Starting phenix.real_space_refine on Sun Mar 17 04:55:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/03_2024/6kz4_0785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/03_2024/6kz4_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_0785/03_2024/6kz4_0785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/03_2024/6kz4_0785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/03_2024/6kz4_0785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz4_0785/03_2024/6kz4_0785.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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-dev-5265/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: 8.92, per 1000 atoms: 0.53 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: 6.03 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: 2.11 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: 5.29 Time building geometry restraints manager: 6.59 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: 2.840 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: 10.110 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 43.770 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.970 ------------------------------------------------------------------------------- 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 % Allowed : 6.88 % Favored : 93.12 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 809 HIS 0.002 0.001 HIS A 558 PHE 0.025 0.002 PHE A 840 TYR 0.009 0.001 TYR D 535 ARG 0.005 0.000 ARG F 793 *********************** 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 : 2.094 Fit side-chains REVERT: F 673 ASN cc_start: 0.8075 (m110) cc_final: 0.7517 (m-40) REVERT: F 814 TYR cc_start: 0.8685 (m-80) cc_final: 0.8402 (m-80) REVERT: F 835 ARG cc_start: 0.6884 (mtm110) cc_final: 0.6379 (ptt90) REVERT: C 798 TYR cc_start: 0.9336 (m-80) cc_final: 0.9071 (m-80) REVERT: D 779 MET cc_start: 0.8634 (mtm) cc_final: 0.8148 (mtm) REVERT: D 870 GLU cc_start: 0.7748 (pp20) cc_final: 0.7504 (pp20) REVERT: B 835 ARG cc_start: 0.7060 (mtm110) cc_final: 0.6650 (ptm-80) outliers start: 0 outliers final: 2 residues processed: 221 average time/residue: 1.4474 time to fit residues: 351.5055 Evaluate side-chains 127 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 551 ASN Chi-restraints excluded: chain F residue 622 ILE 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 673 ASN 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17034 Z= 0.333 Angle : 0.617 7.613 23142 Z= 0.322 Chirality : 0.049 0.177 2658 Planarity : 0.004 0.037 3006 Dihedral : 5.425 43.537 2386 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 3.41 % Allowed : 14.22 % Favored : 82.37 % 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: -3.81 (0.16), residues: 2184 helix: -4.40 (0.21), residues: 192 sheet: -2.70 (0.17), residues: 765 loop : -2.04 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 809 HIS 0.002 0.001 HIS A 558 PHE 0.022 0.002 PHE B 840 TYR 0.011 0.001 TYR B 535 ARG 0.007 0.000 ARG B 672 *********************** 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 : 1.914 Fit side-chains REVERT: E 712 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7905 (p0) REVERT: F 772 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: C 779 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8138 (mtp) REVERT: C 798 TYR cc_start: 0.9325 (m-80) cc_final: 0.9080 (m-80) REVERT: D 673 ASN cc_start: 0.8067 (m-40) cc_final: 0.7853 (m-40) REVERT: D 779 MET cc_start: 0.8418 (mtm) cc_final: 0.8166 (mtm) REVERT: A 779 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7970 (mtp) REVERT: B 835 ARG cc_start: 0.6722 (mtm110) cc_final: 0.6232 (ptm-80) outliers start: 60 outliers final: 32 residues processed: 171 average time/residue: 1.1917 time to fit residues: 229.2614 Evaluate side-chains 147 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 712 ASP Chi-restraints excluded: chain E residue 834 ILE Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 772 GLU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 868 TRP Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR 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: 1.9990 chunk 163 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1545 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= 0.346 Angle : 0.612 8.040 23142 Z= 0.317 Chirality : 0.049 0.178 2658 Planarity : 0.004 0.034 3006 Dihedral : 5.352 45.301 2382 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 4.15 % Allowed : 16.84 % Favored : 79.01 % 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: -3.41 (0.17), residues: 2184 helix: -4.13 (0.25), residues: 192 sheet: -2.46 (0.17), residues: 771 loop : -1.74 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 809 HIS 0.003 0.001 HIS A 558 PHE 0.019 0.002 PHE B 840 TYR 0.012 0.001 TYR F 798 ARG 0.007 0.001 ARG F 672 *********************** 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 193 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 120 time to evaluate : 1.916 Fit side-chains revert: symmetry clash REVERT: E 712 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7923 (p0) REVERT: E 809 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.8017 (p-90) REVERT: F 627 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: