG 597": "NH1" <-> "NH2" Residue "C ARG 616": "NH1" <-> "NH2" Residue "C GLU 709": "OE1" <-> "OE2" Residue "C ASP 712": "OD1" <-> "OD2" Residue "C GLU 722": "OE1" <-> "OE2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "C PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 736": "OE1" <-> "OE2" Residue "C ASP 741": "OD1" <-> "OD2" Residue "C ASP 746": "OD1" <-> "OD2" Residue "C GLU 756": "OE1" <-> "OE2" Residue "C ARG 803": "NH1" <-> "NH2" Residue "C PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 870": "OE1" <-> "OE2" Residue "D ASP 526": "OD1" <-> "OD2" Residue "D GLU 542": "OE1" <-> "OE2" Residue "D ASP 554": "OD1" <-> "OD2" Residue "D ARG 616": "NH1" <-> "NH2" Residue "D PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 709": "OE1" <-> "OE2" Residue "D ARG 729": "NH1" <-> "NH2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D ASP 741": "OD1" <-> "OD2" Residue "D ASP 746": "OD1" <-> "OD2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "D GLU 772": "OE1" <-> "OE2" Residue "D ARG 803": "NH1" <-> "NH2" Residue "D PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ASP 526": "OD1" <-> "OD2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A GLU 542": "OE1" <-> "OE2" Residue "A ARG 597": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A ASP 712": "OD1" <-> "OD2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A ASP 731": "OD1" <-> "OD2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 741": "OD1" <-> "OD2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "A PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 870": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B ASP 526": "OD1" <-> "OD2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B GLU 709": "OE1" <-> "OE2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B ASP 731": "OD1" <-> "OD2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B ASP 741": "OD1" <-> "OD2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "B GLU 772": "OE1" <-> "OE2" Residue "B ARG 803": "NH1" <-> "NH2" Residue "B GLU 870": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 16698 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2783 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 7.87, per 1000 atoms: 0.47 Number of scatterers: 16698 At special positions: 0 Unit cell: (105.07, 105.07, 114.38, 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 24 16.00 O 3138 8.00 N 2922 7.00 C 10614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 5.93 Conformation dependent library (CDL) restraints added in 2.3 seconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 31 sheets defined 9.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'E' and resid 561 through 567 removed outlier: 3.798A pdb=" N ARG E 564 " --> pdb=" O PRO E 561 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASN E 565 " --> pdb=" O GLU E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 601 Processing helix chain 'E' and resid 626 through 632 removed outlier: 3.589A pdb=" N ALA E 630 " --> pdb=" O SER E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 715 removed outlier: 3.575A pdb=" N LEU E 715 " --> pdb=" O ASP E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 802 removed outlier: 3.527A pdb=" N VAL E 802 " --> pdb=" O GLN E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 834 Processing helix chain 'F' and resid 626 through 632 removed outlier: 3.533A pdb=" N ALA F 630 " --> pdb=" O SER F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 710 through 715 removed outlier: 3.689A pdb=" N LEU F 715 " --> pdb=" O ASP F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 798 through 802 Processing helix chain 'F' and resid 830 through 834 Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'C' and resid 596 through 601 Processing helix chain 'C' and resid 626 through 632 removed outlier: 3.643A pdb=" N ALA C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 715 removed outlier: 3.595A pdb=" N LEU C 715 " --> pdb=" O ASP C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.542A pdb=" N VAL C 802 " --> pdb=" O GLN C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 834 Processing helix chain 'C' and resid 867 through 871 Processing helix chain 'D' and resid 626 through 632 removed outlier: 3.541A pdb=" N ALA D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 714 Processing helix chain 'D' and resid 798 through 802 Processing helix chain 'D' and resid 830 through 834 Processing helix chain 'D' and resid 867 through 871 Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.801A pdb=" N ARG A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN A 565 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.652A pdb=" N ALA A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 removed outlier: 3.568A pdb=" N LEU A 715 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.566A pdb=" N VAL A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'B' and resid 563 through 567 removed outlier: 3.542A pdb=" N LEU B 567 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 632 removed outlier: 3.525A pdb=" N ALA B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 647 removed outlier: 4.235A