Starting phenix.real_space_refine on Sun Mar 17 12:42:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/03_2024/6v9y_21130.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/03_2024/6v9y_21130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/03_2024/6v9y_21130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/03_2024/6v9y_21130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/03_2024/6v9y_21130.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/03_2024/6v9y_21130.pdb" } resolution = 3.6 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= 1.000 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 124 5.16 5 C 11628 2.51 5 N 2952 2.21 5 O 3012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A GLU 864": "OE1" <-> "OE2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 1050": "NH1" <-> "NH2" Residue "A GLU 1063": "OE1" <-> "OE2" Residue "A GLU 1073": "OE1" <-> "OE2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B GLU 864": "OE1" <-> "OE2" Residue "B ARG 928": "NH1" <-> "NH2" Residue "B ARG 975": "NH1" <-> "NH2" Residue "B ARG 1050": "NH1" <-> "NH2" Residue "B GLU 1063": "OE1" <-> "OE2" Residue "B GLU 1073": "OE1" <-> "OE2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D GLU 864": "OE1" <-> "OE2" Residue "D ARG 928": "NH1" <-> "NH2" Residue "D ARG 975": "NH1" <-> "NH2" Residue "D ARG 1050": "NH1" <-> "NH2" Residue "D GLU 1063": "OE1" <-> "OE2" Residue "D GLU 1073": "OE1" <-> "OE2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C GLU 864": "OE1" <-> "OE2" Residue "C ARG 928": "NH1" <-> "NH2" Residue "C ARG 975": "NH1" <-> "NH2" Residue "C ARG 1050": "NH1" <-> "NH2" Residue "C GLU 1063": "OE1" <-> "OE2" Residue "C GLU 1073": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17716 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4429 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 18, 'TRANS': 543} Chain breaks: 4 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 4429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4429 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 18, 'TRANS': 543} Chain breaks: 4 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "D" Number of atoms: 4429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4429 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 18, 'TRANS': 543} Chain breaks: 4 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 4429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4429 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 18, 'TRANS': 543} Chain breaks: 4 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Time building chain proxies: 9.23, per 1000 atoms: 0.52 Number of scatterers: 17716 At special positions: 0 Unit cell: (110.62, 109.404, 138.578, 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 124 16.00 O 3012 8.00 N 2952 7.00 C 11628 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: 6.30 Conformation dependent library (CDL) restraints added in 3.0 seconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4304 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 71.8% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.641A pdb=" N CYS A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 464 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 494 through 504 removed outlier: 3.575A pdb=" N LEU A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 4.158A pdb=" N TRP A 515 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.644A pdb=" N HIS A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.508A pdb=" N VAL A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.546A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.583A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 4.142A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 621 through 630 removed outlier: 3.597A pdb=" N GLU A 625 " --> pdb=" O CYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.639A pdb=" N MET A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.801A pdb=" N MET A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 699 removed outlier: 3.514A pdb=" N LEU A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 714 Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.637A pdb=" N HIS A 719 " --> pdb=" O GLY A 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 720 " --> pdb=" O PHE A 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 724 " --> pdb=" O MET A 720 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 725 " --> pdb=" O MET A 721 " (cutoff:3.500A) Proline residue: A 732 - end of helix removed outlier: 3.683A pdb=" N ASN A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 786 removed outlier: 3.697A pdb=" N VAL A 777 " --> pdb=" O CYS A 773 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 778 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 782 " --> pdb=" O PHE A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 819 removed outlier: 3.692A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 823 Processing helix chain 'A' and resid 827 through 850 removed outlier: 3.504A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 857 through 872 removed outlier: 3.514A pdb=" N VAL A 861 " --> pdb=" O GLY A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 892 removed outlier: 5.530A pdb=" N PHE A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.686A pdb=" N PHE A 898 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 911 Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 968 removed outlier: 3.587A pdb=" N ALA A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 988 removed outlier: 3.742A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 4.104A pdb=" N LYS A 997 " --> pdb=" O TRP A 993 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 998 " --> pdb=" O PHE A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1071 removed outlier: 3.544A pdb=" N LYS A1060 " --> pdb=" O PHE A1056 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A1069 " --> pdb=" O ILE A1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.641A pdb=" N CYS B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 464 " --> pdb=" O ASN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 494 through 504 removed outlier: 3.575A pdb=" N LEU B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 removed outlier: 4.158A pdb=" N TRP B 515 " --> pdb=" O HIS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 removed outlier: 3.644A pdb=" N HIS B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 3.508A pdb=" N VAL B 532 " --> pdb=" O GLN B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 559 removed outlier: 3.545A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.583A pdb=" N ASN B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 removed outlier: 4.142A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 Processing helix chain 'B' and resid 621 through 630 removed outlier: 3.597A pdb=" N GLU B 625 " --> pdb=" O CYS B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 640 removed outlier: 3.638A pdb=" N MET B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 692 removed outlier: 3.801A pdb=" N MET B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.514A pdb=" N LEU B 698 " --> pdb=" O ARG B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 714 Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.637A pdb=" N HIS B 719 " --> pdb=" O GLY B 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 720 " --> pdb=" O PHE B 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 724 " --> pdb=" O MET B 720 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 725 " --> pdb=" O MET B 721 " (cutoff:3.500A) Proline residue: B 732 - end of helix removed outlier: 3.683A pdb=" N ASN B 739 " --> pdb=" O ILE B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 786 removed outlier: 3.697A pdb=" N VAL B 777 " --> pdb=" O CYS B 773 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 778 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 782 " --> pdb=" O PHE