Starting phenix.real_space_refine (version: dev) on Tue Dec 13 23:17:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/12_2022/6v9y_21130.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/12_2022/6v9y_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_21130/12_2022/6v9y_21130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/12_2022/6v9y_21130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/12_2022/6v9y_21130.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9y_21130/12_2022/6v9y_21130.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 Convert atoms to be neutral 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-4807/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: 10.23, per 1000 atoms: 0.58 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: 7.10 Conformation dependent library (CDL) restraints added in 2.7 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: 0.90 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: 5.96 Time building geometry restraints manager: 7.66 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 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. 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: 1.160 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: 0.020 Extract box with map and model: 5.500 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.160 Process input model: 47.700 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 2.13 % 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 *********************** 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 : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 12 residues processed: 496 average time/residue: 0.2734 time to fit residues: 207.4521 Evaluate side-chains 338 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 326 time to evaluate : 3.196 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1705 time to fit residues: 6.9518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 203 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 644 HIS ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 ASN B 519 HIS B 644 HIS ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 HIS B 829 HIS ** B 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 HIS D 537 ASN D 644 HIS ** D 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 HIS D 719 HIS ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 940 GLN D 954 ASN C 519 HIS C 644 HIS C 700 HIS C 829 HIS C 845 ASN C 907 GLN C 933 HIS C 954 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 18096 Z= 0.202 Angle : 0.718 11.779 24520 Z= 0.354 Chirality : 0.044 0.314 2900 Planarity : 0.006 0.055 3008 Dihedral : 5.282 23.461 2376 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 4.53 % 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: -2.74 (0.15), residues: 2208 helix: -1.55 (0.11), residues: 1568 sheet: 3.73 (0.72), residues: 40 loop : -2.50 (0.23), residues: 600 *********************** 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 527 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 442 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 44 residues processed: 487 average time/residue: 0.2497 time to fit residues: 191.2061 Evaluate side-chains 398 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 354 time to evaluate : 2.170 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.1632 time to fit residues: 16.1596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 GLN B 933 HIS B1047 GLN B1070 GLN D 549 ASN ** D 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 HIS D 907 GLN D 940 GLN C1047 GLN C1061 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 18096 Z= 0.239 Angle : 0.691 10.240 24520 Z= 0.339 Chirality : 0.044 0.216 2900 Planarity : 0.005 0.050 3008 Dihedral : 4.912 24.685 2376 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 3.57 % 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: -1.34 (0.17), residues: 2208 helix: -0.41 (0.12), residues: 1564 sheet: 4.00 (0.75), residues: 40 loop : -2.27 (0.25), residues: 604 *********************** 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 454 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 387 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 27 residues processed: 424 average time/residue: 0.2340 time to fit residues: 158.7747 Evaluate side-chains 364 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 337 time to evaluate : 2.039 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1730 time to fit residues: 11.0182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 0.0370 chunk 136 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 216 optimal weight: 0.3980 chunk 106 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 58 optimal weight: 0.0170 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 18096 Z= 0.171 Angle : 0.686 10.807 24520 Z= 0.321 Chirality : 0.043 0.200 2900 Planarity : 0.004 0.048 3008 Dihedral : 4.647 23.527 2376 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 2.93 % 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: -0.71 (0.18), residues: 2208 helix: 0.09 (0.13), residues: 1560 sheet: 3.99 (0.74), residues: 40 loop : -2.08 (0.25), residues: 608 *********************** 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 448 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 393 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 19 residues processed: 424 average time/residue: 0.2489 time to fit residues: 168.4235 Evaluate side-chains 367 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 348 time to evaluate : 2.297 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1689 time to fit residues: 9.0321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 0 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 463 GLN B 494 HIS B 577 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS ** D 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 18096 Z= 0.183 Angle : 0.697 12.288 24520 Z= 0.324 Chirality : 0.043 0.203 2900 Planarity : 0.004 0.046 3008 Dihedral : 4.502 23.139 2376 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 2.72 % 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: -0.38 (0.18), residues: 2208 helix: 0.34 (0.13), residues: 1560 sheet: 4.04 (0.75), residues: 40 loop : -1.99 (0.26), residues: 608 *********************** 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 409 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 358 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 22 residues processed: 386 average time/residue: 0.2388 time to fit residues: 148.6776 Evaluate side-chains 347 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 325 time to evaluate : 2.250 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1687 time to fit residues: 9.8837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 