Starting phenix.real_space_refine on Fri Feb 16 23:15:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbo_7846/02_2024/6dbo_7846_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbo_7846/02_2024/6dbo_7846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbo_7846/02_2024/6dbo_7846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbo_7846/02_2024/6dbo_7846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbo_7846/02_2024/6dbo_7846_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbo_7846/02_2024/6dbo_7846_neut.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 128 5.49 5 S 106 5.16 5 C 10178 2.51 5 N 2970 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 849": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C ARG 849": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 999": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16820 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4381 Classifications: {'peptide': 542} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 517} Chain breaks: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4381 Classifications: {'peptide': 542} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 517} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 654 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 658 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "G" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 654 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "H" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 658 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2053 SG CYS A 749 63.024 58.922 98.484 1.00128.59 S ATOM 2074 SG CYS A 752 61.101 58.576 101.316 1.00191.14 S ATOM 9148 SG CYS C 749 57.602 77.984 20.282 1.00123.25 S ATOM 9169 SG CYS C 752 55.168 79.056 17.849 1.00185.95 S Time building chain proxies: 8.84, per 1000 atoms: 0.53 Number of scatterers: 16820 At special positions: 0 Unit cell: (121.324, 143.608, 118.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 4 19.99 S 106 16.00 P 128 15.00 O 3432 8.00 N 2970 7.00 C 10178 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: 7.73 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 752 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " Number of angles added : 4 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 34.5% alpha, 24.5% beta 56 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 5.88 Creating SS restraints... Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 577 through 589 Processing helix chain 'A' and resid 589 through 600 Processing helix chain 'A' and resid 686 through 705 removed outlier: 3.574A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 3.534A pdb=" N MET A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 757 through 762 removed outlier: 3.590A pdb=" N GLN A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 814 through 835 removed outlier: 3.803A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 removed outlier: 3.555A pdb=" N ARG A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 890 removed outlier: 3.688A pdb=" N VAL A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 917 Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.686A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 4.230A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1027 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 519 through 527 removed outlier: 4.018A pdb=" N LYS C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 589 through 600 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.509A pdb=" N SER C 673 " --> pdb=" O SER C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.563A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 757 through 762 removed outlier: 3.628A pdb=" N GLN C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 757 through 762' Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 814 through 835 removed outlier: 3.969A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 889 removed outlier: 3.710A pdb=" N VAL C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 917 Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.637A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 4.265A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.733A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.733A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.679A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LEU B 55 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA B 8 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N TYR B 343 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.214A pdb=" N LEU B 106 