B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 819 removed outlier: 3.692A pdb=" N ILE B 816 " --> pdb=" O TYR B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 823 Processing helix chain 'B' and resid 827 through 850 removed outlier: 3.505A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'B' and resid 857 through 872 removed outlier: 3.514A pdb=" N VAL B 861 " --> pdb=" O GLY B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 892 removed outlier: 5.531A pdb=" N PHE B 879 " --> pdb=" O VAL B 875 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.686A pdb=" N PHE B 898 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 911 Processing helix chain 'B' and resid 922 through 927 Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 968 removed outlier: 3.587A pdb=" N ALA B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 988 removed outlier: 3.742A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 988 " --> pdb=" O THR B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 removed outlier: 4.105A pdb=" N LYS B 997 " --> pdb=" O TRP B 993 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 998 " --> pdb=" O PHE B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1071 removed outlier: 3.543A pdb=" N LYS B1060 " --> pdb=" O PHE B1056 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B1069 " --> pdb=" O ILE B1065 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 Processing helix chain 'D' and resid 458 through 466 removed outlier: 3.641A pdb=" N CYS D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 464 " --> pdb=" O ASN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 492 Processing helix chain 'D' and resid 494 through 504 removed outlier: 3.575A pdb=" N LEU D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 removed outlier: 4.158A pdb=" N TRP D 515 " --> pdb=" O HIS D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 523 removed outlier: 3.643A pdb=" N HIS D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 535 removed outlier: 3.508A pdb=" N VAL D 532 " --> pdb=" O GLN D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 559 removed outlier: 3.545A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 569 Processing helix chain 'D' and resid 582 through 590 removed outlier: 3.583A pdb=" N ASN D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 removed outlier: 4.142A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 611 Processing helix chain 'D' and resid 621 through 630 removed outlier: 3.597A pdb=" N GLU D 625 " --> pdb=" O CYS D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.638A pdb=" N MET D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 692 removed outlier: 3.801A pdb=" N MET D 689 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 690 " --> pdb=" O LEU D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 699 removed outlier: 3.513A pdb=" N LEU D 698 " --> pdb=" O ARG D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 714 Processing helix chain 'D' and resid 714 through 739 removed outlier: 3.637A pdb=" N HIS D 719 " --> pdb=" O GLY D 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET D 720 " --> pdb=" O PHE D 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY D 724 " --> pdb=" O MET D 720 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 725 " --> pdb=" O MET D 721 " (cutoff:3.500A) Proline residue: D 732 - end of helix removed outlier: 3.684A pdb=" N ASN D 739 " --> pdb=" O ILE D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 786 removed outlier: 3.697A pdb=" N VAL D 777 " --> pdb=" O CYS D 773 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 778 " --> pdb=" O MET D 774 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 782 " --> pdb=" O PHE D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 819 removed outlier: 3.692A pdb=" N ILE D 816 " --> pdb=" O TYR D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 823 Processing helix chain 'D' and resid 827 through 850 removed outlier: 3.505A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 853 No H-bonds generated for 'chain 'D' and resid 851 through 853' Processing helix chain 'D' and resid 857 through 872 removed outlier: 3.514A pdb=" N VAL D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 892 removed outlier: 5.530A pdb=" N PHE D 879 " --> pdb=" O VAL D 875 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU D 880 " --> pdb=" O VAL D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.687A pdb=" N PHE D 898 " --> pdb=" O GLN D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 911 Processing helix chain 'D' and resid 922 through 927 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 968 removed outlier: 3.587A pdb=" N ALA D 960 " --> pdb=" O LEU D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 988 removed outlier: 3.743A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS D 988 " --> pdb=" O THR D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 removed outlier: 4.104A pdb=" N LYS D 997 " --> pdb=" O TRP D 993 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 998 " --> pdb=" O PHE D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1071 removed outlier: 3.544A pdb=" N LYS D1060 " --> pdb=" O PHE D1056 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D1069 " --> pdb=" O ILE D1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 458 through 466 removed outlier: 3.641A pdb=" N CYS C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 464 " --> pdb=" O ASN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 494 through 504 removed outlier: 3.574A pdb=" N LEU C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 removed outlier: 4.158A pdb=" N TRP C 515 " --> pdb=" O HIS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 523 removed outlier: 3.644A pdb=" N HIS C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 535 removed outlier: 3.507A pdb=" N VAL C 532 " --> pdb=" O GLN C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 559 removed outlier: 3.546A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 569 Processing helix chain 'C' and resid 582 through 590 removed outlier: 3.583A pdb=" N ASN C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 removed outlier: 4.142A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 611 Processing helix chain 'C' and resid 621 through 630 removed outlier: 3.598A pdb=" N GLU C 625 " --> pdb=" O CYS C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 640 removed outlier: 3.639A pdb=" N MET C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 692 removed outlier: 3.800A pdb=" N MET C 689 " --> pdb=" O ALA C 685 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 690 " --> pdb=" O LEU C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 699 removed outlier: 3.514A pdb=" N LEU C 698 " --> pdb=" O ARG C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 714 Processing helix chain 'C' and resid 714 through 739 removed outlier: 3.638A pdb=" N HIS C 719 " --> pdb=" O GLY C 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET C 720 " --> pdb=" O PHE C 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 724 " --> pdb=" O MET C 720 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 725 " --> pdb=" O MET C 721 " (cutoff:3.500A) Proline residue: C 732 - end of helix removed outlier: 3.683A pdb=" N ASN C 739 " --> pdb=" O ILE C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 786 removed outlier: 3.697A pdb=" N VAL C 777 " --> pdb=" O CYS C 773 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 778 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 782 " --> pdb=" O PHE C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 819 removed outlier: 3.691A pdb=" N ILE C 816 " --> pdb=" O TYR C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 823 Processing helix chain 'C' and resid 827 through 850 removed outlier: 3.505A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 853 No H-bonds generated for 'chain 'C' and resid 851 through 