F 772 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: F 798 TYR cc_start: 0.8972 (m-80) cc_final: 0.8555 (m-80) REVERT: F 835 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6883 (ptt90) REVERT: C 779 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8179 (mtp) REVERT: A 779 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7839 (mtp) outliers start: 73 outliers final: 42 residues processed: 164 average time/residue: 1.1382 time to fit residues: 211.0282 Evaluate side-chains 162 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 113 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 551 ASN Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 712 ASP Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 824 VAL Chi-restraints excluded: chain E residue 834 ILE Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 627 GLU Chi-restraints excluded: chain F residue 772 GLU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 868 TRP Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 868 TRP Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 208 optimal weight: 0.0970 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.8348 moved from start: 0.1794 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= 0.253 Angle : 0.566 7.338 23142 Z= 0.293 Chirality : 0.047 0.169 2658 Planarity : 0.003 0.034 3006 Dihedral : 5.087 42.417 2382 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 4.32 % Allowed : 18.49 % Favored : 77.19 % 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: -3.12 (0.17), residues: 2184 helix: -3.80 (0.29), residues: 174 sheet: -2.28 (0.17), residues: 774 loop : -1.60 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 809 HIS 0.002 0.000 HIS A 558 PHE 0.015 0.002 PHE D 840 TYR 0.009 0.001 TYR F 798 ARG 0.005 0.000 ARG A 672 *********************** 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 200 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 124 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: E 809 TRP cc_start: 0.8174 (OUTLIER) cc_final: 0.7892 (p-90) REVERT: E 830 PHE cc_start: 0.3576 (OUTLIER) cc_final: 0.3296 (m-80) REVERT: F 772 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: F 798 TYR cc_start: 0.8954 (m-80) cc_final: 0.8598 (m-80) REVERT: F 809 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7272 (p-90) REVERT: F 835 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6906 (ptt90) REVERT: C 595 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8944 (tm) REVERT: C 779 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: C 798 TYR cc_start: 0.9333 (m-80) cc_final: 0.9089 (m-80) REVERT: D 534 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8305 (mp) REVERT: D 560 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8147 (mtpt) REVERT: D 627 GLU cc_start: 0.7755 (tp30) cc_final: 0.7264 (tp30) REVERT: A 809 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.8038 (p-90) REVERT: A 840 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7138 (t80) REVERT: B 627 GLU cc_start: 0.8175 (tp30) cc_final: 0.7692 (tp30) REVERT: B 678 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8707 (mmtm) outliers start: 76 outliers final: 39 residues processed: 172 average time/residue: 1.0454 time to fit residues: 204.8360 Evaluate side-chains 165 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 114 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 551 ASN Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 619 ASP Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 830 PHE Chi-restraints excluded: chain E residue 834 ILE Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 772 GLU Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 178 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 187 optimal weight: 0.0000 chunk 52 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17034 Z= 0.246 Angle : 0.560 7.279 23142 Z= 0.289 Chirality : 0.047 0.184 2658 Planarity : 0.003 0.026 3006 Dihedral : 4.968 39.938 2382 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.84 % Allowed : 19.28 % Favored : 75.88 % 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: -2.88 (0.17), residues: 2184 helix: -3.44 (0.33), residues: 156 sheet: -2.10 (0.17), residues: 807 loop : -1.48 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 809 HIS 0.002 0.000 HIS A 558 PHE 0.016 0.002 PHE B 553 TYR 0.009 0.001 TYR F 798 ARG 0.004 0.000 ARG B 672 *********************** 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 205 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 120 time to evaluate : 1.973 Fit side-chains revert: symmetry clash REVERT: E 809 TRP cc_start: 0.8178 (OUTLIER) cc_final: 0.7846 (p-90) REVERT: E 830 PHE cc_start: 0.3612 (OUTLIER) cc_final: 0.3306 (m-80) REVERT: E 864 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: F 772 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: F 798 TYR cc_start: 0.8940 (m-80) cc_final: 0.8634 (m-80) REVERT: F 809 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.7319 (p-90) REVERT: F 835 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6914 (ptt90) REVERT: F 864 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6833 (tm-30) REVERT: C 595 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8931 (tm) REVERT: C 779 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: C 798 TYR cc_start: 0.9331 (m-80) cc_final: 0.9072 (m-80) REVERT: D 534 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8277 (mp) REVERT: D 560 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8177 (mtpt) REVERT: D 627 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: D 809 TRP cc_start: 0.8064 (OUTLIER) cc_final: 0.7766 (p-90) REVERT: A 651 MET cc_start: 0.9089 (ttp) cc_final: 0.8825 (ttp) REVERT: A 779 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7945 (mtp) REVERT: A 809 TRP cc_start: 0.8413 (OUTLIER) cc_final: 0.7058 (p-90) REVERT: A 840 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7155 (t80) REVERT: B 627 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: B 835 ARG cc_start: 0.7283 (mtm110) cc_final: 0.6797 (ptt90) outliers start: 85 outliers final: 49 residues processed: 172 average time/residue: 1.0634 time to fit residues: 208.4756 Evaluate side-chains 173 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 107 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 551 ASN Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 619 ASP Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 824 VAL Chi-restraints excluded: chain E residue 830 PHE Chi-restraints excluded: chain E residue 834 ILE Chi-restraints excluded: chain E residue 864 GLU Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 772 GLU Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 864 GLU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 868 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.0170 chunk 188 optimal weight: 0.0270 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 0.0040 chunk 69 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 overall best weight: 0.2488 ------------------------------------------------------------------------------- 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: 0.8303 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17034 Z= 0.155 Angle : 0.522 8.655 23142 Z= 0.267 Chirality : 0.045 0.186 2658 Planarity : 0.003 0.024 3006 Dihedral : 4.582 37.194 2382 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.53 % Allowed : 20.88 % Favored : 75.60 % 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: -2.66 (0.18), residues: 2184 helix: -3.14 (0.35), residues: 156 sheet: -1.92 (0.17), residues: 801 loop : -1.38 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 809 HIS 0.001 0.000 HIS A 558 PHE 0.012 0.001 PHE C 605 TYR 0.007 0.001 TYR F 798 ARG 0.003 0.000 ARG B 672 *********************** 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 197 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 135 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: E 809 TRP cc_start: 0.8104 (OUTLIER) cc_final: 0.7716 (p-90) REVERT: F 655 TYR cc_start: 0.9051 (t80) cc_final: 0.8683 (t80) REVERT: F 772 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: F 809 TRP cc_start: 0.7946 (OUTLIER) cc_final: 0.7370 (p-90) REVERT: F 835 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7097 (ptt90) REVERT: F 864 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: C 655 TYR cc_start: 0.9247 (t80) cc_final: 0.8707 (t80) REVERT: C 798 TYR cc_start: 0.9300 (m-80) cc_final: 0.9020 (m-80) REVERT: D 534 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8321 (mp) REVERT: D 560 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8051 (mtpt) REVERT: D 627 GLU cc_start: 0.7721 (tp30) cc_final: 0.7231 (tp30) REVERT: D 809 TRP cc_start: 0.7913 (OUTLIER) cc_final: 0.7500 (p-90) REVERT: A 651 MET cc_start: 0.9128 (ttp) cc_final: 0.8925 (ttp) REVERT: A 789 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8190 (mtp) REVERT: A 809 TRP cc_start: 0.8463 (OUTLIER) cc_final: 0.7143 (p-90) REVERT: B 626 SER cc_start: 0.8916 (p) cc_final: 0.8715 (m) REVERT: B 627 GLU cc_start: 0.8040 (tp30) cc_final: 0.7557 (tp30) REVERT: B 835 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6868 (ptt90) outliers start: 62 outliers final: 32 residues processed: 177 average time/residue: 1.0206 time to fit residues: 206.7084 Evaluate side-chains 155 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 112 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 824 VAL Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 772 GLU Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 864 GLU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 846 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 152 optimal weight: 0.0870 chunk 118 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 831 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17034 Z= 0.303 Angle : 0.589 8.991 23142 Z= 0.300 Chirality : 0.048 0.205 2658 Planarity : 0.003 0.027 3006 Dihedral : 4.882 40.799 2382 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 3.92 % Allowed : 21.22 % Favored : 74.86 % 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: -2.58 (0.18), residues: 2184 helix: -3.07 (0.36), residues: 156 sheet: -1.92 (0.17), residues: 798 loop : -1.29 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 809 HIS 0.002 0.001 HIS E 558 PHE 0.018 0.002 PHE F 840 TYR 0.009 0.001 TYR A 718 ARG 0.003 0.000 ARG B 672 *********************** 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 