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA8, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AA9, first strand: chain 'B' and resid 277 through 279 Processing sheet with id=AB1, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.524A pdb=" N PHE C 611 " --> pdb=" O SER C 719 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 617 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 727 " --> pdb=" O GLU C 617 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N CYS C 619 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 677 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.524A pdb=" N PHE C 611 " --> pdb=" O SER C 719 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 617 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 727 " --> pdb=" O GLU C 617 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N CYS C 619 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.689A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.060A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'D' and resid 209 through 212 removed outlier: 3.573A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 263 through 265 Processing sheet with id=AB9, first strand: chain 'D' and resid 277 through 279 666 hydrogen bonds defined for protein. 1869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 268 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 8.20 Time building geometry restraints manager: 8.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3784 1.33 - 1.46: 5162 1.46 - 1.58: 8092 1.58 - 1.71: 250 1.71 - 1.84: 158 Bond restraints: 17446 Sorted by residual: bond pdb=" CA VAL A 965 " pdb=" CB VAL A 965 " ideal model delta sigma weight residual 1.539 1.569 -0.030 5.40e-03 3.43e+04 3.00e+01 bond pdb=" CA VAL C 965 " pdb=" CB VAL C 965 " ideal model delta sigma weight residual 1.539 1.567 -0.028 5.40e-03 3.43e+04 2.62e+01 bond pdb=" CA PRO D 70 " pdb=" C PRO D 70 " ideal model delta sigma weight residual 1.517 1.549 -0.032 6.70e-03 2.23e+04 2.33e+01 bond pdb=" N LEU C 751 " pdb=" CA LEU C 751 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.35e-02 5.49e+03 8.35e+00 bond pdb=" C CYS A 674 " pdb=" N ARG A 675 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.63e-02 3.76e+03 8.22e+00 ... (remaining 17441 not shown) Histogram of bond angle deviations from ideal: 98.46 - 107.00: 1515 107.00 - 115.53: 10294 115.53 - 124.07: 11344 124.07 - 132.61: 942 132.61 - 141.15: 35 Bond angle restraints: 24130 Sorted by residual: angle pdb=" C GLY A 512 " pdb=" N ARG A 513 " pdb=" CA ARG A 513 " ideal model delta sigma weight residual 121.70 132.72 -11.02 1.80e+00 3.09e-01 3.75e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 127.00 141.15 -14.15 2.40e+00 1.74e-01 3.48e+01 angle pdb=" C GLY C 512 " pdb=" N ARG C 513 " pdb=" CA ARG C 513 " ideal model delta sigma weight residual 121.70 132.31 -10.61 1.80e+00 3.09e-01 3.47e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CA PRO D 340 " ideal model delta sigma weight residual 127.00 140.80 -13.80 2.40e+00 1.74e-01 3.31e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CD PRO B 340 " ideal model delta sigma weight residual 120.60 109.21 11.39 2.20e+00 2.07e-01 2.68e+01 ... (remaining 24125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.91: 8437 21.91 - 43.82: 1161 43.82 - 65.73: 537 65.73 - 87.64: 46 87.64 - 109.55: 3 Dihedral angle restraints: 10184 sinusoidal: 5014 harmonic: 5170 Sorted by residual: dihedral pdb=" CA ALA D 76 " pdb=" C ALA D 76 " pdb=" N ILE D 77 " pdb=" CA ILE D 77 " ideal model delta harmonic sigma weight residual -180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ALA A 509 " pdb=" C ALA A 509 " pdb=" N THR A 510 " pdb=" CA THR A 510 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLU A 617 " pdb=" C GLU A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual -180.00 -151.20 -28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 10181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1852 0.064 - 0.128: 623 0.128 - 0.191: 136 0.191 - 0.255: 25 0.255 - 0.319: 4 Chirality restraints: 2640 Sorted by residual: chirality pdb=" CB VAL C 562 " pdb=" CA VAL C 562 " pdb=" CG1 VAL C 562 " pdb=" CG2 VAL C 562 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB VAL A 562 " pdb=" CA VAL A 562 " pdb=" CG1 VAL A 562 " pdb=" CG2 VAL A 562 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CG LEU A 653 " pdb=" CB LEU A 653 " pdb=" CD1 LEU A 653 " pdb=" CD2 LEU A 653 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2637 not shown) Planarity restraints: 2670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C1007 " -0.025 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C