853' Processing helix chain 'C' and resid 857 through 872 removed outlier: 3.514A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 892 removed outlier: 5.530A pdb=" N PHE C 879 " --> pdb=" O VAL C 875 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 removed outlier: 3.686A pdb=" N PHE C 898 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 911 Processing helix chain 'C' and resid 922 through 927 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 968 removed outlier: 3.586A pdb=" N ALA C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 988 removed outlier: 3.743A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 988 " --> pdb=" O THR C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 removed outlier: 4.104A pdb=" N LYS C 997 " --> pdb=" O TRP C 993 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 998 " --> pdb=" O PHE C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1071 removed outlier: 3.544A pdb=" N LYS C1060 " --> pdb=" O PHE C1056 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C1069 " --> pdb=" O ILE C1065 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 645 removed outlier: 3.729A pdb=" N TYR A 655 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A1003 " --> pdb=" O TYR A 658 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.729A pdb=" N TYR B 655 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B1003 " --> pdb=" O TYR B 658 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 642 through 645 removed outlier: 3.729A pdb=" N TYR D 655 " --> pdb=" O SER D 645 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D1003 " --> pdb=" O TYR D 658 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 642 through 645 removed outlier: 3.729A pdb=" N TYR C 655 " --> pdb=" O SER C 645 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C1003 " --> pdb=" O TYR C 658 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2838 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: 4.91 Time building geometry restraints manager: 6.92 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: 5462 1.34 - 1.46: 3982 1.46 - 1.58: 8444 1.58 - 1.70: 4 1.70 - 1.82: 204 Bond restraints: 18096 Sorted by residual: bond pdb=" C LEU A 820 " pdb=" N PRO A 821 " ideal model delta sigma weight residual 1.337 1.369 -0.033 9.80e-03 1.04e+04 1.12e+01 bond pdb=" C LEU D 820 " pdb=" N PRO D 821 " ideal model delta sigma weight residual 1.337 1.369 -0.032 9.80e-03 1.04e+04 1.10e+01 bond pdb=" C LEU C 820 " pdb=" N PRO C 821 " ideal model delta sigma weight residual 1.337 1.369 -0.032 9.80e-03 1.04e+04 1.09e+01 bond pdb=" C LEU B 820 " pdb=" N PRO B 821 " ideal model delta sigma weight residual 1.337 1.369 -0.032 9.80e-03 1.04e+04 1.08e+01 bond pdb=" CB VAL C 948 " pdb=" CG2 VAL C 948 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.74e+00 ... (remaining 18091 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.55: 528 106.55 - 114.11: 10706 114.11 - 121.68: 9779 121.68 - 129.24: 3339 129.24 - 136.80: 168 Bond angle restraints: 24520 Sorted by residual: angle pdb=" CG LYS C 503 " pdb=" CD LYS C 503 " pdb=" CE LYS C 503 " ideal model delta sigma weight residual 111.30 123.84 -12.54 2.30e+00 1.89e-01 2.97e+01 angle pdb=" CG LYS A 503 " pdb=" CD LYS A 503 " pdb=" CE LYS A 503 " ideal model delta sigma weight residual 111.30 123.81 -12.51 2.30e+00 1.89e-01 2.96e+01 angle pdb=" CG LYS D 503 " pdb=" CD LYS D 503 " pdb=" CE LYS D 503 " ideal model delta sigma weight residual 111.30 123.80 -12.50 2.30e+00 1.89e-01 2.95e+01 angle pdb=" CG LYS B 503 " pdb=" CD LYS B 503 " pdb=" CE LYS B 503 " ideal model delta sigma weight residual 111.30 123.79 -12.49 2.30e+00 1.89e-01 2.95e+01 angle pdb=" CD LYS B 503 " pdb=" CE LYS B 503 " pdb=" NZ LYS B 503 " ideal model delta sigma weight residual 111.90 128.42 -16.52 3.20e+00 9.77e-02 2.67e+01 ... (remaining 24515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 9605 15.97 - 31.94: 911 31.94 - 47.92: 232 47.92 - 63.89: 52 63.89 - 79.86: 16 Dihedral angle restraints: 10816 sinusoidal: 4204 harmonic: 6612 Sorted by residual: dihedral pdb=" CA LEU C 576 " pdb=" C LEU C 576 " pdb=" N ASN C 577 " pdb=" CA ASN C 577 " ideal model delta harmonic sigma weight residual 180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA LEU A 576 " pdb=" C LEU A 576 " pdb=" N ASN A 577 " pdb=" CA ASN A 577 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA LEU D 576 " pdb=" C LEU D 576 " pdb=" N ASN D 577 " pdb=" CA ASN D 577 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 10813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2601 0.098 - 0.195: 280 0.195 - 0.293: 11 0.293 - 0.391: 4 0.391 - 0.489: 4 Chirality restraints: 2900 Sorted by residual: chirality pdb=" CB ILE C 811 " pdb=" CA ILE C 811 " pdb=" CG1 ILE C 811 " pdb=" CG2 ILE C 811 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" CB ILE D 811 " pdb=" CA ILE D 811 " pdb=" CG1 ILE D 811 " pdb=" CG2 ILE D 811 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CB ILE A 811 " pdb=" CA ILE A 811 " pdb=" CG1 ILE A 811 " pdb=" CG2 ILE A 811 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.89e+00 ... (remaining 2897 not shown) Planarity restraints: 3008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 820 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 821 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 821 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 821 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 820 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.10e+01 pdb=" N PRO A 821 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 821 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 821 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 820 " -0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO D 821 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO D 821 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 821 " -0.046 5.00e-02 4.00e+02 ... (remaining 3005 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4863 2.79 - 3.32: 16694 3.32 - 3.84: 28789 3.84 - 4.37: 34410 4.37 - 4.90: 55778 Nonbonded interactions: 140534 Sorted by model distance: nonbonded pdb=" NH1 ARG D 458 " pdb=" O MET C1072 " model vdw 2.262 2.520 nonbonded pdb=" OG1 THR D 814 " pdb=" O CYS D 834 " model vdw 2.318 2.440 nonbonded pdb=" OG1 THR B 814 " pdb=" O CYS B 834 " model vdw 2.319 2.440 nonbonded pdb=" OG1 THR A 814 " pdb=" O CYS A 834 " model vdw 2.319 2.440 nonbonded pdb=" OG1 THR C 814 " pdb=" O CYS C 834 " model vdw 2.319 2.440 ... (remaining 140529 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 4.410 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 44.910 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.009 0.092 18096 Z= 0.579 Angle : 1.182 17.130 24520 Z= 0.590 Chirality : 0.065 0.489 2900 Planarity : 0.008 0.083 3008 Dihedral : 14.212 79.858 6512 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.13 % Allowed : 10.02 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.18 (0.13), residues: 2208 helix: -3.75 (0.07), residues: 1460 sheet: 1.08 (0.73), residues: 60 loop : -2.57 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 605 HIS 0.011 0.002 HIS B 719 PHE 0.017 0.002 PHE A 944 TYR 0.024 0.003 TYR C 842 ARG 0.004 0.001 ARG D 852 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 474 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.9391 (mt) cc_final: 0.9151 (pp) REVERT: A 491 LYS cc_start: 0.9396 (tttt) cc_final: 0.9141 (ttmm) REVERT: A 509 LEU cc_start: 0.9000 (mm) cc_final: 0.8761 (mm) REVERT: A 634 MET cc_start: 0.9464 (tpt) cc_final: 0.9177 (tpt) REVERT: A 704 LYS cc_start: 0.9530 (mttt) cc_final: 0.9300 (mtmm) REVERT: A 721 MET cc_start: 0.8372 (mmm) cc_final: 0.7958 (tmm) REVERT: A 808 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8270 (mp0) REVERT: A 834 CYS cc_start: 0.9015 (m) cc_final: 0.8745 (m) REVERT: A 840 TYR cc_start: 0.9142 (t80) cc_final: 0.8868 (t80) REVERT: A 845 ASN cc_start: 0.8777 (t0) cc_final: 