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: 0.7980 chunk 113 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 494 HIS A 549 ASN B 933 HIS ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS D 699 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 18096 Z= 0.250 Angle : 0.726 14.220 24520 Z= 0.340 Chirality : 0.043 0.240 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.498 22.545 2376 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 2.56 % 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: -0.22 (0.18), residues: 2208 helix: 0.42 (0.13), residues: 1568 sheet: 4.09 (0.73), residues: 40 loop : -1.83 (0.26), residues: 600 *********************** 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 399 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 351 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 374 average time/residue: 0.2514 time to fit residues: 151.1662 Evaluate side-chains 353 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 331 time to evaluate : 2.358 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1573 time to fit residues: 9.5586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 158 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 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 512 HIS ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 18096 Z= 0.196 Angle : 0.723 11.974 24520 Z= 0.333 Chirality : 0.043 0.179 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.459 23.664 2376 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 1.55 % 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: -0.06 (0.19), residues: 2208 helix: 0.51 (0.13), residues: 1576 sheet: 4.10 (0.72), residues: 40 loop : -1.68 (0.27), residues: 592 *********************** 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 395 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 366 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 379 average time/residue: 0.2523 time to fit residues: 152.4885 Evaluate side-chains 359 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 343 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1889 time to fit residues: 8.1262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 0.0060 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 HIS ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 940 GLN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1070 GLN D 481 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 18096 Z= 0.200 Angle : 0.729 15.114 24520 Z= 0.337 Chirality : 0.043 0.290 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.428 21.550 2376 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 1.23 % 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: 0.53 (0.13), residues: 1572 sheet: 4.10 (0.72), residues: 40 loop : -1.70 (0.27), residues: 596 *********************** 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 379 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 356 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 366 average time/residue: 0.2568 time to fit residues: 150.4101 Evaluate side-chains 353 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 338 time to evaluate : 2.130 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1687 time to fit residues: 7.6244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.8980 chunk 206 optimal weight: 0.3980 chunk 188 optimal weight: 20.0000 chunk 201 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 181 optimal weight: 0.0870 chunk 190 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN B 512 HIS ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1070 GLN D 467 GLN D 481 HIS ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4562 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= 0.201 Angle : 0.747 13.691 24520 Z= 0.343 Chirality : 0.043 0.203 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.407 19.896 2376 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.96 % 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: 0.53 (0.13), residues: 1576 sheet: 4.15 (0.71), residues: 40 loop : -1.70 (0.27), residues: 592 *********************** 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 375 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 357 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 366 average time/residue: 0.2437 time to fit residues: 143.6296 Evaluate side-chains 354 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 342 time to evaluate : 2.386 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1778 time to fit residues: 6.9747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 100 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 177 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 0.0370 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 GLN B1070 GLN D 481 HIS C 512 HIS ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4725 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= 0.198 Angle : 0.757 14.357 24520 Z= 0.347 Chirality : 0.044 0.206 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.372 19.014 2376 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.27 % 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: -0.04 (0.19), residues: 2208 helix: 0.55 (0.13), residues: 1568 sheet: 4.25 (0.71), residues: 40 loop : -1.75 (0.27), residues: 600 ********************** 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 377 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 372 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 373 average time/residue: 0.2555 time to fit residues: 158.0990 Evaluate side-chains 354 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 351 time to evaluate : 2.328 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1991 time to fit residues: 4.1804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 163 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 182 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS C 467 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.080481 restraints weight = 48744.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083019 restraints weight = 25217.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.084756 restraints weight = 16328.334| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 18096 Z= 0.185 Angle : 0.774 13.869 24520 Z= 0.351 Chirality : 0.043 0.243 2900 Planarity : 0.004 0.047 3008 Dihedral : 4.320 18.543 2376 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.75 % 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: -0.02 (0.19), residues: 2208 helix: 0.56 (0.13), residues: 1568 sheet: 4.38 (0.74), residues: 40 loop : -1.75 (0.27), residues: 600 =============================================================================== Job complete usr+sys time: 3525.32 seconds wall clock time: 65 minutes 10.04 seconds (3910.04 seconds total)