GLU C1007 " 0.087 2.00e-02 2.50e+03 pdb=" O GLU C1007 " -0.033 2.00e-02 2.50e+03 pdb=" N ASP C1008 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 713 " 0.024 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C VAL C 713 " -0.086 2.00e-02 2.50e+03 pdb=" O VAL C 713 " 0.033 2.00e-02 2.50e+03 pdb=" N GLY C 714 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 713 " -0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C VAL A 713 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL A 713 " -0.032 2.00e-02 2.50e+03 pdb=" N GLY A 714 " -0.029 2.00e-02 2.50e+03 ... (remaining 2667 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 158 2.48 - 3.08: 11500 3.08 - 3.69: 27296 3.69 - 4.29: 37822 4.29 - 4.90: 59597 Nonbonded interactions: 136373 Sorted by model distance: nonbonded pdb=" OE2 GLU A 617 " pdb=" NH1 ARG A 701 " model vdw 1.874 2.520 nonbonded pdb=" NH1 ARG A 860 " pdb=" C LYS A 864 " model vdw 1.951 3.350 nonbonded pdb=" OD2 ASP A 566 " pdb=" OH TYR B 138 " model vdw 1.964 2.440 nonbonded pdb=" O ILE C 975 " pdb=" N ALA C 977 " model vdw 1.990 2.520 nonbonded pdb=" O ARG C 783 " pdb=" OG SER D 67 " model vdw 2.006 2.440 ... (remaining 136368 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 2.500 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 54.990 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.120 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 0.090 17446 Z= 0.547 Angle : 1.346 14.149 24130 Z= 0.743 Chirality : 0.067 0.319 2640 Planarity : 0.010 0.076 2670 Dihedral : 22.321 109.545 6856 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.82 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 26.24 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.15), residues: 1774 helix: -2.79 (0.16), residues: 560 sheet: -2.10 (0.24), residues: 330 loop : -2.99 (0.15), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP A 549 HIS 0.019 0.005 HIS C 964 PHE 0.066 0.005 PHE C 576 TYR 0.043 0.005 TYR A 747 ARG 0.033 0.002 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 MET cc_start: 0.9268 (mmm) cc_final: 0.8887 (mmm) REVERT: A 727 THR cc_start: 0.9328 (p) cc_final: 0.8944 (t) REVERT: A 738 GLU cc_start: 0.8356 (tp30) cc_final: 0.8111 (tp30) REVERT: A 743 SER cc_start: 0.8708 (t) cc_final: 0.8450 (p) REVERT: A 808 GLU cc_start: 0.9340 (tt0) cc_final: 0.8528 (tm-30) REVERT: A 905 MET cc_start: 0.9247 (tpp) cc_final: 0.8804 (mmm) REVERT: A 918 THR cc_start: 0.8973 (m) cc_final: 0.8740 (p) REVERT: A 1025 MET cc_start: 0.8302 (tpp) cc_final: 0.7931 (tpp) REVERT: B 185 ILE cc_start: 0.9404 (mt) cc_final: 0.9202 (tp) REVERT: C 499 GLN cc_start: 0.8237 (mt0) cc_final: 0.7873 (mp10) REVERT: C 733 MET cc_start: 0.8840 (ttm) cc_final: 0.8459 (tpp) REVERT: C 743 SER cc_start: 0.8697 (t) cc_final: 0.8259 (p) REVERT: C 782 TRP cc_start: 0.8801 (t-100) cc_final: 0.8335 (t-100) REVERT: C 794 LEU cc_start: 0.9599 (tp) cc_final: 0.8958 (tp) REVERT: C 808 GLU cc_start: 0.9340 (tt0) cc_final: 0.8828 (tm-30) REVERT: C 922 ARG cc_start: 0.9105 (ttp-170) cc_final: 0.8800 (ptm-80) REVERT: C 941 LEU cc_start: 0.9322 (tp) cc_final: 0.9007 (pp) REVERT: C 1006 LEU cc_start: 0.8486 (mt) cc_final: 0.8099 (mm) REVERT: C 1016 TYR cc_start: 0.8187 (t80) cc_final: 0.7831 (t80) REVERT: C 1024 PHE cc_start: 0.8945 (m-10) cc_final: 0.8695 (m-10) REVERT: D 185 ILE cc_start: 0.9505 (mt) cc_final: 0.9220 (tp) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3130 time to fit residues: 169.6391 Evaluate side-chains 191 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 172 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN A 956 ASN A1013 HIS B 16 GLN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 204 GLN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 ASN ** C1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN D 79 HIS D 99 ASN D 171 ASN D 222 HIS ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17446 Z= 0.273 Angle : 0.808 14.283 24130 Z= 0.435 Chirality : 0.045 0.193 2640 Planarity : 0.007 0.111 2670 Dihedral : 23.852 105.412 3364 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.32 % Allowed : 3.30 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -2.13 (0.18), residues: 1774 helix: -0.55 (0.20), residues: 560 sheet: -1.11 (0.27), residues: 332 loop : -2.12 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 317 HIS 0.010 0.002 HIS A1013 PHE 0.014 0.002 PHE A 576 TYR 0.024 0.002 TYR A 747 ARG 0.009 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 283 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LEU cc_start: 0.9470 (mp) cc_final: 0.9059 (mm) REVERT: A 700 GLU cc_start: 0.9081 (tt0) cc_final: 