0.7579 (t0) REVERT: A 978 MET cc_start: 0.8118 (ttp) cc_final: 0.7469 (ttm) REVERT: A 1053 ASP cc_start: 0.8481 (t70) cc_final: 0.8169 (t0) REVERT: A 1071 LYS cc_start: 0.9325 (mttm) cc_final: 0.8938 (mmmm) REVERT: B 491 LYS cc_start: 0.9394 (tttt) cc_final: 0.9121 (ttpp) REVERT: B 509 LEU cc_start: 0.9035 (mm) cc_final: 0.8789 (mm) REVERT: B 522 SER cc_start: 0.9344 (m) cc_final: 0.9116 (p) REVERT: B 635 LYS cc_start: 0.9481 (tttt) cc_final: 0.9262 (ttmt) REVERT: B 721 MET cc_start: 0.8176 (mmm) cc_final: 0.7953 (tmm) REVERT: B 834 CYS cc_start: 0.9010 (m) cc_final: 0.8653 (m) REVERT: B 845 ASN cc_start: 0.8887 (t0) cc_final: 0.7950 (t0) REVERT: B 849 TYR cc_start: 0.8990 (m-80) cc_final: 0.8748 (m-10) REVERT: B 978 MET cc_start: 0.7992 (ttp) cc_final: 0.7441 (ttm) REVERT: B 1045 LEU cc_start: 0.9439 (tp) cc_final: 0.9133 (tt) REVERT: B 1053 ASP cc_start: 0.8207 (t70) cc_final: 0.7957 (t70) REVERT: B 1059 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8228 (mm-30) REVERT: B 1071 LYS cc_start: 0.9257 (mttm) cc_final: 0.9043 (mmmm) REVERT: B 1072 MET cc_start: 0.7499 (ttp) cc_final: 0.7201 (tmm) REVERT: D 464 ARG cc_start: 0.9184 (mtm110) cc_final: 0.8946 (mtm110) REVERT: D 491 LYS cc_start: 0.9434 (tttt) cc_final: 0.9142 (ttpp) REVERT: D 522 SER cc_start: 0.9490 (m) cc_final: 0.9247 (p) REVERT: D 634 MET cc_start: 0.9431 (tpt) cc_final: 0.8957 (tpp) REVERT: D 704 LYS cc_start: 0.9402 (mttt) cc_final: 0.9080 (mttm) REVERT: D 721 MET cc_start: 0.8184 (mmm) cc_final: 0.7682 (tmm) REVERT: D 834 CYS cc_start: 0.8814 (m) cc_final: 0.8612 (m) REVERT: D 844 MET cc_start: 0.9217 (mmt) cc_final: 0.8676 (tpp) REVERT: D 845 ASN cc_start: 0.8760 (t0) cc_final: 0.8524 (t0) REVERT: D 862 MET cc_start: 0.8861 (mtt) cc_final: 0.8646 (mtt) REVERT: D 978 MET cc_start: 0.8242 (ttp) cc_final: 0.7582 (ttp) REVERT: D 1053 ASP cc_start: 0.8140 (t70) cc_final: 0.7930 (t70) REVERT: D 1059 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8101 (mm-30) REVERT: C 459 ILE cc_start: 0.9437 (mm) cc_final: 0.9217 (tt) REVERT: C 491 LYS cc_start: 0.9376 (tttt) cc_final: 0.9099 (ptmm) REVERT: C 522 SER cc_start: 0.9535 (m) cc_final: 0.9198 (p) REVERT: C 544 LEU cc_start: 0.9174 (mt) cc_final: 0.8926 (tp) REVERT: C 635 LYS cc_start: 0.9539 (tttt) cc_final: 0.9265 (ttmt) REVERT: C 834 CYS cc_start: 0.8964 (m) cc_final: 0.8644 (m) REVERT: C 845 ASN cc_start: 0.8741 (t0) cc_final: 0.7784 (t0) REVERT: C 1045 LEU cc_start: 0.9378 (tp) cc_final: 0.8966 (tt) REVERT: C 1053 ASP cc_start: 0.8308 (t70) cc_final: 0.8065 (t70) REVERT: C 1059 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8248 (mm-30) outliers start: 40 outliers final: 12 residues processed: 496 average time/residue: 0.2731 time to fit residues: 206.7214 Evaluate side-chains 351 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 339 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1073 GLU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 644 HIS A 700 HIS A 831 GLN A 954 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 644 HIS ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 HIS B 829 HIS B 831 GLN ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 HIS D 537 ASN D 644 HIS D 700 HIS D 719 HIS ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN C 519 HIS C 644 HIS C 700 HIS C 829 HIS C 831 GLN C 907 GLN C 933 HIS C 954 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18096 Z= 0.203 Angle : 0.706 11.856 24520 Z= 0.352 Chirality : 0.044 0.314 2900 Planarity : 0.006 0.056 3008 Dihedral : 6.281 52.096 2402 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.42 % Allowed : 16.15 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.15), residues: 2208 helix: -1.58 (0.11), residues: 1568 sheet: 3.74 (0.73), residues: 40 loop : -2.50 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 711 HIS 0.005 0.001 HIS D 589 PHE 0.015 0.001 PHE A 583 TYR 0.015 0.001 TYR C 456 ARG 0.006 0.000 ARG D 473 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 434 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 LEU cc_start: 0.8962 (mm) cc_final: 0.8707 (mm) REVERT: A 586 LEU cc_start: 0.9556 (tp) cc_final: 0.9170 (tp) REVERT: A 634 MET cc_start: 0.9487 (tpt) cc_final: 0.9230 (tpt) REVERT: A 721 MET cc_start: 0.8473 (mmm) cc_final: 0.7871 (tmm) REVERT: A 1045 LEU cc_start: 0.9418 (tp) cc_final: 0.9065 (tt) REVERT: A 1053 ASP cc_start: 0.8488 (t70) cc_final: 0.8141 (t0) REVERT: A 1061 GLN cc_start: 0.8867 (tt0) cc_final: 0.8283 (tt0) REVERT: A 1066 LYS cc_start: 0.9202 (mttt) cc_final: 0.8901 (ttmm) REVERT: A 1071 LYS cc_start: 0.9272 (mttm) cc_final: 0.8960 (mmmm) REVERT: B 463 GLN cc_start: 0.9086 (mt0) cc_final: 0.8882 (mt0) REVERT: B 491 LYS cc_start: 0.9365 (tttt) cc_final: 0.9138 (ptmm) REVERT: B 509 LEU cc_start: 0.8933 (mm) cc_final: 0.8675 (mm) REVERT: B 518 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9034 (tt) REVERT: B 530 MET cc_start: 0.9170 (mtp) cc_final: 0.8951 (mmm) REVERT: B 534 LEU cc_start: 0.9344 (mm) cc_final: 0.9142 (mm) REVERT: B 544 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8845 (tp) REVERT: B 586 LEU cc_start: 0.9587 (tp) cc_final: 0.9368 (tp) REVERT: B 635 LYS cc_start: 0.9358 (tttt) cc_final: 0.9099 (ttmt) REVERT: B 720 MET cc_start: 0.8413 (mmp) cc_final: 0.7991 (mmm) REVERT: B 834 CYS cc_start: 0.8888 (m) cc_final: 0.8605 (m) REVERT: B 845 ASN cc_start: 0.8299 (t0) cc_final: 0.7880 (t0) REVERT: B 1045 LEU cc_start: 0.9364 (tp) cc_final: 0.9087 (tt) REVERT: B 1056 PHE cc_start: 0.8766 (t80) cc_final: 0.8559 (t80) REVERT: B 1059 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7979 (mm-30) REVERT: D 464 ARG cc_start: 0.9142 (mtm110) cc_final: 0.8872 (mtm110) REVERT: D 491 LYS cc_start: 0.9433 (tttt) cc_final: 0.9167 (ttpp) REVERT: D 522 SER cc_start: 0.9496 (m) cc_final: 0.9145 (p) REVERT: D 577 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.6472 (p0) REVERT: D 634 MET cc_start: 0.9306 (tpt) cc_final: 0.8985 (tpt) REVERT: D 686 LEU cc_start: 0.9230 (tp) cc_final: 0.8993 (tp) REVERT: D 704 LYS cc_start: 0.9416 (mttt) cc_final: 0.9178 (mttm) REVERT: D 721 MET cc_start: 0.8171 (mmm) cc_final: 0.7689 (tmt) REVERT: D 844 MET cc_start: 0.9261 (mmt) cc_final: 0.8683 (tpp) REVERT: D 845 ASN cc_start: 0.8726 (t0) cc_final: 0.8489 (t0) REVERT: D 891 LEU cc_start: 0.9346 (mt) cc_final: 0.8868 (mt) REVERT: D 1053 ASP cc_start: 0.8134 (t70) cc_final: 0.7877 (t70) REVERT: D 1060 LYS cc_start: 0.9045 (mtmm) cc_final: 0.8622 (ptpp) REVERT: C 459 ILE cc_start: 0.9529 (mm) cc_final: 0.9289 (tt) REVERT: C 466 LEU cc_start: 0.9497 (mt) cc_final: 0.9268 (mt) REVERT: C 491 LYS cc_start: 0.9353 (tttt) cc_final: 0.9129 (ptmm) REVERT: C 577 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.6972 (p0) REVERT: C 721 MET cc_start: 0.7874 (tmm) cc_final: 0.7311 (tmm) REVERT: C 727 CYS cc_start: 0.9106 (t) cc_final: 0.8870 (t) REVERT: C 805 ASN cc_start: 0.8738 (m110) cc_final: 0.8498 (t0) REVERT: C 816 ILE cc_start: 0.9462 (pt) cc_final: 0.9179 (pt) REVERT: C 840 TYR cc_start: 0.9255 (t80) cc_final: 0.8954 (t80) REVERT: C 1000 GLN cc_start: 0.7591 (mp10) cc_final: 0.7390 (mp10) REVERT: C 1045 LEU cc_start: 0.9464 (tp) cc_final: 0.9158 (tt) REVERT: C 1059 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8233 (mm-30) outliers start: 83 outliers final: 45 residues processed: 484 average time/residue: 0.2805 time to fit residues: 203.8067 Evaluate side-chains 408 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 359 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 1068 ILE Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 571 ASN Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 856 CYS Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 951 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 0.0170 chunk 181 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS A 907 GLN B 907 GLN B 933 HIS ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18096 Z= 0.197 Angle : 0.642 10.011 24520 Z= 0.318 Chirality : 0.042 