pdb=" N LYS B 646 " --> pdb=" O ASP B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 830 through 834 Processing sheet with id=AA1, first strand: chain 'E' and resid 517 through 521 removed outlier: 3.820A pdb=" N VAL E 517 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 555 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR E 545 " --> pdb=" O ASP E 556 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS E 558 " --> pdb=" O VAL E 543 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL E 543 " --> pdb=" O HIS E 558 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL E 533 " --> pdb=" O VAL E 540 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL E 532 " --> pdb=" O ILE E 603 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N PHE E 605 " --> pdb=" O VAL E 532 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU E 534 " --> pdb=" O PHE E 605 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ASN E 607 " --> pdb=" O LEU E 534 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 583 through 584 Processing sheet with id=AA3, first strand: chain 'E' and resid 667 through 669 removed outlier: 6.489A pdb=" N ILE E 653 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR E 718 " --> pdb=" O VAL E 699 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE E 696 " --> pdb=" O GLN E 735 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N PHE E 732 " --> pdb=" O GLN E 636 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR E 638 " --> pdb=" O PHE E 732 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU E 734 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N HIS E 640 " --> pdb=" O LEU E 734 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 702 through 704 removed outlier: 3.577A pdb=" N GLY E 707 " --> pdb=" O SER E 704 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 809 through 811 removed outlier: 6.215A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL E 776 " --> pdb=" O ARG E 793 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG E 793 " --> pdb=" O VAL E 776 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N PHE E 858 " --> pdb=" O SER E 749 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE E 751 " --> pdb=" O PHE E 858 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 553 through 559 removed outlier: 6.836A pdb=" N ASP F 554 " --> pdb=" O VAL F 546 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL F 546 " --> pdb=" O ASP F 554 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP F 556 " --> pdb=" O ILE F 544 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL F 533 " --> pdb=" O VAL F 540 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL F 532 " --> pdb=" O ILE F 603 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE F 605 " --> pdb=" O VAL F 532 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU F 534 " --> pdb=" O PHE F 605 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ASN F 607 " --> pdb=" O LEU F 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 667 through 669 removed outlier: 6.603A pdb=" N ILE F 653 " --> pdb=" O ILE F 660 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE F 696 " --> pdb=" O GLN F 735 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N PHE F 732 " --> pdb=" O GLN F 636 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR F 638 " --> pdb=" O PHE F 732 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU F 734 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS F 640 " --> pdb=" O LEU F 734 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 702 through 704 removed outlier: 3.512A pdb=" N SER F 704 " --> pdb=" O GLY F 707 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 747 through 748 removed outlier: 6.182A pdb=" N MET F 789 " --> pdb=" O MET F 779 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N MET F 779 " --> pdb=" O MET F 789 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA F 791 " --> pdb=" O THR F 777 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL F 773 " --> pdb=" O SER F 795 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL F 766 " --> pdb=" O VAL F 773 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 747 through 748 removed outlier: 7.006A pdb=" N ILE F 751 " --> pdb=" O PHE F 858 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 517 through 521 removed outlier: 3.820A pdb=" N VAL C 517 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 555 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP C 554 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL C 546 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP C 556 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL C 532 " --> pdb=" O ILE C 603 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE C 605 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU C 534 " --> pdb=" O PHE C 605 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N ASN C 607 " --> pdb=" O LEU C 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 583 through 584 Processing sheet with id=AB4, first strand: chain 'C' and resid 667 through 669 removed outlier: 6.540A pdb=" N ILE C 653 " --> pdb=" O ILE C 660 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE C 696 " --> pdb=" O GLN C 735 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 734 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS C 640 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.643A pdb=" N GLY C 707 " --> pdb=" O SER C 704 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 809 through 811 removed outlier: 6.306A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 791 " --> pdb=" O THR C 777 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET C 779 " --> pdb=" O MET C 789 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N MET C 789 " --> pdb=" O MET C 779 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N PHE C 858 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 751 " --> pdb=" O PHE C 858 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 518 through 521 removed outlier: 3.570A pdb=" N ILE D 555 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP D 554 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL D 546 " --> pdb=" O ASP D 554 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP D 556 " --> pdb=" O ILE D 544 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 533 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 605 " --> pdb=" O LEU D 534 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'D' and resid 667 through 669 removed outlier: 6.616A pdb=" N ILE D 653 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR D 718 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE D 696 " --> pdb=" O GLN D 735 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE D 732 " --> pdb=" O GLN D 636 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR D 638 " --> pdb=" O PHE D 732 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU D 734 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS D 640 " --> pdb=" O LEU D 734 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 702 through 704 Processing sheet with id=AC2, first strand: chain 'D' and resid 747 through 748 removed outlier: 6.595A pdb=" N ARG D 793 " --> pdb=" O VAL D 776 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL D 776 " --> pdb=" O ARG D 793 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER D 795 " --> pdb=" O GLY D 774 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY D 774 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 766 " --> pdb=" O VAL D 773 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 747 through 748 removed outlier: 7.001A pdb=" N ILE D 751 " --> pdb=" O PHE D 858 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 517 through 521 removed outlier: 3.778A pdb=" N VAL A 517 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 555 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A 545 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS A 558 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL A 543 " --> pdb=" O HIS A 558 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 533 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 532 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE A 605 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 534 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N ASN A 607 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AC6, first strand: chain 'A' and resid 667 through 669 removed outlier: 6.529A pdb=" N ILE A 653 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 696 " --> pdb=" O GLN A 735 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N PHE A 732 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR A 638 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 734 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS A 640 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'A' and resid 838 through 839 removed outlier: 6.286A pdb=" N PHE A 768 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 791 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET A 779 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N MET A 789 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N PHE A 858 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 751 " --> pdb=" O PHE A 858 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 518 through 521 removed outlier: 3.601A pdb=" N PHE B 553 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL B 546 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP B 556 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 533 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 532 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N PHE B 605 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 534 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ASN B 607 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 667 through 669 removed outlier: 6.625A pdb=" N ILE B 653 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR B 718 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE B 696 " --> pdb=" O GLN B 735 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N PHE B 732 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 638 " --> pdb=" O PHE B 732 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 734 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS B 640 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 747 through 748 removed outlier: 6.666A pdb=" N ARG B 793 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 776 " --> pdb=" O ARG B 793 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER B 795 " --> pdb=" O GLY B 774 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLY B 774 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 766 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 747 through 748 removed outlier: 6.981A pdb=" N ILE B 751 " --> pdb=" O PHE B 858 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 957 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: 5.60 Time building geometry restraints manager: 6.48 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: 5548 1.34 - 1.45: 2085 1.45 - 1.57: 9353 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 17034 Sorted by residual: bond pdb=" C SER A 531 " pdb=" N VAL A 532 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.24e-02 6.50e+03 1.41e+00 bond pdb=" CA VAL D 802 " pdb=" CB VAL D 802 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.39e+00 bond pdb=" CA VAL A 802 " pdb=" CB VAL A 802 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.34e+00 bond pdb=" CB PHE E 840 " pdb=" CG PHE E 840 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.27e+00 bond pdb=" CB PRO B 594 " pdb=" CG PRO B 594 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 9.91e-01 ... (remaining 17029 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.88: 405 105.88 - 112.92: 9261 112.92 - 119.95: 5389 119.95 - 126.99: 7895 126.99 - 134.03: 192 Bond angle restraints: 23142 Sorted by residual: angle pdb=" N VAL F 773 " pdb=" CA VAL F 773 " pdb=" C VAL F 773 " ideal model delta sigma weight residual 113.71 108.81 4.90 9.50e-01 1.11e+00 2.66e+01 angle pdb=" N ASN B 551 " pdb=" CA ASN B 551 " pdb=" C ASN B 551 " ideal model delta sigma weight residual 114.75 108.70 6.05 1.26e+00 6.30e-01 2.31e+01 angle pdb=" N ILE B 660 " pdb=" CA ILE B 660 " pdb=" C ILE B 660 " ideal model delta sigma weight residual 112.96 108.45 4.51 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N ASN F 551 " pdb=" CA ASN F 551 " pdb=" C ASN F 551 " ideal model delta sigma weight residual 114.75 109.86 4.89 1.26e+00 6.30e-01 1.51e+01 angle pdb=" N LEU B 595 " pdb=" CA LEU B 595 " pdb=" C LEU B 595 " ideal model delta sigma weight residual 114.62 110.24 4.38 1.14e+00 7.69e-01 1.48e+01 ... (remaining 23137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9268 17.91 - 35.81: 715 35.81 - 53.72: 107 53.72 - 71.62: 36 71.62 - 89.53: 14 Dihedral angle restraints: 10140 sinusoidal: 3954 harmonic: 6186 Sorted by residual: dihedral pdb=" CA ARG F 536 " pdb=" C ARG F 536 " pdb=" N LYS F 537 " pdb=" CA LYS F 537 " ideal model delta harmonic sigma weight residual 180.00 135.62 44.38 0 5.00e+00 4.00e-02 7.88e+01 dihedral pdb=" CA ARG B 536 " pdb=" C ARG B 536 " pdb=" N LYS B 537 " pdb=" CA LYS B 537 " ideal model delta harmonic sigma weight residual 180.00 137.95 42.05 0 5.00e+00 4.00e-02 7.07e+01 dihedral pdb=" CA ARG D 536 " pdb=" C ARG D 536 " pdb=" N LYS D 537 " pdb=" CA LYS D 537 " ideal model delta harmonic sigma weight residual 180.00 139.19 40.81 0 5.00e+00 4.00e-02 6.66e+01 ... (remaining 10137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1756 0.040 - 0.081: 623 0.081 - 0.121: 242 0.121 - 0.161: 36 0.161 - 0.202: 1 Chirality restraints: 2658 Sorted by residual: chirality pdb=" CB ILE E 750 " pdb=" CA ILE E 750 " pdb=" CG1 ILE E 750 " pdb=" CG2 ILE E 750 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE B 653 " pdb=" N ILE B 653 " pdb=" C ILE B 653 " pdb=" CB ILE B 653 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE E 653 " pdb=" N ILE E 653 " pdb=" C ILE E 653 " pdb=" CB ILE E 653 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 2655 not shown) Planarity restraints: 3006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 547 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 548 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 548 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 548 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 536 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C ARG A 536 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG A 536 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 537 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 536 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C ARG E 536 " -0.026 2.00e-02 2.50e+03 pdb=" O ARG E 536 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS E 537 " 0.009 2.00e-02 2.50e+03 ... (remaining 3003 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 832 2.72 - 3.26: 16099 3.26 - 3.81: 25168 3.81 - 4.35: 32785 4.35 - 4.90: 56650 Nonbonded interactions: 131534 Sorted by model distance: nonbonded pdb=" OH TYR F 744 " pdb=" OE1 GLU F 772 " model vdw 2.170 2.440 nonbonded pdb=" OH TYR D 744 " pdb=" OE2 GLU D 772 " model vdw 2.193 2.440 nonbonded pdb=" O HIS A 710 " pdb=" OG1 THR A 713 " model vdw 2.237 2.440 nonbonded pdb=" O HIS B 710 " pdb=" OG1 THR B 713 " model vdw 2.262 2.440 nonbonded pdb=" O HIS F 710 " pdb=" OG1 THR F 713 " model vdw 2.264 