0.8608 (tm-30) REVERT: A 704 MET cc_start: 0.8706 (ptm) cc_final: 0.8397 (ptm) REVERT: A 727 THR cc_start: 0.9288 (p) cc_final: 0.8988 (t) REVERT: A 738 GLU cc_start: 0.8619 (tp30) cc_final: 0.8247 (tp30) REVERT: A 743 SER cc_start: 0.8396 (t) cc_final: 0.8163 (p) REVERT: A 808 GLU cc_start: 0.9200 (tt0) cc_final: 0.8900 (tm-30) REVERT: A 989 LEU cc_start: 0.9220 (mm) cc_final: 0.8900 (mm) REVERT: A 1013 HIS cc_start: 0.7840 (t-90) cc_final: 0.7560 (t-170) REVERT: A 1016 TYR cc_start: 0.8220 (t80) cc_final: 0.7702 (t80) REVERT: B 146 ASN cc_start: 0.9047 (p0) cc_final: 0.8767 (t0) REVERT: B 155 LEU cc_start: 0.9379 (tp) cc_final: 0.9137 (tp) REVERT: B 236 LEU cc_start: 0.9426 (pp) cc_final: 0.9116 (mp) REVERT: B 274 PHE cc_start: 0.8665 (m-10) cc_final: 0.8392 (m-10) REVERT: C 487 LEU cc_start: 0.9373 (tp) cc_final: 0.8920 (tp) REVERT: C 496 SER cc_start: 0.8498 (m) cc_final: 0.7741 (t) REVERT: C 677 LEU cc_start: 0.8845 (tt) cc_final: 0.8435 (tp) REVERT: C 727 THR cc_start: 0.9339 (p) cc_final: 0.9091 (t) REVERT: C 743 SER cc_start: 0.8559 (t) cc_final: 0.8274 (p) REVERT: C 782 TRP cc_start: 0.8947 (t-100) cc_final: 0.8422 (t-100) REVERT: C 794 LEU cc_start: 0.9570 (tp) cc_final: 0.8914 (tp) REVERT: C 808 GLU cc_start: 0.9234 (tt0) cc_final: 0.9024 (tm-30) REVERT: C 847 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9139 (mp0) REVERT: C 905 MET cc_start: 0.9011 (tpt) cc_final: 0.8748 (tpt) REVERT: C 911 MET cc_start: 0.8934 (ttm) cc_final: 0.8619 (mmt) REVERT: C 922 ARG cc_start: 0.9098 (ttp-110) cc_final: 0.8801 (ptm-80) REVERT: C 941 LEU cc_start: 0.9307 (tp) cc_final: 0.8990 (pp) REVERT: C 945 MET cc_start: 0.8881 (tpt) cc_final: 0.8524 (tpp) REVERT: C 1010 LEU cc_start: 0.8629 (tp) cc_final: 0.8371 (tp) REVERT: D 146 ASN cc_start: 0.9497 (p0) cc_final: 0.8870 (t0) REVERT: D 236 LEU cc_start: 0.9443 (pp) cc_final: 0.8967 (mp) outliers start: 5 outliers final: 4 residues processed: 288 average time/residue: 0.3469 time to fit residues: 142.5521 Evaluate side-chains 179 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.0270 chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS C 501 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17446 Z= 0.257 Angle : 0.735 12.137 24130 Z= 0.399 Chirality : 0.043 0.210 2640 Planarity : 0.006 0.101 2670 Dihedral : 23.470 103.899 3364 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.36 (0.19), residues: 1774 helix: 0.01 (0.21), residues: 574 sheet: -0.49 (0.28), residues: 332 loop : -1.70 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 317 HIS 0.009 0.002 HIS C 501 PHE 0.015 0.002 PHE A 681 TYR 0.020 0.002 TYR A 931 ARG 0.007 0.001 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LEU cc_start: 0.9232 (mp) cc_final: 0.8960 (mm) REVERT: A 622 MET cc_start: 0.7624 (mtt) cc_final: 0.7414 (mtt) REVERT: A 677 LEU cc_start: 0.7929 (tp) cc_final: 0.7706 (tp) REVERT: A 738 GLU cc_start: 0.8762 (tp30) cc_final: 0.8295 (tp30) REVERT: A 743 SER cc_start: 0.8468 (t) cc_final: 0.8219 (p) REVERT: A 871 MET cc_start: 0.8905 (mmp) cc_final: 0.8680 (tpp) REVERT: A 880 MET cc_start: 0.9204 (mmp) cc_final: 0.8964 (mmm) REVERT: A 911 MET cc_start: 0.8894 (tpp) cc_final: 0.8645 (tpp) REVERT: A 1016 TYR cc_start: 0.8154 (t80) cc_final: 0.7888 (t80) REVERT: B 109 LEU cc_start: 0.8287 (tp) cc_final: 0.7826 (pp) REVERT: B 146 ASN cc_start: 0.9048 (p0) cc_final: 0.8513 (t0) REVERT: B 236 LEU cc_start: 0.9436 (pp) cc_final: 0.9142 (mp) REVERT: B 271 TYR cc_start: 0.9129 (m-80) cc_final: 0.8917 (m-80) REVERT: C 700 GLU cc_start: 0.9135 (tt0) cc_final: 0.8749 (tm-30) REVERT: C 737 MET cc_start: 0.8839 (tpp) cc_final: 0.8592 (tpp) REVERT: C 743 SER cc_start: 0.8487 (t) cc_final: 0.8142 (p) REVERT: C 782 TRP cc_start: 0.8972 (t-100) cc_final: 0.8472 (t-100) REVERT: C 794 LEU cc_start: 0.9573 (tp) cc_final: 0.8725 (tp) REVERT: C 808 GLU cc_start: 0.9260 (tt0) cc_final: 0.9002 (tm-30) REVERT: C 847 GLU cc_start: 0.9394 (mt-10) cc_final: 0.9111 (mp0) REVERT: C 852 ARG cc_start: 0.9005 (ttp-170) cc_final: 0.8513 (mtt-85) REVERT: C 878 ARG cc_start: 0.9199 (mtt180) cc_final: 0.8911 (mmp80) REVERT: C 922 ARG cc_start: 0.9044 (ttp-110) cc_final: 0.8608 (ttp80) REVERT: C 941 LEU cc_start: 0.9301 (tp) cc_final: 0.8953 (pp) REVERT: C 945 MET cc_start: 0.8962 (tpt) cc_final: 0.8532 (tpp) REVERT: C 1010 LEU cc_start: 0.8669 (tp) cc_final: 0.8463 (tp) REVERT: C 1024 PHE cc_start: 0.8997 (m-80) cc_final: 0.8756 (m-10) REVERT: D 142 LEU cc_start: 0.8554 (tp) cc_final: 0.8351 (tp) REVERT: D 155 LEU cc_start: 0.9469 (tp) cc_final: 0.9186 (tp) REVERT: D 236 LEU cc_start: 0.9455 (pp) cc_final: 0.9138 (mp) REVERT: D 271 TYR cc_start: 0.9193 (m-80) cc_final: 0.8900 (m-80) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.3102 time to fit residues: 109.0654 Evaluate side-chains 159 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS C 501 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 GLN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17446 Z= 0.224 Angle : 0.713 10.911 24130 Z= 0.383 Chirality : 0.043 0.193 2640 Planarity : 0.005 0.073 2670 Dihedral : 23.286 105.217 3364 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.19 % Allowed : 4.07 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.09 (0.19), residues: 1774 helix: 0.22 (0.21), residues: 580 sheet: -0.25 (0.29), residues: 332 loop : -1.58 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 317 HIS 0.006 0.001 HIS D 237 PHE 0.017 0.001 PHE D 62 TYR 0.019 0.002 TYR C 931 ARG 0.009 0.001 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LEU cc_start: 0.9344 (mp) cc_final: 0.9082 (mm) REVERT: A 736 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 743 SER cc_start: 0.8428 (t) cc_final: 0.8180 (p) REVERT: A 871 MET cc_start: 0.8848 (mmp) cc_final: 0.8606 (tpp) REVERT: A 880 MET cc_start: 0.9180 (mmp) cc_final: 0.8946 (mmm) REVERT: A 1015 LEU cc_start: 0.8644 (tp) cc_final: 0.8349 (tp) REVERT: B 56 LYS cc_start: 0.9205 (mmpt) cc_final: 0.8959 (tttp) REVERT: B 69 LEU cc_start: 0.8315 (tp) cc_final: 0.7952 (tp) REVERT: B 109 LEU cc_start: 0.8315 (tp) cc_final: 0.7922 (pp) REVERT: B 146 ASN cc_start: 0.9105 (p0) cc_final: 0.8519 (t0) REVERT: B 236 LEU cc_start: 0.9425 (pp) cc_final: 0.9224 (mp) REVERT: C 700 GLU cc_start: 0.9029 (tt0) cc_final: 0.8726 (tm-30) REVERT: C 738 GLU cc_start: 0.8465 (tp30) cc_final: 0.8213 (tp30) REVERT: C 743 SER cc_start: 0.8533 (t) cc_final: 0.8150 (p) REVERT: C 782 TRP cc_start: 0.8979 (t-100) cc_final: 0.8491 (t-100) REVERT: C 794 LEU cc_start: 0.9548 (tp) cc_final: 0.8823 (tp) REVERT: C 808 GLU cc_start: 0.9279 (tt0) cc_final: 0.9014 (tm-30) REVERT: C 817 HIS cc_start: 0.9252 (m-70) cc_final: 0.8681 (m90) REVERT: C 847 GLU cc_start: 0.9396 (mt-10) cc_final: 0.9117 (mp0) REVERT: C 852 ARG cc_start: 0.9045 (ttp-170) cc_final: 0.8498 (mtt-85) REVERT: C 922 ARG cc_start: 0.9053 (ttp-110) cc_final: 0.8615 (ttp80) REVERT: C 941 LEU cc_start: 0.9281 (tp) cc_final: 0.8938 (pp) REVERT: C 945 MET cc_start: 0.9098 (tpt) cc_final: 0.8676 (tpp) REVERT: C 995 LYS cc_start: 0.9077 (ptpt) cc_final: 0.8779 (ptmt) REVERT: C 1010 LEU cc_start: 0.8644 (tp) cc_final: 0.8438 (tp) REVERT: D 155 LEU cc_start: 0.9476 (tp) cc_final: 0.9198 (tp) REVERT: D 236 LEU cc_start: 0.9456 (pp) cc_final: 0.9158 (mp) REVERT: D 285 MET cc_start: 0.8051 (mmp) cc_final: 0.7851 (tpp) outliers start: 3 outliers final: 0 residues processed: 228 average time/residue: 0.2997 time to fit residues: 101.6554 Evaluate side-chains 163 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17446 Z= 0.284 Angle : 0.725 10.670 24130 Z= 0.391 Chirality : 0.043 0.193 2640 Planarity : 0.005 0.075 2670 Dihedral : 23.209 105.547 3364 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.01 (0.19), residues: 1774 helix: 0.22 (0.21), residues: 586 sheet: -0.11 (0.29), residues: 332 loop : -1.52 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 782 HIS 0.008 0.002 HIS C 959 PHE 0.020 0.002 PHE C 724 TYR 0.019 0.002 TYR C1020 ARG 0.011 0.001 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.8674 (ppp) cc_final: 0.8402 (tmm) REVERT: A 522 LEU cc_start: 0.9436 (mp) cc_final: 0.9122 (mp) REVERT: A 711 ILE cc_start: 0.9145 (pt) cc_final: 0.8701 (mp) REVERT: A 743 SER cc_start: 0.8567 (t) cc_final: 0.8231 (p) REVERT: A 782 TRP cc_start: 0.8839 (t-100) cc_final: 0.8595 (t-100) REVERT: A 871 MET cc_start: 0.8629 (mmp) cc_final: 0.8335 (tpp) REVERT: A 880 MET cc_start: 0.9268 (mmp) cc_final: 0.8992 (mmm) REVERT: A 1015 LEU cc_start: 0.8658 (tp) cc_final: 0.8404 (tp) REVERT: B 56 LYS cc_start: 0.9403 (mmpt) cc_final: 0.8928 (tttp) REVERT: B 109 LEU cc_start: 0.8423 (tp) cc_final: 0.7981 (pp) REVERT: C 598 ARG cc_start: 0.9540 (ppt170) cc_final: 0.9288 (ttp80) REVERT: C 700 GLU cc_start: 0.9084 (tt0) cc_final: 0.8704 (tm-30) REVERT: C 733 MET cc_start: 0.8346 (mmm) cc_final: 0.8063 (tpp) REVERT: C 737 MET cc_start: 0.8906 (tpp) cc_final: 0.8389 (tpp) REVERT: C 738 GLU cc_start: 0.8449 (tp30) cc_final: 0.8233 (tp30) REVERT: C 743 SER cc_start: 0.8629 (t) cc_final: 0.8263 (p) REVERT: C 782 TRP cc_start: 0.9022 (t-100) cc_final: 0.8793 (t-100) REVERT: C 794 LEU cc_start: 0.9572 (tp) cc_final: 0.8904 (mt) REVERT: C 808 GLU cc_start: 0.9293 (tt0) cc_final: 0.9069 (tm-30) REVERT: C 852 ARG cc_start: 0.8967 (ttp-170) cc_final: 0.8391 (mtt-85) REVERT: C 