177 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 108 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 809 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.7864 (p-90) REVERT: F 772 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: F 809 TRP cc_start: 0.8055 (OUTLIER) cc_final: 0.7288 (p-90) REVERT: F 835 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7057 (ptt90) REVERT: F 864 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: C 798 TYR cc_start: 0.9343 (m-80) cc_final: 0.9054 (m-80) REVERT: D 627 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: D 660 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8750 (mp) REVERT: D 809 TRP cc_start: 0.8070 (OUTLIER) cc_final: 0.7710 (p-90) REVERT: A 789 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8296 (mtp) REVERT: A 809 TRP cc_start: 0.8410 (OUTLIER) cc_final: 0.7249 (p-90) REVERT: B 627 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7666 (tp30) outliers start: 69 outliers final: 45 residues processed: 153 average time/residue: 1.0467 time to fit residues: 182.9763 Evaluate side-chains 158 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 102 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 551 ASN Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain E residue 824 VAL Chi-restraints excluded: chain E residue 834 ILE Chi-restraints excluded: chain E residue 868 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 772 GLU Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain F residue 864 GLU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 840 PHE Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 846 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.0670 chunk 83 optimal weight: 0.0370 chunk 124 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 0.0470 chunk 141 optimal weight: 0.0370 chunk 102 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 0.0980 chunk 189 optimal weight: 0.6980 overall best weight: 0.0572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 636 GLN C 664 GLN B 799 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2698 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= 0.134 Angle : 0.523 7.629 23142 Z= 0.263 Chirality : 0.045 0.211 2658 Planarity : 0.003 0.024 3006 Dihedral : 4.373 36.512 2382 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.79 % Allowed : 22.75 % Favored : 74.46 % 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: -2.43 (0.18), residues: 2184 helix: -2.99 (0.33), residues: 192 sheet: -1.67 (0.18), residues: 750 loop : -1.27 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 809 HIS 0.001 0.000 HIS D 800 PHE 0.010 0.001 PHE C 605 TYR 0.007 0.001 TYR E 535 ARG 0.003 0.000 ARG B 672 *********************** 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 186 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: E 809 TRP cc_start: 0.8092 (OUTLIER) cc_final: 0.7825 (p-90) REVERT: F 655 TYR cc_start: 0.8983 (t80) cc_final: 0.8528 (t80) REVERT: F 809 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.7266 (p-90) REVERT: F 835 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7135 (ptt90) REVERT: C 655 TYR cc_start: 0.9263 (t80) cc_final: 0.8614 (t80) REVERT: C 798 TYR cc_start: 0.9291 (m-80) cc_final: 0.9007 (m-80) REVERT: D 537 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7512 (mptt) REVERT: D 582 GLN cc_start: 0.7808 (tt0) cc_final: 0.7593 (tt0) REVERT: D 627 GLU cc_start: 0.7651 (tp30) cc_final: 0.7126 (tp30) REVERT: D 809 TRP cc_start: 0.7856 (OUTLIER) cc_final: 0.7087 (p-90) REVERT: A 809 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.6969 (p-90) REVERT: B 627 GLU cc_start: 0.7965 (tp30) cc_final: 0.7472 (tp30) REVERT: B 835 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6999 (ptt90) outliers start: 49 outliers final: 26 residues processed: 171 average time/residue: 1.0972 time to fit residues: 212.3727 Evaluate side-chains 148 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 846 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 116 optimal weight: 0.0030 chunk 84 optimal weight: 0.9980 chunk 152 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 664 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17034 Z= 0.212 Angle : 0.558 8.500 23142 Z= 0.282 Chirality : 0.046 0.201 2658 Planarity : 0.003 0.032 3006 Dihedral : 4.481 37.199 2382 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 2.56 % Allowed : 23.44 % Favored : 74.00 % 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: -2.23 (0.18), residues: 2184 helix: -2.77 (0.38), residues: 156 sheet: -1.77 (0.18), residues: 756 loop : -1.03 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 809 HIS 0.002 0.000 HIS E 558 PHE 0.015 0.001 PHE E 830 TYR 0.012 0.001 TYR C 718 ARG 0.006 0.000 ARG F 729 *********************** 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 166 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 121 time to evaluate : 1.991 Fit side-chains revert: symmetry clash REVERT: E 767 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9191 (mt) REVERT: E 809 TRP cc_start: 0.8186 (OUTLIER) cc_final: 0.7875 (p-90) REVERT: E 835 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.7124 (ptt90) REVERT: F 772 