2.440 ... (remaining 131529 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 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: 10.900 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 42.280 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 0.050 17034 Z= 0.337 Angle : 0.643 7.712 23142 Z= 0.372 Chirality : 0.047 0.202 2658 Planarity : 0.003 0.045 3006 Dihedral : 13.568 89.529 6204 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.51 (0.15), residues: 2184 helix: -4.80 (0.15), residues: 186 sheet: -3.15 (0.16), residues: 762 loop : -2.59 (0.15), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.146 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 221 average time/residue: 1.4855 time to fit residues: 361.6440 Evaluate side-chains 125 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.3110 time to fit residues: 3.1054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 662 GLN E 716 GLN F 702 GLN F 716 GLN F 720 ASN C 662 GLN C 716 GLN C 720 ASN C 857 HIS D 673 ASN D 710 HIS D 716 GLN A 662 GLN A 716 GLN A 720 ASN B 710 HIS B 716 GLN B 800 HIS B 832 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 17034 Z= 0.333 Angle : 0.618 7.607 23142 Z= 0.322 Chirality : 0.049 0.177 2658 Planarity : 0.004 0.041 3006 Dihedral : 5.403 43.450 2382 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.80 (0.16), residues: 2184 helix: -4.39 (0.21), residues: 192 sheet: -2.69 (0.17), residues: 765 loop : -2.04 (0.17), residues: 1227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 136 time to evaluate : 1.768 Fit side-chains outliers start: 60 outliers final: 34 residues processed: 170 average time/residue: 1.1620 time to fit residues: 222.8865 Evaluate side-chains 145 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 1.957 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 21 residues processed: 17 average time/residue: 0.2440 time to fit residues: 9.1227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 163 optimal weight: 0.1980 chunk 133 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 196 optimal weight: 0.3980 chunk 212 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 194 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 17034 Z= 0.236 Angle : 0.564 7.769 23142 Z= 0.291 Chirality : 0.047 0.168 2658 Planarity : 0.003 0.030 3006 Dihedral : 5.074 42.250 2382 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer Outliers : 3.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.36 (0.17), residues: 2184 helix: -4.00 (0.27), residues: 174 sheet: -2.44 (0.17), residues: 774 loop : -1.76 (0.18), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 130 time to evaluate : 1.928 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 30 residues processed: 173 average time/residue: 1.1610 time to fit residues: 226.8535 Evaluate side-chains 139 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 20 residues processed: 12 average time/residue: 0.2280 time to fit residues: 6.7071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 208 optimal weight: 0.4980 chunk 103 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 17034 Z= 0.260 Angle : 0.566 7.675 23142 Z= 0.292 Chirality : 0.047 0.167 2658 Planarity : 0.003 0.033 3006 Dihedral : 5.007 41.733 2382 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer Outliers : 3.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.10 (0.17), residues: 2184 helix: -3.77 (0.29), residues: 174 sheet: -2.28 (0.17), residues: 774 loop : -1.57 (0.18), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 118 time to evaluate : 1.756 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 34 residues processed: 164 average time/residue: 1.1891 time to fit residues: 220.5288 Evaluate side-chains 135 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 25 residues processed: 10 average time/residue: 0.2276 time to fit residues: 6.1400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 155 optimal weight: 0.0870 chunk 86 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 106 optimal weight: 0.0370 chunk 187 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 17034 Z= 0.241 Angle : 0.558 8.665 23142 Z= 0.287 Chirality : 0.047 0.178 2658 Planarity : 0.003 0.024 3006 Dihedral : 4.912 41.081 2382 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.84 (0.18), residues: 2184 helix: -3.35 (0.34), residues: 156 sheet: -2.11 (0.17), residues: 792 loop : -1.46 (0.18), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 114 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 44 residues processed: 158 average time/residue: 1.0518 time to fit residues: 190.4133 Evaluate side-chains 147 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 103 time to evaluate : 1.831 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 35 residues processed: 10 average time/residue: 0.4536 time to fit residues: 8.3279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.0050 chunk 188 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 208 optimal weight: 0.0010 chunk 173 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 overall best weight: 0.