0.213 2900 Planarity : 0.004 0.050 3008 Dihedral : 5.524 58.473 2389 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.58 % Allowed : 19.24 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2208 helix: -0.41 (0.12), residues: 1568 sheet: 4.03 (0.75), residues: 40 loop : -2.29 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 711 HIS 0.003 0.001 HIS B 719 PHE 0.035 0.001 PHE D 944 TYR 0.015 0.001 TYR A 840 ARG 0.006 0.000 ARG C 473 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 398 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 LEU cc_start: 0.8915 (mm) cc_final: 0.8649 (mm) REVERT: A 586 LEU cc_start: 0.9557 (tp) cc_final: 0.9191 (tp) REVERT: A 721 MET cc_start: 0.8548 (mmm) cc_final: 0.8026 (tmm) REVERT: A 808 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8250 (mp0) REVERT: A 842 TYR cc_start: 0.8434 (m-80) cc_final: 0.7926 (t80) REVERT: A 1045 LEU cc_start: 0.9410 (tp) cc_final: 0.9137 (tt) REVERT: A 1053 ASP cc_start: 0.8500 (t70) cc_final: 0.8128 (t0) REVERT: A 1056 PHE cc_start: 0.8830 (t80) cc_final: 0.8581 (t80) REVERT: B 491 LYS cc_start: 0.9328 (tttt) cc_final: 0.9074 (ptmm) REVERT: B 509 LEU cc_start: 0.8791 (mm) cc_final: 0.8510 (mm) REVERT: B 518 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9055 (tt) REVERT: B 544 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8810 (tp) REVERT: B 635 LYS cc_start: 0.9278 (tttt) cc_final: 0.9013 (ttmt) REVERT: B 720 MET cc_start: 0.8440 (mmp) cc_final: 0.8058 (mmm) REVERT: B 805 ASN cc_start: 0.8806 (m110) cc_final: 0.8450 (t0) REVERT: B 834 CYS cc_start: 0.8834 (m) cc_final: 0.8583 (m) REVERT: B 840 TYR cc_start: 0.9061 (t80) cc_final: 0.8796 (t80) REVERT: B 845 ASN cc_start: 0.8468 (t0) cc_final: 0.7904 (t0) REVERT: B 1053 ASP cc_start: 0.8294 (t70) cc_final: 0.8058 (t70) REVERT: B 1059 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7931 (mm-30) REVERT: D 491 LYS cc_start: 0.9378 (tttt) cc_final: 0.9132 (ttpp) REVERT: D 522 SER cc_start: 0.9504 (m) cc_final: 0.9131 (p) REVERT: D 704 LYS cc_start: 0.9483 (mttt) cc_final: 0.9232 (mttm) REVERT: D 721 MET cc_start: 0.8198 (mmm) cc_final: 0.7813 (tmt) REVERT: D 844 MET cc_start: 0.9246 (mmt) cc_final: 0.8720 (tpp) REVERT: D 845 ASN cc_start: 0.8660 (t0) cc_final: 0.8439 (t0) REVERT: D 978 MET cc_start: 0.8131 (ttp) cc_final: 0.7634 (ttp) REVERT: D 1053 ASP cc_start: 0.8175 (t70) cc_final: 0.7939 (t70) REVERT: D 1059 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7975 (mm-30) REVERT: D 1060 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8563 (ptpp) REVERT: D 1072 MET cc_start: 0.7676 (tmm) cc_final: 0.7341 (tmm) REVERT: C 459 ILE cc_start: 0.9563 (mm) cc_final: 0.9321 (tt) REVERT: C 488 LEU cc_start: 0.9468 (mp) cc_final: 0.9254 (mp) REVERT: C 491 LYS cc_start: 0.9325 (tttt) cc_final: 0.9055 (ptmm) REVERT: C 544 LEU cc_start: 0.9143 (mt) cc_final: 0.8936 (tp) REVERT: C 586 LEU cc_start: 0.9612 (tp) cc_final: 0.9370 (tp) REVERT: C 721 MET cc_start: 0.7880 (tmm) cc_final: 0.7249 (tmm) REVERT: C 727 CYS cc_start: 0.9101 (t) cc_final: 0.8874 (t) REVERT: C 776 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9206 (tp) REVERT: C 805 ASN cc_start: 0.8747 (m110) cc_final: 0.8500 (t0) REVERT: C 816 ILE cc_start: 0.9486 (pt) cc_final: 0.9218 (pt) REVERT: C 840 TYR cc_start: 0.9292 (t80) cc_final: 0.9068 (t80) REVERT: C 1045 LEU cc_start: 0.9459 (tp) cc_final: 0.9126 (tt) REVERT: C 1059 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7917 (mm-30) REVERT: C 1072 MET cc_start: 0.7429 (tmm) cc_final: 0.7228 (tmm) outliers start: 86 outliers final: 54 residues processed: 449 average time/residue: 0.2505 time to fit residues: 177.7577 Evaluate side-chains 413 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 356 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 571 ASN Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 97 optimal weight: 0.0970 chunk 136 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 216 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 HIS D 907 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18096 Z= 0.178 Angle : 0.655 11.242 24520 Z= 0.313 Chirality : 0.042 0.222 2900 Planarity : 0.004 0.048 3008 Dihedral : 5.193 56.261 2387 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.74 % Allowed : 21.06 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2208 helix: 0.14 (0.13), residues: 1560 sheet: 4.03 (0.75), residues: 40 loop : -2.11 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 711 HIS 0.002 0.000 HIS A 933 PHE 0.024 0.001 PHE D 944 TYR 0.011 0.001 TYR A 840 ARG 0.002 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 388 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8918 (mmp) cc_final: 0.8268 (mmm) REVERT: A 509 LEU cc_start: 0.8906 (mm) cc_final: 0.8662 (mm) REVERT: A 586 LEU cc_start: 0.9596 (tp) cc_final: 0.9275 (tp) REVERT: A 642 MET cc_start: 0.8662 (mtp) cc_final: 0.8425 (mtt) REVERT: A 721 MET cc_start: 0.8498 (mmm) cc_final: 0.8016 (tmm) REVERT: A 803 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7748 (tp) REVERT: A 842 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7972 (t80) REVERT: A 1045 LEU cc_start: 0.9443 (tp) cc_final: 0.8933 (tt) REVERT: A 1053 ASP cc_start: 0.8432 (t70) cc_final: 0.8045 (t0) REVERT: A 1056 PHE cc_start: 0.8828 (t80) cc_final: 0.8577 (t80) REVERT: B 509 LEU cc_start: 0.8759 (mm) cc_final: 0.8499 (mm) REVERT: B 544 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8722 (tp) REVERT: B 635 LYS cc_start: 0.9284 (tttt) cc_final: 0.8983 (ttmt) REVERT: B 720 MET cc_start: 0.8461 (mmp) cc_final: 0.8105 (mmm) REVERT: B 805 ASN cc_start: 0.8792 (m110) cc_final: 0.8399 (t0) REVERT: B 834 CYS cc_start: 0.8823 (m) cc_final: 0.8584 (m) REVERT: B 840 TYR cc_start: 0.9115 (t80) cc_final: 0.8906 (t80) REVERT: B 1053 ASP cc_start: 0.8280 (t70) cc_final: 0.8065 (t70) REVERT: B 1059 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7952 (mm-30) REVERT: D 504 LYS cc_start: 0.9322 (mmmm) cc_final: 0.9001 (mmtm) REVERT: D 522 SER cc_start: 0.9476 (m) cc_final: 0.9100 (p) REVERT: D 704 LYS cc_start: 0.9443 (mttt) cc_final: 0.9211 (mttm) REVERT: D 721 MET cc_start: 0.8216 (mmm) cc_final: 0.7777 (tmm) REVERT: D 844 MET cc_start: 0.9224 (mmt) cc_final: 0.8755 (tpp) REVERT: D 845 ASN cc_start: 0.8635 (t0) cc_final: 0.7670 (t0) REVERT: D 1053 ASP cc_start: 0.8188 (t70) cc_final: 0.7946 (t70) REVERT: D 1059 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8049 (mm-30) REVERT: D 1060 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8665 (ptpp) REVERT: D 1072 MET cc_start: 0.7660 (tmm) cc_final: 0.7264 (tmm) REVERT: C 459 ILE cc_start: 0.9535 (mm) cc_final: 0.9091 (tt) REVERT: C 491 LYS cc_start: 0.9300 (tttt) cc_final: 0.9021 (ptmm) REVERT: C 577 ASN cc_start: 0.7209 (OUTLIER) cc_final: 0.6783 (p0) REVERT: C 586 LEU cc_start: 0.9644 (tp) cc_final: 0.9426 (tp) REVERT: C 721 MET cc_start: 0.7884 (tmm) cc_final: 0.7534 (ppp) REVERT: C 727 CYS cc_start: 0.9065 (t) cc_final: 0.8820 (t) REVERT: C 776 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9259 (tp) REVERT: C 805 ASN cc_start: 0.8714 (m110) cc_final: 0.8487 (t0) REVERT: C 808 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7969 (mm-30) REVERT: C 816 ILE cc_start: 0.9454 (pt) cc_final: 0.9182 (pt) REVERT: C 840 TYR cc_start: 0.9263 (t80) cc_final: 0.9002 (t80) REVERT: C 1045 LEU cc_start: 0.9314 (tp) cc_final: 0.8921 (tt) REVERT: C 1059 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7885 (mm-30) outliers start: 89 outliers final: 59 residues processed: 437 average time/residue: 0.2458 time to fit residues: 169.4725 Evaluate side-chains 413 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 348 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 571 ASN Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 184 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 HIS B 845 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 GLN D 481 HIS C 494 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18096 