Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 10:28:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/04_2023/6dbq_7847_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/04_2023/6dbq_7847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/04_2023/6dbq_7847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/04_2023/6dbq_7847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/04_2023/6dbq_7847_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/04_2023/6dbq_7847_neut.pdb" } resolution = 4.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 222 5.49 5 S 112 5.16 5 C 11837 2.51 5 N 3565 2.21 5 O 4214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 114": "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 239": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "C PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 ARG 232": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 19956 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4999 Classifications: {'peptide': 621} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 596} 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: 4972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4972 Classifications: {'peptide': 616} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} 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: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1023 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "G" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1245 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1256 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} 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 2680 SG CYS A 749 57.331 83.908 33.106 1.00 74.96 S ATOM 10357 SG CYS C 749 61.990 61.912 113.881 1.00 62.00 S Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" P DA E 39 " occ=0.80 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.80 residue: pdb=" P DA E 40 " occ=0.71 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.71 residue: pdb=" P DA E 41 " occ=0.70 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.70 residue: pdb=" P DA E 42 " occ=0.48 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.48 residue: pdb=" P DC E 44 " occ=0.47 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.47 residue: pdb=" P DG F 7 " occ=0.62 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.62 residue: pdb=" P DG F 8 " occ=0.72 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.72 residue: pdb=" P DT F 9 " occ=0.66 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.66 residue: pdb=" P DT F 10 " occ=0.76 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.76 residue: pdb=" P DT F 11 " occ=0.70 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.70 residue: pdb=" P DT F 12 " occ=0.74 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.74 residue: pdb=" P DT F 13 " occ=0.76 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.76 ... (remaining 16 not shown) Time building chain proxies: 10.41, per 1000 atoms: 0.52 Number of scatterers: 19956 At special positions: 0 Unit cell: (154.75, 149.798, 134.942, 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 112 16.00 P 222 15.00 O 4214 8.00 N 3565 7.00 C 11837 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: 9.51 Conformation dependent library (CDL) restraints added in 2.3 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 749 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 18 sheets defined 37.5% alpha, 23.0% beta 86 base pairs and 171 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.510A pdb=" N SER A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.784A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 461 removed outlier: 3.511A pdb=" N VAL A 449 " --> pdb=" O ASP A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.605A pdb=" N ALA A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 497 through 511 Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 577 through 601 removed outlier: 4.901A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.603A pdb=" N CYS A 607 " --> pdb=" O ASP A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 687 through 704 Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.680A pdb=" N ALA A 759 " --> pdb=" O THR A 755 " (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 819 through 835 Processing helix chain 'A' and resid 844 through 863 removed outlier: 3.919A 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 889 Processing helix chain 'A' and resid 894 through 912 Processing helix chain 'A' and resid 912 through 917 removed outlier: 4.024A pdb=" N ARG A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 946 removed outlier: 3.759A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.560A pdb=" N HIS A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.603A pdb=" N GLU A 984 " --> pdb=" O SER A 980 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1018 through 1025 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 419 through 442 removed outlier: 6.074A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 461 removed outlier: 4.021A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 526 removed outlier: 3.757A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN C 524 " --> pdb=" O HIS C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 529 No H-bonds generated for 'chain 'C' and resid 527 through 529' Processing helix chain 'C' and resid 577 through 600 removed outlier: 5.022A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 Proline residue: C 696 - end of helix removed outlier: 3.744A pdb=" N MET C 705 " --> pdb=" O ARG C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 757 through 762 removed outlier: 3.579A pdb=" N GLN C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 815 through 835 removed outlier: 4.226A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 Processing helix chain 'C' and resid 894 through 912 Processing helix chain 'C' and resid 912 through 917 removed outlier: 3.701A pdb=" N ARG C 916 " --> pdb=" O LYS C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 930 removed outlier: 4.048A pdb=" N LEU C 928 " --> pdb=" O CYS C 924 " (cutoff:3.500A) 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 972 Processing helix chain 'C' and resid 980 through 985 removed outlier: 3.578A pdb=" N GLU C 984 " --> pdb=" O SER C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 997 removed outlier: 4.004A pdb=" N PHE C 990 " --> pdb=" O GLY C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 4.665A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 3.513A pdb=" N GLN C1022 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C1027 " --> pdb=" O LYS