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: F 809 TRP cc_start: 0.7816 (OUTLIER) cc_final: 0.6963 (p-90) REVERT: F 835 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7172 (ptt90) REVERT: C 798 TYR cc_start: 0.9315 (m-80) cc_final: 0.9022 (m-80) REVERT: D 537 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7482 (mptt) REVERT: D 627 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7207 (tp30) REVERT: D 809 TRP cc_start: 0.7894 (OUTLIER) cc_final: 0.7013 (p-90) REVERT: A 779 MET cc_start: 0.8601 (mtm) cc_final: 0.8308 (mpp) REVERT: A 809 TRP cc_start: 0.8355 (OUTLIER) cc_final: 0.7132 (p-90) REVERT: B 627 GLU cc_start: 0.8043 (tp30) cc_final: 0.7554 (tp30) REVERT: B 835 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6912 (ptt90) outliers start: 45 outliers final: 28 residues processed: 156 average time/residue: 1.1188 time to fit residues: 198.5116 Evaluate side-chains 148 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 110 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 767 LEU Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 809 TRP Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 772 GLU Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG 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: 0.5980 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 0.0570 chunk 215 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 171 optimal weight: 0.0570 chunk 17 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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: 0.8311 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17034 Z= 0.195 Angle : 0.554 8.865 23142 Z= 0.280 Chirality : 0.046 0.216 2658 Planarity : 0.003 0.029 3006 Dihedral : 4.528 38.708 2382 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.45 % Allowed : 23.83 % Favored : 73.72 % 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: -2.17 (0.18), residues: 2184 helix: -2.79 (0.38), residues: 156 sheet: -1.72 (0.18), residues: 756 loop : -0.99 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 809 HIS 0.001 0.000 HIS A 558 PHE 0.012 0.001 PHE C 605 TYR 0.012 0.001 TYR C 718 ARG 0.006 0.000 ARG F 729 ********************** 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 161 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 118 time to evaluate : 1.862 Fit side-chains revert: symmetry clash REVERT: E 767 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9184 (mt) REVERT: E 835 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7146 (ptt90) REVERT: F 809 TRP cc_start: 0.7794 (OUTLIER) cc_final: 0.7010 (p-90) REVERT: F 835 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7188 (ptt90) REVERT: C 798 TYR cc_start: 0.9309 (m-80) cc_final: 0.9014 (m-80) REVERT: D 627 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7227 (tp30) REVERT: D 809 TRP cc_start: 0.7951 (OUTLIER) cc_final: 0.7488 (p-90) REVERT: A 779 MET cc_start: 0.8586 (mtm) cc_final: 0.8302 (mpp) REVERT: A 809 TRP cc_start: 0.8340 (OUTLIER) cc_final: 0.7122 (p-90) REVERT: B 627 GLU cc_start: 0.8037 (tp30) cc_final: 0.7556 (tp30) REVERT: B 835 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6927 (ptt90) outliers start: 43 outliers final: 29 residues processed: 150 average time/residue: 1.0566 time to fit residues: 180.5484 Evaluate side-chains 147 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 526 ASP Chi-restraints excluded: chain E residue 545 THR Chi-restraints excluded: chain E residue 551 ASN Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 767 LEU Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 547 ARG Chi-restraints excluded: chain F residue 809 TRP Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 834 ILE Chi-restraints excluded: chain F residue 835 ARG Chi-restraints excluded: chain F residue 838 ILE Chi-restraints excluded: chain F residue 846 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 627 GLU Chi-restraints excluded: chain D residue 712 ASP Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 809 TRP Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 809 TRP Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 835 ARG 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: 0.9990 chunk 158 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 176 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.112203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.088996 restraints weight = 24797.425| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.74 r_work: 0.2904 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17034 Z= 0.268 Angle : 0.591 9.236 23142 Z= 0.298 Chirality : 0.047 0.221 2658 Planarity : 0.003 0.028 3006 Dihedral : 4.757 40.620 2382 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.67 % Allowed : 23.78 % Favored : 73.55 % 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: -2.04 (0.18), residues: 2184 helix: -2.64 (0.42), residues: 132 sheet: -1.73 (0.18), residues: 762 loop : -0.88 (0.19), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 809 HIS 0.002 0.000 HIS A 558 PHE 0.017 0.002 PHE B 553 TYR 0.014 0.001 TYR C 718 ARG 0.006 0.000 ARG F 729 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4464.53 seconds wall clock time: 80 minutes 19.86 seconds (4819.86 seconds total)