Z= 0.181 Angle : 0.650 11.326 24520 Z= 0.311 Chirality : 0.042 0.191 2900 Planarity : 0.004 0.046 3008 Dihedral : 4.973 49.868 2387 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.22 % Allowed : 21.59 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2208 helix: 0.39 (0.13), residues: 1568 sheet: 4.12 (0.76), residues: 40 loop : -1.96 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 605 HIS 0.002 0.000 HIS B 719 PHE 0.019 0.001 PHE D 944 TYR 0.011 0.001 TYR B 842 ARG 0.002 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 361 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8921 (mmp) cc_final: 0.8337 (mmm) REVERT: A 509 LEU cc_start: 0.8882 (mm) cc_final: 0.8638 (mm) REVERT: A 586 LEU cc_start: 0.9595 (tp) cc_final: 0.9283 (tp) REVERT: A 642 MET cc_start: 0.8665 (mtp) cc_final: 0.8453 (mtt) REVERT: A 721 MET cc_start: 0.8517 (mmm) cc_final: 0.8009 (tmm) REVERT: A 842 TYR cc_start: 0.8482 (m-80) cc_final: 0.8026 (t80) REVERT: A 978 MET cc_start: 0.8032 (ttm) cc_final: 0.7612 (ttp) REVERT: A 1045 LEU cc_start: 0.9328 (tp) cc_final: 0.8892 (tt) REVERT: A 1053 ASP cc_start: 0.8498 (t70) cc_final: 0.8124 (t0) REVERT: A 1056 PHE cc_start: 0.8807 (t80) cc_final: 0.8580 (t80) REVERT: B 509 LEU cc_start: 0.8782 (mm) cc_final: 0.8531 (mm) REVERT: B 635 LYS cc_start: 0.9266 (tttt) cc_final: 0.8957 (ttmt) REVERT: B 720 MET cc_start: 0.8574 (mmp) cc_final: 0.8190 (mmm) REVERT: B 805 ASN cc_start: 0.8841 (m110) cc_final: 0.8435 (t0) REVERT: B 834 CYS cc_start: 0.8865 (m) cc_final: 0.8613 (m) REVERT: B 840 TYR cc_start: 0.9098 (t80) cc_final: 0.8884 (t80) REVERT: B 1053 ASP cc_start: 0.8282 (t70) cc_final: 0.8070 (t70) REVERT: B 1059 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8049 (mm-30) REVERT: D 504 LYS cc_start: 0.9330 (mmmm) cc_final: 0.9005 (mmtm) REVERT: D 721 MET cc_start: 0.8233 (mmm) cc_final: 0.7763 (tmm) REVERT: D 844 MET cc_start: 0.9226 (mmt) cc_final: 0.8717 (tpp) REVERT: D 978 MET cc_start: 0.8141 (ttp) cc_final: 0.7709 (ttp) REVERT: D 1053 ASP cc_start: 0.8216 (t70) cc_final: 0.7948 (t70) REVERT: D 1060 LYS cc_start: 0.9031 (mtmm) cc_final: 0.8664 (ptpp) REVERT: D 1072 MET cc_start: 0.7639 (tmm) cc_final: 0.7261 (tmm) REVERT: C 491 LYS cc_start: 0.9254 (tttt) cc_final: 0.8991 (ptmm) REVERT: C 544 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8739 (tp) REVERT: C 586 LEU cc_start: 0.9653 (tp) cc_final: 0.9443 (tp) REVERT: C 720 MET cc_start: 0.8194 (mmm) cc_final: 0.7960 (mmm) REVERT: C 721 MET cc_start: 0.7917 (tmm) cc_final: 0.7307 (tmm) REVERT: C 727 CYS cc_start: 0.9070 (t) cc_final: 0.8818 (t) REVERT: C 776 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9237 (tp) REVERT: C 805 ASN cc_start: 0.8725 (m110) cc_final: 0.8505 (t0) REVERT: C 808 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: C 816 ILE cc_start: 0.9467 (pt) cc_final: 0.9210 (pt) REVERT: C 840 TYR cc_start: 0.9269 (t80) cc_final: 0.9008 (t80) REVERT: C 842 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: C 1045 LEU cc_start: 0.9329 (tp) cc_final: 0.8915 (tt) REVERT: C 1059 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7977 (mm-30) outliers start: 98 outliers final: 67 residues processed: 415 average time/residue: 0.2424 time to fit residues: 161.2374 Evaluate side-chains 404 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 333 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 571 ASN Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 856 CYS Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.0020 chunk 194 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 HIS B 933 HIS B1047 GLN B1070 GLN D 481 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18096 Z= 0.175 Angle : 0.661 14.000 24520 Z= 0.312 Chirality : 0.042 0.322 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.764 43.321 2385 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.80 % Allowed : 23.19 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2208 helix: 0.54 (0.13), residues: 1564 sheet: 4.28 (0.76), residues: 40 loop : -1.92 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 605 HIS 0.002 0.000 HIS D 933 PHE 0.020 0.001 PHE B 783 TYR 0.012 0.001 TYR B 842 ARG 0.003 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 362 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 LEU cc_start: 0.9454 (mt) cc_final: 0.9213 (mt) REVERT: A 483 MET cc_start: 0.8962 (mmp) cc_final: 0.8392 (mmm) REVERT: A 504 LYS cc_start: 0.9253 (mmmt) cc_final: 0.8819 (tppp) REVERT: A 509 LEU cc_start: 0.8849 (mm) cc_final: 0.8606 (mm) REVERT: A 586 LEU cc_start: 0.9607 (tp) cc_final: 0.9311 (tp) REVERT: A 642 MET cc_start: 0.8659 (mtp) cc_final: 0.8451 (mtt) REVERT: A 721 MET cc_start: 0.8515 (mmm) cc_final: 0.7994 (tmm) REVERT: A 840 TYR cc_start: 0.8824 (t80) cc_final: 0.8618 (t80) REVERT: A 842 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8036 (t80) REVERT: A 1045 LEU cc_start: 0.9373 (tp) cc_final: 0.8871 (tt) REVERT: A 1053 ASP cc_start: 0.8497 (t70) cc_final: 0.8127 (t0) REVERT: A 1056 PHE cc_start: 0.8805 (t80) cc_final: 0.8601 (t80) REVERT: B 509 LEU cc_start: 0.8792 (mm) cc_final: 0.8540 (mm) REVERT: B 530 MET cc_start: 0.9462 (mmm) cc_final: 0.9237 (mmm) REVERT: B 635 LYS cc_start: 0.9258 (tttt) cc_final: 0.8940 (ttmt) REVERT: B 720 MET cc_start: 0.8577 (mmp) cc_final: 0.8165 (mmm) REVERT: B 805 ASN cc_start: 0.8828 (m110) cc_final: 0.8409 (t0) REVERT: B 834 CYS cc_start: 0.8861 (m) cc_final: 0.8614 (m) REVERT: B 1053 ASP cc_start: 0.8284 (t70) cc_final: 0.8068 (t70) REVERT: D 504 LYS cc_start: 0.9314 (mmmm) cc_final: 0.8987 (mmtm) REVERT: D 577 ASN cc_start: 0.6784 (OUTLIER) cc_final: 0.6469 (p0) REVERT: D 721 MET cc_start: 0.8176 (mmm) cc_final: 0.7786 (tmm) REVERT: D 842 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: D 1053 ASP cc_start: 0.8254 (t70) cc_final: 0.7994 (t70) REVERT: D 1060 LYS cc_start: 0.9045 (mtmm) cc_final: 0.8664 (ptpp) REVERT: D 1073 GLU cc_start: 0.8018 (pm20) cc_final: 0.7747 (pm20) REVERT: C 491 LYS cc_start: 0.9272 (tttt) cc_final: 0.8974 (ptmm) REVERT: C 544 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8718 (tp) REVERT: C 586 LEU cc_start: 0.9647 (tp) cc_final: 0.9440 (tp) REVERT: C 720 MET cc_start: 0.8184 (mmm) cc_final: 0.7968 (mmm) REVERT: C 721 MET cc_start: 0.7928 (tmm) cc_final: 0.7272 (tmm) REVERT: C 727 CYS cc_start: 0.9063 (t) cc_final: 0.8853 (t) REVERT: C 776 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9239 (tp) REVERT: C 803 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8108 (tp) REVERT: C 805 ASN cc_start: 0.8715 (m110) cc_final: 0.8489 (t0) REVERT: C 808 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: C 816 ILE cc_start: 0.9457 (pt) cc_final: 0.9207 (pt) REVERT: C 840 TYR cc_start: 0.9273 (t80) cc_final: 0.8987 (t80) REVERT: C 842 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: C 1045 LEU cc_start: 0.9301 (tp) cc_final: 0.8885 (tt) REVERT: C 1059 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8040 (mm-30) outliers start: 90 outliers final: 60 residues processed: 407 average time/residue: 0.2394 time to fit residues: 156.1145 Evaluate side-chains 412 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 344 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 571 ASN Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 856 CYS Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1065 ILE Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 856 CYS Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 121 optimal weight: 0.0050 chunk 215 optimal weight: 0.4980 chunk 135 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN B1070 GLN D 481 HIS D 494 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18096 Z= 0.171 Angle : 0.655 11.520 24520 Z= 0.308 Chirality : 0.041 0.243 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.613 43.668 2385 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.90 % Allowed : 23.61 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 2208 helix: 0.63 (0.14), residues: 