905 MET cc_start: 0.9147 (tpt) cc_final: 0.8367 (tpt) REVERT: C 945 MET cc_start: 0.9210 (tpt) cc_final: 0.8944 (tpp) REVERT: D 155 LEU cc_start: 0.9530 (tp) cc_final: 0.9257 (tp) REVERT: D 162 MET cc_start: 0.8500 (mmp) cc_final: 0.8231 (mmp) REVERT: D 236 LEU cc_start: 0.9422 (pp) cc_final: 0.9096 (mp) REVERT: D 285 MET cc_start: 0.8154 (mmp) cc_final: 0.7896 (tpp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2936 time to fit residues: 91.2196 Evaluate side-chains 149 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 282 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17446 Z= 0.283 Angle : 0.713 10.416 24130 Z= 0.386 Chirality : 0.042 0.193 2640 Planarity : 0.005 0.072 2670 Dihedral : 23.169 106.609 3364 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -1.02 (0.19), residues: 1774 helix: 0.18 (0.21), residues: 590 sheet: -0.17 (0.28), residues: 358 loop : -1.52 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 317 HIS 0.008 0.001 HIS D 207 PHE 0.017 0.002 PHE B 274 TYR 0.026 0.002 TYR B 271 ARG 0.004 0.001 ARG C 523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.923 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 486 CYS cc_start: 0.8571 (t) cc_final: 0.8368 (t) REVERT: A 503 MET cc_start: 0.8712 (ppp) cc_final: 0.8432 (tmm) REVERT: A 522 LEU cc_start: 0.9403 (mp) cc_final: 0.9011 (mp) REVERT: A 622 MET cc_start: 0.8005 (mtt) cc_final: 0.7662 (mtt) REVERT: A 700 GLU cc_start: 0.9323 (pp20) cc_final: 0.9110 (pp20) REVERT: A 743 SER cc_start: 0.8612 (t) cc_final: 0.8265 (p) REVERT: A 880 MET cc_start: 0.9212 (mmp) cc_final: 0.9004 (mmp) REVERT: A 1015 LEU cc_start: 0.8692 (tp) cc_final: 0.8428 (tp) REVERT: B 56 LYS cc_start: 0.9392 (mmpt) cc_final: 0.8958 (tttp) REVERT: B 109 LEU cc_start: 0.8577 (tp) cc_final: 0.8024 (pp) REVERT: B 146 ASN cc_start: 0.9288 (p0) cc_final: 0.8586 (t0) REVERT: B 271 TYR cc_start: 0.9250 (m-80) cc_final: 0.8957 (m-80) REVERT: C 598 ARG cc_start: 0.9548 (ppt170) cc_final: 0.9303 (ttp80) REVERT: C 622 MET cc_start: 0.8203 (mtt) cc_final: 0.7971 (mtt) REVERT: C 700 GLU cc_start: 0.9101 (tt0) cc_final: 0.8752 (tm-30) REVERT: C 737 MET cc_start: 0.9000 (tpp) cc_final: 0.8515 (tpp) REVERT: C 738 GLU cc_start: 0.8566 (tp30) cc_final: 0.8319 (tp30) REVERT: C 743 SER cc_start: 0.8640 (t) cc_final: 0.8269 (p) REVERT: C 808 GLU cc_start: 0.9271 (tt0) cc_final: 0.8995 (tm-30) REVERT: C 852 ARG cc_start: 0.8978 (ttp-170) cc_final: 0.8362 (mtt-85) REVERT: C 905 MET cc_start: 0.9249 (tpt) cc_final: 0.8770 (tpt) REVERT: C 922 ARG cc_start: 0.9048 (ttp-110) cc_final: 0.8692 (ttp80) REVERT: C 945 MET cc_start: 0.9184 (tpt) cc_final: 0.8938 (tpp) REVERT: D 155 LEU cc_start: 0.9559 (tp) cc_final: 0.9274 (tp) REVERT: D 236 LEU cc_start: 0.9461 (pp) cc_final: 0.9135 (mp) REVERT: D 285 MET cc_start: 0.8359 (mmp) cc_final: 0.7929 (tpp) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2960 time to fit residues: 89.7424 Evaluate side-chains 149 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 113 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17446 Z= 0.215 Angle : 0.695 10.831 24130 Z= 0.371 Chirality : 0.043 0.222 2640 Planarity : 0.004 0.062 2670 Dihedral : 23.089 108.312 3364 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -0.89 (0.19), residues: 1774 helix: 0.27 (0.21), residues: 590 sheet: -0.02 (0.28), residues: 358 loop : -1.46 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 782 HIS 0.007 0.001 HIS C 501 PHE 0.023 0.001 PHE A 681 TYR 0.023 0.002 TYR B 271 ARG 0.004 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.8732 (ppp) cc_final: 0.8472 (tmm) REVERT: A 522 LEU cc_start: 0.9436 (mp) cc_final: 0.9058 (mp) REVERT: A 622 MET cc_start: 0.7857 (mtt) cc_final: 0.7285 (mtt) REVERT: A 743 SER cc_start: 0.8494 (t) cc_final: 0.8204 (p) REVERT: A 922 ARG cc_start: 0.9137 (ttp-110) cc_final: 0.8725 (ttp80) REVERT: A 1015 LEU cc_start: 0.8680 (tp) cc_final: 0.8329 (tp) REVERT: B 56 LYS cc_start: 0.9386 (mmpt) cc_final: 0.8959 (tttp) REVERT: B 69 LEU cc_start: 0.8431 (tp) cc_final: 0.8201 (tp) REVERT: B 109 LEU cc_start: 0.8574 (tp) cc_final: 0.8042 (pp) REVERT: B 146 ASN cc_start: 0.9299 (p0) cc_final: 0.8495 (t0) REVERT: C 594 MET cc_start: 0.9010 (mmt) cc_final: 0.8668 (mpp) REVERT: C 598 ARG cc_start: 0.9499 (ppt170) cc_final: 0.9257 (ttp80) REVERT: C 622 MET cc_start: 0.8093 (mtt) cc_final: 0.7893 (mtt) REVERT: C 700 GLU cc_start: 0.9082 (tt0) cc_final: 0.8766 (tm-30) REVERT: C 705 MET cc_start: 0.8594 (mpp) cc_final: 0.8132 (mmt) REVERT: C 738 GLU cc_start: 0.8572 (tp30) cc_final: 0.8292 (tp30) REVERT: C 743 SER cc_start: 0.8581 (t) cc_final: 0.8195 (p) REVERT: C 782 TRP cc_start: 0.8900 (t60) cc_final: 0.8512 (t60) REVERT: C 808 GLU cc_start: 0.9233 (tt0) cc_final: 0.8947 (tm-30) REVERT: C 852 ARG cc_start: 0.8945 (ttp-170) cc_final: 0.8353 (mtt-85) REVERT: C 905 MET cc_start: 0.9187 (tpt) cc_final: 0.8716 (tpt) REVERT: C 922 ARG cc_start: 0.9110 (ttp-110) cc_final: 0.8693 (ttp80) REVERT: C 945 MET cc_start: 0.9187 (tpt) cc_final: 0.8814 (tpp) REVERT: C 1010 LEU cc_start: 0.8649 (tp) cc_final: 0.8411 (tp) REVERT: C 1024 PHE cc_start: 0.9033 (m-80) cc_final: 0.8742 (m-80) REVERT: D 155 LEU cc_start: 0.9533 (tp) cc_final: 0.9257 (tp) REVERT: D 236 LEU cc_start: 0.9381 (pp) cc_final: 0.9158 (mp) REVERT: D 285 MET cc_start: 0.8406 (mmp) cc_final: 0.7978 (tpp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2723 time to fit residues: 86.8686 Evaluate side-chains 162 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 116 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 143 optimal weight: 0.0000 chunk 166 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS A 544 ASN A 858 GLN ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17446 Z= 0.175 Angle : 0.699 9.336 24130 Z= 0.369 Chirality : 0.043 0.189 2640 Planarity : 0.004 0.053 2670 Dihedral : 22.973 110.256 3364 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.06 % Allowed : 0.89 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -0.74 (0.19), residues: 1774 helix: 0.35 (0.21), residues: 586 sheet: 0.20 (0.28), residues: 358 loop : -1.42 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 782 HIS 0.008 0.001 HIS A 501 PHE 0.018 0.001 PHE D 62 TYR 0.020 0.001 TYR C1020 ARG 0.009 0.000 ARG C 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8623 (t) cc_final: 0.8361 (t) REVERT: A 522 LEU cc_start: 0.9436 (mp) cc_final: 0.9048 (mp) REVERT: A 622 MET cc_start: 0.7737 (mtt) cc_final: 0.7036 (mtt) REVERT: A 737 MET cc_start: 0.7750 (tpt) cc_final: 0.6431 (tpt) REVERT: A 743 SER cc_start: 0.8352 (t) cc_final: 0.8094 (p) REVERT: A 922 ARG cc_start: 0.9128 (ttp-110) cc_final: 0.8790 (ttp80) REVERT: A 1015 LEU cc_start: 0.8613 (tp) cc_final: 0.8270 (tp) REVERT: B 56 LYS cc_start: 0.9447 (mmpt) cc_final: 0.9004 (tttp) REVERT: B 69 LEU cc_start: 0.8554 (tp) cc_final: 0.8264 (tp) REVERT: B 109 LEU cc_start: 0.8484 (tp) cc_final: 0.8018 (pp) REVERT: B 146 ASN cc_start: 0.9220 (p0) cc_final: 0.8432 (t0) REVERT: B 162 MET cc_start: 0.8761 (mmp) cc_final: 0.8538 (mmp) REVERT: C 523 ARG cc_start: 0.9112 (mtm-85) cc_final: 0.8831 (mtt180) REVERT: C 594 MET cc_start: 0.8934 (mmt) cc_final: 0.8663 (mpp) REVERT: C 598 ARG cc_start: 0.9517 (ppt170) cc_final: 0.9267 (ttp80) REVERT: C 700 GLU cc_start: 0.9012 (tt0) cc_final: 0.8736 (tm-30) REVERT: C 737 MET cc_start: 0.9015 (tpp) cc_final: 0.8685 (tpp) REVERT: C 738 GLU cc_start: 0.8397 (tp30) cc_final: 0.8148 (tp30) REVERT: C 743 SER cc_start: 0.8390 (t) cc_final: 0.8027 (p) REVERT: C 782 TRP cc_start: 0.8868 (t60) cc_final: 0.8446 (t60) REVERT: C 808 GLU cc_start: 0.9146 (tt0) cc_final: 0.8775 (tm-30) REVERT: C 852 ARG cc_start: 0.8994 (ttp-170) cc_final: 0.8447 (ttt-90) REVERT: C 905 MET cc_start: 0.9123 (tpt) cc_final: 0.8467 (tpt) REVERT: C 922 ARG cc_start: 0.9080 (ttp-110) cc_final: 0.8671 (ttp80) REVERT: C 945 MET cc_start: 0.9170 (tpt) cc_final: 0.8863 (tpp) REVERT: C 1010 LEU cc_start: 0.8589 (tp) cc_final: 0.8366 (tp) REVERT: D 155 LEU cc_start: 0.9456 (tp) cc_final: 0.9193 (tp) REVERT: D 285 MET cc_start: 0.8268 (mmp) cc_final: 0.7902 (tpp) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.2962 time to fit residues: 99.7568 Evaluate side-chains 169 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.2980 chunk 170 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17446 Z= 0.259 Angle : 0.699 9.243 24130 Z= 0.375 Chirality : 0.043 0.191 2640 Planarity : 0.005 0.062 2670 Dihedral : 22.967 107.290 3364 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -0.79 (0.19), residues: 1774 helix: 0.37 (0.21), residues: 588 sheet: 0.11 (0.28), residues: 358 loop : -1.47 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 915 HIS 0.012 0.001 HIS C 501 PHE 0.025 0.002 PHE A1024 TYR 0.023 0.002 TYR A1020 ARG 0.006 0.001 ARG C 916 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8660 (t) cc_final: 0.8432 (t) REVERT: A 522 LEU cc_start: 0.9493 (mp) cc_final: 0.9202 (mp) REVERT: A 622 MET cc_start: 0.7698 (mtt) cc_final: 0.7025 (mtt) REVERT: A 738 GLU cc_start: 0.8398 (tp30) cc_final: 0.7889 (tp30) REVERT: A 743 SER cc_start: 0.8728 (t) cc_final: 0.8384 (p) REVERT: A 922 ARG cc_start: 0.9162 (ttp-110) cc_final: 0.8756 (ttp80) REVERT: A 1015 LEU cc_start: 0.8728 (tp) cc_final: 0.8404 (tp) REVERT: B 56 LYS cc_start: 0.9459 (mmpt) cc_final: 