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 17034 Z= 0.154 Angle : 0.515 7.846 23142 Z= 0.264 Chirality : 0.045 0.214 2658 Planarity : 0.003 0.024 3006 Dihedral : 4.547 36.659 2382 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.59 (0.18), residues: 2184 helix: -3.10 (0.35), residues: 156 sheet: -1.95 (0.18), residues: 768 loop : -1.31 (0.18), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 137 time to evaluate : 1.727 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 32 residues processed: 181 average time/residue: 1.0196 time to fit residues: 211.4802 Evaluate side-chains 153 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 4 average time/residue: 0.1916 time to fit residues: 3.7055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 152 optimal weight: 0.0010 chunk 118 optimal weight: 0.0010 chunk 175 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 130 optimal weight: 0.0270 chunk 126 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.3050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 17034 Z= 0.174 Angle : 0.542 8.763 23142 Z= 0.273 Chirality : 0.046 0.223 2658 Planarity : 0.003 0.025 3006 Dihedral : 4.493 35.992 2382 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.41 (0.18), residues: 2184 helix: -2.94 (0.36), residues: 156 sheet: -1.89 (0.18), residues: 750 loop : -1.16 (0.18), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 126 time to evaluate : 1.924 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 38 residues processed: 165 average time/residue: 0.9942 time to fit residues: 189.8032 Evaluate side-chains 151 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 113 time to evaluate : 1.901 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 8 average time/residue: 0.2038 time to fit residues: 5.2546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 0.0980 chunk 163 optimal weight: 0.4980 chunk 189 optimal weight: 0.0870 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17034 Z= 0.184 Angle : 0.544 7.725 23142 Z= 0.274 Chirality : 0.046 0.222 2658 Planarity : 0.003 0.025 3006 Dihedral : 4.485 34.832 2382 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.18), residues: 2184 helix: -2.98 (0.34), residues: 174 sheet: -1.82 (0.18), residues: 750 loop : -1.15 (0.18), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 1.968 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 33 residues processed: 157 average time/residue: 0.9883 time to fit residues: 179.2225 Evaluate side-chains 147 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 4 average time/residue: 0.2186 time to fit residues: 3.7991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 193 optimal weight: 0.4980 chunk 127 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 17034 Z= 0.302 Angle : 0.603 8.469 23142 Z= 0.306 Chirality : 0.048 0.224 2658 Planarity : 0.003 0.024 3006 Dihedral : 4.853 39.563 2382 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.30 (0.18), residues: 2184 helix: -2.86 (0.37), residues: 156 sheet: -1.85 (0.18), residues: 762 loop : -1.05 (0.18), residues: 1266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 1.765 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 35 residues processed: 147 average time/residue: 1.0659 time to fit residues: 179.1304 Evaluate side-chains 137 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 34 residues processed: 3 average time/residue: 0.2083 time to fit residues: 3.4493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 125 optimal weight: 0.0970 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 0.0370 chunk 215 optimal weight: 0.4980 chunk 198 optimal weight: 0.9980 chunk 171 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17034 Z= 0.187 Angle : 0.558 9.102 23142 Z= 0.281 Chirality : 0.046 0.227 2658 Planarity : 0.003 0.024 3006 Dihedral : 4.655 39.045 2382 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.33 (0.18), residues: 2184 helix: -3.00 (0.34), residues: 174 sheet: -1.74 (0.18), residues: 792 loop : -1.08 (0.19), residues: 1218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 117 time to evaluate : 1.866 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 32 residues processed: 152 average time/residue: 1.0157 time to fit residues: 178.8497 Evaluate side-chains 141 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 0.3425 time to fit residues: 3.0985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 171 optimal weight: 0.0020 chunk 71 optimal weight: 0.0980 chunk 176 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090221 restraints weight = 24674.443| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.76 r_work: 0.2924 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17034 Z= 0.207 Angle : 0.564 9.426 23142 Z= 0.283 Chirality : 0.046 0.225 2658 Planarity : 0.003 0.023 3006 Dihedral : 4.635 39.251 2382 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.19 (0.18), residues: 2184 helix: -2.77 (0.37), residues: 156 sheet: -1.70 (0.18), residues: 792 loop : -1.00 (0.19), residues: 1236 =============================================================================== Job complete usr+sys time: 4376.38 seconds wall clock time: 79 minutes 31.90 seconds (4771.90 seconds total)