1572 sheet: 4.36 (0.75), residues: 40 loop : -1.81 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 605 HIS 0.002 0.000 HIS D 933 PHE 0.010 0.001 PHE B 944 TYR 0.028 0.001 TYR B 840 ARG 0.003 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 371 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 465 LEU cc_start: 0.9452 (mt) cc_final: 0.9207 (mt) REVERT: A 483 MET cc_start: 0.8985 (mmp) cc_final: 0.8434 (mmm) REVERT: A 504 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8810 (tppp) REVERT: A 509 LEU cc_start: 0.8809 (mm) cc_final: 0.8559 (mm) REVERT: A 586 LEU cc_start: 0.9610 (tp) cc_final: 0.9315 (tp) REVERT: A 721 MET cc_start: 0.8513 (mmm) cc_final: 0.7983 (tmm) REVERT: A 840 TYR cc_start: 0.8872 (t80) cc_final: 0.8661 (t80) REVERT: A 842 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.8055 (t80) REVERT: A 1045 LEU cc_start: 0.9345 (tp) cc_final: 0.8808 (tt) REVERT: A 1053 ASP cc_start: 0.8479 (t70) cc_final: 0.8113 (t0) REVERT: A 1056 PHE cc_start: 0.8806 (t80) cc_final: 0.8590 (t80) REVERT: B 466 LEU cc_start: 0.9445 (mt) cc_final: 0.9196 (pp) REVERT: B 483 MET cc_start: 0.8997 (mmp) cc_final: 0.8777 (mmm) REVERT: B 509 LEU cc_start: 0.8765 (mm) cc_final: 0.8487 (mm) REVERT: B 635 LYS cc_start: 0.9231 (tttt) cc_final: 0.8909 (ttmt) REVERT: B 720 MET cc_start: 0.8609 (mmp) cc_final: 0.8213 (mmm) REVERT: B 805 ASN cc_start: 0.8824 (m110) cc_final: 0.8397 (t0) REVERT: B 834 CYS cc_start: 0.8864 (m) cc_final: 0.8609 (m) REVERT: B 1053 ASP cc_start: 0.8281 (t70) cc_final: 0.8065 (t70) REVERT: D 504 LYS cc_start: 0.9316 (mmmm) cc_final: 0.8988 (mmmt) REVERT: D 577 ASN cc_start: 0.6965 (OUTLIER) cc_final: 0.6632 (p0) REVERT: D 721 MET cc_start: 0.8184 (mmm) cc_final: 0.7799 (tmm) REVERT: D 842 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: D 844 MET cc_start: 0.8531 (mmm) cc_final: 0.8238 (mmt) REVERT: D 978 MET cc_start: 0.8075 (ttp) cc_final: 0.7633 (ttp) REVERT: D 1053 ASP cc_start: 0.8261 (t70) cc_final: 0.8007 (t70) REVERT: D 1060 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8554 (ptpp) REVERT: C 463 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.9086 (pm20) REVERT: C 544 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8671 (tp) REVERT: C 720 MET cc_start: 0.8175 (mmm) cc_final: 0.7954 (mmm) REVERT: C 721 MET cc_start: 0.7893 (tmm) cc_final: 0.7181 (tmm) REVERT: C 727 CYS cc_start: 0.9086 (t) cc_final: 0.8851 (t) REVERT: C 778 PHE cc_start: 0.9357 (t80) cc_final: 0.9146 (t80) REVERT: C 803 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8078 (tp) REVERT: C 805 ASN cc_start: 0.8669 (m110) cc_final: 0.8462 (t0) REVERT: C 808 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: C 816 ILE cc_start: 0.9455 (pt) cc_final: 0.9177 (pt) REVERT: C 840 TYR cc_start: 0.9270 (t80) cc_final: 0.8989 (t80) REVERT: C 842 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: C 1045 LEU cc_start: 0.9274 (tp) cc_final: 0.8857 (tt) REVERT: C 1072 MET cc_start: 0.7605 (tmm) cc_final: 0.7324 (tmm) outliers start: 92 outliers final: 58 residues processed: 422 average time/residue: 0.2402 time to fit residues: 161.8354 Evaluate side-chains 411 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 345 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 571 ASN Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 633 CYS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 856 CYS Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 chunk 169 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1070 GLN D 481 HIS C1047 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18096 Z= 0.200 Angle : 0.680 12.901 24520 Z= 0.320 Chirality : 0.043 0.206 2900 Planarity : 0.004 0.046 3008 Dihedral : 4.524 42.424 2381 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.37 % Allowed : 24.73 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 2208 helix: 0.57 (0.13), residues: 1580 sheet: 4.43 (0.75), residues: 40 loop : -1.69 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 605 HIS 0.003 0.001 HIS D 933 PHE 0.040 0.001 PHE C 944 TYR 0.021 0.001 TYR B 840 ARG 0.002 0.000 ARG D 872 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 363 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 465 LEU cc_start: 0.9446 (mt) cc_final: 0.9202 (mt) REVERT: A 483 MET cc_start: 0.8972 (mmp) cc_final: 0.8431 (mmm) REVERT: A 504 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8839 (tppp) REVERT: A 509 LEU cc_start: 0.8849 (mm) cc_final: 0.8616 (mm) REVERT: A 586 LEU cc_start: 0.9615 (tp) cc_final: 0.9326 (tp) REVERT: A 721 MET cc_start: 0.8547 (mmm) cc_final: 0.7987 (tmm) REVERT: A 840 TYR cc_start: 0.8917 (t80) cc_final: 0.8698 (t80) REVERT: A 842 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8061 (t80) REVERT: A 978 MET cc_start: 0.7924 (ttm) cc_final: 0.7541 (ttp) REVERT: A 1045 LEU cc_start: 0.9322 (tp) cc_final: 0.8819 (tt) REVERT: A 1053 ASP cc_start: 0.8499 (t70) cc_final: 0.8144 (t0) REVERT: A 1056 PHE cc_start: 0.8829 (t80) cc_final: 0.8618 (t80) REVERT: B 466 LEU cc_start: 0.9453 (mt) cc_final: 0.9199 (pp) REVERT: B 483 MET cc_start: 0.9049 (mmp) cc_final: 0.8842 (mmm) REVERT: B 509 LEU cc_start: 0.8808 (mm) cc_final: 0.8557 (mm) REVERT: B 635 LYS cc_start: 0.9245 (tttt) cc_final: 0.8929 (ttmt) REVERT: B 720 MET cc_start: 0.8645 (mmp) cc_final: 0.8255 (mmm) REVERT: B 805 ASN cc_start: 0.8756 (m110) cc_final: 0.8379 (t0) REVERT: B 834 CYS cc_start: 0.8877 (m) cc_final: 0.8619 (m) REVERT: B 1053 ASP cc_start: 0.8299 (t70) cc_final: 0.8076 (t70) REVERT: D 504 LYS cc_start: 0.9329 (mmmm) cc_final: 0.8987 (mmmt) REVERT: D 530 MET cc_start: 0.9295 (mmm) cc_final: 0.9034 (mmt) REVERT: D 577 ASN cc_start: 0.7091 (OUTLIER) cc_final: 0.6782 (p0) REVERT: D 721 MET cc_start: 0.8186 (mmm) cc_final: 0.7879 (tmt) REVERT: D 842 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: D 1053 ASP cc_start: 0.8261 (t70) cc_final: 0.8019 (t70) REVERT: C 544 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8592 (tp) REVERT: C 721 MET cc_start: 0.7963 (tmm) cc_final: 0.7225 (tmm) REVERT: C 727 CYS cc_start: 0.9074 (t) cc_final: 0.8851 (t) REVERT: C 803 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8076 (tp) REVERT: C 805 ASN cc_start: 0.8686 (m110) cc_final: 0.8471 (t0) REVERT: C 808 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7885 (mm-30) REVERT: C 816 ILE cc_start: 0.9454 (pt) cc_final: 0.9181 (pt) REVERT: C 840 TYR cc_start: 0.9258 (t80) cc_final: 0.8933 (t80) REVERT: C 842 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: C 1045 LEU cc_start: 0.9261 (tp) cc_final: 0.8858 (tt) REVERT: C 1072 MET cc_start: 0.7673 (tmm) cc_final: 0.7362 (tmm) outliers start: 82 outliers final: 65 residues processed: 406 average time/residue: 0.2392 time to fit residues: 154.7825 Evaluate side-chains 412 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 340 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 571 ASN Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 856 CYS Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.0030 chunk 206 optimal weight: 0.7980 chunk 188 optimal weight: 20.0000 chunk 201 optimal weight: 2.9990 chunk 121 optimal weight: 0.0270 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.7650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS D 481 HIS ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18096 Z= 0.185 Angle : 0.690 12.830 24520 Z= 0.323 Chirality : 0.043 0.244 2900 Planarity : 0.004 0.046 3008 Dihedral : 4.493 43.168 2381 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.37 % Allowed : 25.21 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.19), residues: 2208 helix: 0.63 (0.13), residues: 1576 sheet: 4.43 (0.74), residues: 40 loop : -1.67 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 605 HIS 0.003 0.000 HIS D 933 PHE 0.022 0.001 PHE B 944 TYR 0.027 0.001 TYR D 840 ARG 0.001 0.000 ARG C 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 367 time to evaluate : 2.280 Fit side-chains revert: symmetry clash REVERT: A 465 LEU cc_start: 0.9435 (mt) cc_final: 0.9201 (mt) REVERT: A 483 MET cc_start: 0.8952 (mmp) cc_final: 0.8503 (mmm) REVERT: A 504 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8812 (tppp) REVERT: A 509 LEU cc_start: 0.8861 (mm) cc_final: 0.8635 (mm) REVERT: A 586 LEU cc_start: 0.9602 (tp) cc_final: 0.9321 (tp) REVERT: A 721 MET cc_start: 0.8532 (mmm) cc_final: 0.7969 (tmm) REVERT: A 842 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.8063 (t80) REVERT: A 1045 LEU cc_start: 0.9314 (tp) cc_final: 0.8810 (tt) REVERT: A 1053 ASP cc_start: 0.8478 (t70) cc_final: 0.8047 (t0) REVERT: A 1056 PHE cc_start: 0.8815 (t80) cc_final: 0.8603 (t80) REVERT: B 466 LEU cc_start: 0.9468 (mt) cc_final: 0.9206 (pp) REVERT: B 483 MET cc_start: 0.8991 (mmp) cc_final: 0.8736 (mmm) REVERT: B 509 LEU cc_start: 0.8825 (mm) cc_final: 0.8577 (mm) REVERT: B 530 MET cc_start: 0.9322 (mmm) cc_final: 0.9035 (mmm) REVERT: B 635 LYS cc_start: 0.9233 (tttt) cc_final: 0.8905 (ttmt) REVERT: B 720 MET cc_start: 0.8636 (mmp) cc_final: 0.8234 (mmm) REVERT: B 774 MET cc_start: 0.8654 (ttt) cc_final: 0.8451 (ptm) REVERT: B 805 ASN cc_start: 0.8728 (m110) cc_final: 0.8343 (t0) REVERT: B 834 CYS cc_start: 0.8859 (m) cc_final: 0.8597 (m) REVERT: B 1053 ASP cc_start: 0.8291 (t70) cc_final: 0.8063 (t70) REVERT: D 504 LYS cc_start: 0.9327 (mmmm) cc_final: 0.9009 (mmmt) REVERT: D 530 MET cc_start: 0.9258 (mmm) cc_final: 0.9043 (mmt) REVERT: D 721 MET cc_start: 0.8219 (mmm) cc_final: 0.7890 (tmt) REVERT: D 842 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: D 844 MET cc_start: 0.8819 (mmm) cc_final: 0.8183 (mmm) REVERT: D 1049 TYR cc_start: 0.8608 (m-80) cc_final: 0.8382 (m-80) REVERT: D 1053 ASP cc_start: 0.8260 (t70) cc_final: 0.8036 (t70) REVERT: C 544 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8563 (tp) REVERT: C 721 MET cc_start: 0.7965 (tmm) cc_final: 0.7280 (tmm) REVERT: C 727 CYS cc_start: 0.9108 (t) cc_final: 0.8851 (t) REVERT: C 803 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8047 (tp) REVERT: C 805 ASN cc_start: 0.8675 (m110) cc_final: 0.8466 (t0) REVERT: C 808 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8009 (mm-30) REVERT: C 840 TYR cc_start: 0.9274 (t80) cc_final: 0.8912 (t80) REVERT: C 842 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: C 1045 LEU cc_start: 0.9249 (tp) cc_final: 0.8842 (tt) REVERT: C 1072 MET cc_start: 0.7576 (tmm) cc_final: 0.7254 (tmm) outliers start: 82 outliers final: 68 residues processed: 412 average time/residue: 0.2374 time to fit residues: 156.9890 Evaluate side-chains 424 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 350 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 571 ASN Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 633 CYS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 641 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 20.0000 chunk 212 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 100 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN B 512 HIS B 907 GLN D 481 HIS ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18096 Z= 0.179 Angle : 0.711 13.743 24520 Z= 0.330 Chirality : 0.043 0.221 2900 Planarity : 0.004 0.046 3008 Dihedral : 4.479 43.265 2381 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.73 % Allowed : 26.60 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 2208 helix: 0.65 (0.14), residues: 1576 sheet: 4.46 (0.74), residues: 40 loop : -1.63 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 605 HIS 0.003 0.000 HIS D 933 PHE 0.021 0.001 PHE B 783 TYR 0.026 0.001 TYR B 840 ARG 0.001 0.000 ARG D 919 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 373 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 483 MET cc_start: 0.8909 (mmp) cc_final: 0.8447 (mmm) REVERT: A 504 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8750 (tppp) REVERT: A 509 LEU cc_start: 0.8824 (mm) cc_final: 0.8609 (mm) REVERT: A 586 LEU cc_start: 0.9582 (tp) cc_final: 0.9310 (tp) REVERT: A 721 MET cc_start: 0.8471 (mmm) cc_final: 0.7890 (tmm) REVERT: A 842 TYR cc_start: 0.8367 (m-80) cc_final: 0.7992 (t80) REVERT: A 912 MET cc_start: 0.8879 (ppp) cc_final: 0.8619 (ppp) REVERT: A 978 MET cc_start: 0.7934 (ttm) cc_final: 0.7691 (ttp) REVERT: A 1045 LEU cc_start: 0.9323 (tp) cc_final: 0.8828 (tt) REVERT: A 1053 ASP cc_start: 0.8469 (t70) cc_final: 0.8032 (t0) REVERT: A 1056 PHE cc_start: 0.8806 (t80) cc_final: 0.8586 (t80) REVERT: B 466 LEU cc_start: 0.9470 (mt) cc_final: 0.9203 (pp) REVERT: B 509 LEU cc_start: 0.8801 (mm) cc_final: 0.8550 (mm) REVERT: B 523 MET cc_start: 0.8719 (tpp) cc_final: 0.8127 (tpp) REVERT: B 635 LYS cc_start: 0.9220 (tttt) cc_final: 0.8894 (ttmt) REVERT: B 720 MET cc_start: 0.8659 (mmp) cc_final: 0.8211 (mmm) REVERT: B 774 MET cc_start: 0.8830 (ttt) cc_final: 0.8589 (ptm) REVERT: B 805 ASN cc_start: 0.8758 (m110) cc_final: 0.8345 (t0) REVERT: B 834 CYS cc_start: 0.8836 (m) cc_final: 0.8587 (m) REVERT: B 844 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8359 (mmm) REVERT: B 990 LEU cc_start: 0.9067 (tp) cc_final: 0.8727 (tt) REVERT: B 1053 ASP cc_start: 0.8252 (t70) cc_final: 0.8022 (t70) REVERT: D 504 LYS cc_start: 0.9322 (mmmm) cc_final: 0.8999 (mmmt) REVERT: D 530 MET cc_start: 0.9280 (mmm) cc_final: 0.9069 (mmt) REVERT: D 586 LEU cc_start: 0.9587 (tp) cc_final: 0.9307 (tp) REVERT: D 721 MET cc_start: 0.8187 (mmm) cc_final: 0.7873 (tmt) REVERT: D 842 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: D 844 MET cc_start: 0.8823 (mmm) cc_final: 0.8532 (mmm) REVERT: D 1049 TYR cc_start: 0.8602 (m-80) cc_final: 0.8392 (m-80) REVERT: D 1053 ASP cc_start: 0.8258 (t70) cc_final: 0.8026 (t70) REVERT: D 1060 LYS cc_start: 0.9320 (ptpt) cc_final: 0.9008 (ptpp) REVERT: C 544 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8513 (tp) REVERT: C 721 MET cc_start: 0.7925 (tmm) cc_final: 0.7285 (tmm) REVERT: C 727 CYS cc_start: 0.9103 (t) cc_final: 0.8841 (t) REVERT: C 805 ASN cc_start: 0.8683 (m110) cc_final: 0.8480 (t0) REVERT: C 808 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: C 840 TYR cc_start: 0.9268 (t80) cc_final: 0.8923 (t80) REVERT: C 842 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: C 1045 LEU cc_start: 0.9224 (tp) cc_final: 0.8811 (tt) REVERT: C 1072 MET cc_start: 0.7524 (tmm) cc_final: 0.7204 (tmm) outliers start: 70 outliers final: 61 residues processed: 410 average time/residue: 0.2390 time to fit residues: 156.3316 Evaluate side-chains 426 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 360 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 571 ASN Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 583 PHE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 633 CYS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1074 ILE Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.9980 chunk 189 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 182 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS D 940 GLN C 907 GLN C 940 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.100475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.078637 restraints weight = 49335.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.081088 restraints weight = 26323.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.082764 restraints weight = 17459.251| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18096 Z= 0.184 Angle : 0.730 13.973 24520 Z= 0.336 Chirality : 0.043 0.217 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.473 42.833 2381 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.73 % Allowed : 26.81 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 2208 helix: 0.68 (0.14), residues: 1576 sheet: 4.55 (0.75), residues: 40 loop : -1.62 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 605 HIS 0.003 0.000 HIS D 933 PHE 0.023 0.001 PHE A 783 TYR 0.029 0.001 TYR D 840 ARG 0.003 0.000 ARG D 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3643.81 seconds wall clock time: 66 minutes 51.78 seconds (4011.78 seconds total)