0.9010 (tttp) REVERT: B 109 LEU cc_start: 0.8535 (tp) cc_final: 0.8024 (pp) REVERT: C 598 ARG cc_start: 0.9531 (ppt170) cc_final: 0.9278 (ttp80) REVERT: C 700 GLU cc_start: 0.9126 (tt0) cc_final: 0.8806 (tm-30) REVERT: C 737 MET cc_start: 0.8853 (tpp) cc_final: 0.8382 (tpp) REVERT: C 738 GLU cc_start: 0.8469 (tp30) cc_final: 0.8230 (tp30) REVERT: C 743 SER cc_start: 0.8398 (t) cc_final: 0.8064 (p) REVERT: C 808 GLU cc_start: 0.9191 (tt0) cc_final: 0.8769 (tm-30) REVERT: C 852 ARG cc_start: 0.8919 (ttp-170) cc_final: 0.8302 (mtt-85) REVERT: C 905 MET cc_start: 0.9174 (tpt) cc_final: 0.8715 (tpt) REVERT: C 922 ARG cc_start: 0.9087 (ttp-110) cc_final: 0.8688 (ttp80) REVERT: C 945 MET cc_start: 0.9272 (tpt) cc_final: 0.8911 (tpp) REVERT: D 155 LEU cc_start: 0.9559 (tp) cc_final: 0.9267 (tp) REVERT: D 236 LEU cc_start: 0.9371 (mp) cc_final: 0.9002 (tt) REVERT: D 285 MET cc_start: 0.8422 (mmp) cc_final: 0.8172 (tpp) outliers start: 1 outliers final: 1 residues processed: 204 average time/residue: 0.2796 time to fit residues: 87.8996 Evaluate side-chains 161 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17446 Z= 0.220 Angle : 0.698 8.992 24130 Z= 0.370 Chirality : 0.043 0.186 2640 Planarity : 0.004 0.060 2670 Dihedral : 22.948 108.757 3364 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -0.78 (0.19), residues: 1774 helix: 0.37 (0.21), residues: 588 sheet: 0.16 (0.28), residues: 358 loop : -1.48 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 782 HIS 0.008 0.001 HIS A 501 PHE 0.022 0.002 PHE A1024 TYR 0.018 0.002 TYR B 271 ARG 0.004 0.000 ARG C 523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LEU cc_start: 0.9479 (mp) cc_final: 0.9161 (mp) REVERT: A 622 MET cc_start: 0.7633 (mtt) cc_final: 0.7012 (mtt) REVERT: A 700 GLU cc_start: 0.9097 (pm20) cc_final: 0.8695 (pm20) REVERT: A 738 GLU cc_start: 0.8315 (tp30) cc_final: 0.7772 (tp30) REVERT: A 743 SER cc_start: 0.8689 (t) cc_final: 0.8344 (p) REVERT: A 794 LEU cc_start: 0.9412 (pp) cc_final: 0.8956 (pp) REVERT: A 1015 LEU cc_start: 0.8720 (tp) cc_final: 0.8336 (tp) REVERT: B 56 LYS cc_start: 0.9419 (mmpt) cc_final: 0.8991 (tttp) REVERT: B 109 LEU cc_start: 0.8521 (tp) cc_final: 0.8016 (pp) REVERT: B 146 ASN cc_start: 0.9193 (p0) cc_final: 0.8500 (t0) REVERT: C 594 MET cc_start: 0.8928 (mmt) cc_final: 0.8510 (mpp) REVERT: C 598 ARG cc_start: 0.9529 (ppt170) cc_final: 0.9271 (ttp80) REVERT: C 622 MET cc_start: 0.7933 (mtt) cc_final: 0.7702 (mtt) REVERT: C 700 GLU cc_start: 0.9103 (tt0) cc_final: 0.8760 (tm-30) REVERT: C 737 MET cc_start: 0.9166 (tpp) cc_final: 0.8909 (tpp) REVERT: C 738 GLU cc_start: 0.8499 (tp30) cc_final: 0.8228 (tp30) REVERT: C 743 SER cc_start: 0.8531 (t) cc_final: 0.8166 (p) REVERT: C 808 GLU cc_start: 0.9217 (tt0) cc_final: 0.8633 (tm-30) REVERT: C 852 ARG cc_start: 0.8911 (ttp-170) cc_final: 0.8282 (mtt-85) REVERT: C 905 MET cc_start: 0.9174 (tpt) cc_final: 0.8758 (tpt) REVERT: C 922 ARG cc_start: 0.9099 (ttp-110) cc_final: 0.8740 (tmm-80) REVERT: C 945 MET cc_start: 0.9220 (tpt) cc_final: 0.8870 (tpp) REVERT: D 155 LEU cc_start: 0.9546 (tp) cc_final: 0.9243 (tp) REVERT: D 236 LEU cc_start: 0.9370 (mp) cc_final: 0.9008 (tt) REVERT: D 285 MET cc_start: 0.8549 (mmp) cc_final: 0.8283 (tpp) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.2649 time to fit residues: 85.1411 Evaluate side-chains 161 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.0770 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 41 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.0370 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 0.0270 overall best weight: 0.4454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.060153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044870 restraints weight = 94382.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.046328 restraints weight = 58896.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047321 restraints weight = 42975.689| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17446 Z= 0.177 Angle : 0.693 8.298 24130 Z= 0.363 Chirality : 0.043 0.188 2640 Planarity : 0.004 0.053 2670 Dihedral : 22.830 111.715 3364 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.54 % 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: -0.64 (0.19), residues: 1774 helix: 0.50 (0.21), residues: 584 sheet: 0.27 (0.27), residues: 380 loop : -1.46 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 782 HIS 0.005 0.001 HIS D 237 PHE 0.023 0.001 PHE A1024 TYR 0.017 0.001 TYR A 578 ARG 0.003 0.000 ARG A 897 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3002.80 seconds wall clock time: 56 minutes 14.69 seconds (3374.69 seconds total)