C1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.659A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 612 " --> pdb=" O SER A 650 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE A 644 " --> pdb=" O PRO A 676 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 575 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.659A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 612 " --> pdb=" O SER A 650 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.275A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 55 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.364A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS B 89 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB1, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.589A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR C 727 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLU C 617 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 639 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.589A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR C 727 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLU C 617 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 639 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 7.016A 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 23 removed outlier: 4.498A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D 318 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 61 through 62 removed outlier: 6.774A pdb=" N SER D 61 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N CYS D 124 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.517A pdb=" N GLU D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 138 through 147 removed outlier: 6.830A pdb=" N GLY D 139 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 158 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 147 removed outlier: 6.830A pdb=" N GLY D 139 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 158 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY D 157 " --> pdb=" O GLN D 181 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLN D 181 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265 715 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 212 hydrogen bonds 408 hydrogen bond angles 0 basepair planarities 86 basepair parallelities 171 stacking parallelities Total time for adding SS restraints: 10.10 Time building geometry restraints manager: 10.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4309 1.33 - 1.45: 5718 1.45 - 1.57: 10198 1.57 - 1.70: 441 1.70 - 1.82: 168 Bond restraints: 20834 Sorted by residual: bond pdb=" CG GLN D 83 " pdb=" CD GLN D 83 " ideal model delta sigma weight residual 1.516 1.380 0.136 2.50e-02 1.60e+03 2.95e+01 bond pdb=" CG HIS C 817 " pdb=" CD2 HIS C 817 " ideal model delta sigma weight residual 1.354 1.409 -0.055 1.10e-02 8.26e+03 2.53e+01 bond pdb=" CG ASN B 10 " pdb=" OD1 ASN B 10 " ideal model delta sigma weight residual 1.231 1.321 -0.090 1.90e-02 2.77e+03 2.25e+01 bond pdb=" CB ILE D 234 " pdb=" CG1 ILE D 234 " ideal model delta sigma weight residual 1.530 1.444 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CB GLN A 423 " pdb=" CG GLN A 423 " ideal model delta sigma weight residual 1.520 1.398 0.122 3.00e-02 1.11e+03 1.66e+01 ... (remaining 20829 not shown) Histogram of bond angle deviations from ideal: 66.60 - 87.52: 2 87.52 - 108.44: 3073 108.44 - 129.36: 25799 129.36 - 150.29: 225 150.29 - 171.21: 2 Bond angle restraints: 29101 Sorted by residual: angle pdb=" CB ASN C 432 " pdb=" CG ASN C 432 " pdb=" ND2 ASN C 432 " ideal model delta sigma weight residual 116.40 66.60 49.80 1.50e+00 4.44e-01 1.10e+03 angle pdb=" CB ASN C 432 " pdb=" CG ASN C 432 " pdb=" OD1 ASN C 432 " ideal model delta sigma weight residual 120.80 171.21 -50.41 2.00e+00 2.50e-01 6.35e+02 angle pdb=" CG GLN A 423 " pdb=" CD GLN A 423 " pdb=" NE2 GLN A 423 " ideal model delta sigma weight residual 116.40 79.13 37.27 1.50e+00 4.44e-01 6.17e+02 angle pdb=" CG GLN A 423 " pdb=" CD GLN A 423 " pdb=" OE1 GLN A 423 " ideal model delta sigma weight residual 120.80 157.58 -36.78 2.00e+00 2.50e-01 3.38e+02 angle pdb=" OD1 ASN C 432 " pdb=" CG ASN C 432 " pdb=" ND2 ASN C 432 " ideal model delta sigma weight residual 122.60 106.78 15.82 1.00e+00 1.00e+00 2.50e+02 ... (remaining 29096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 10566 35.53 - 71.05: 1155 71.05 - 106.58: 30 106.58 - 142.10: 2 142.10 - 177.63: 5 Dihedral angle restraints: 11758 sinusoidal: 6160 harmonic: 5598 Sorted by residual: dihedral pdb=" CA SER A 511 " pdb=" C SER A 511 " pdb=" N GLY A 512 " pdb=" CA GLY A 512 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" N HIS B 344 " pdb=" C HIS B 344 " pdb=" CA HIS B 344 " pdb=" CB HIS B 344 " ideal model delta harmonic sigma weight residual 122.80 109.89 12.91 0 2.50e+00 1.60e-01 2.67e+01 dihedral pdb=" CA PRO D 98 " pdb=" C PRO D 98 " pdb=" N ASN D 99 " pdb=" CA ASN D 99 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 11755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2690 0.060 - 0.120: 449 0.120 - 0.180: 41 0.180 - 0.240: 5 0.240 - 0.300: 2 Chirality restraints: 3187 Sorted by residual: chirality pdb=" CA HIS C 817 " pdb=" N HIS C 817 " pdb=" C HIS C 817 " pdb=" CB HIS C 817 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA GLN D 83 " pdb=" N GLN D 83 " pdb=" C GLN D 83 " pdb=" CB GLN D 83 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA HIS B 344 " pdb=" N HIS B 344 " pdb=" C HIS B 344 " pdb=" CB HIS B 344 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3184 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 817 " 0.149 2.00e-02 2.50e+03 1.49e-01 3.33e+02 pdb=" CG HIS C 817 " -0.313 2.00e-02 2.50e+03 pdb=" ND1 HIS C 817 " 0.088 2.00e-02 2.50e+03 pdb=" CD2 HIS C 817 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS C 817 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS C 817 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 344 " 0.085 2.00e-02 2.50e+03 1.12e-01 1.88e+02 pdb=" CG HIS B 344 " -0.237 2.00e-02 2.50e+03 pdb=" ND1 HIS B 344 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS B 344 " 0.080 2.00e-02 2.50e+03 pdb=" CE1 HIS B 344 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 344 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 10 " 0.058 2.00e-02 2.50e+03 1.18e-01 1.40e+02 pdb=" CG ASN B 10 " -0.204 2.00e-02 2.50e+03 pdb=" OD1 ASN B 10 " 0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN B 10 " 0.069 2.00e-02 2.50e+03 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 118 2.34 - 2.98: 10527 2.98 - 3.62: 32798 3.62 - 4.26: 48285 4.26 - 4.90: 72855 Nonbonded interactions: 164583 Sorted by model distance: nonbonded pdb=" NH1 ARG D 123 " pdb=" OE2 GLU D 125 " model vdw 1.700 2.520 nonbonded pdb=" OD1 ASN B 99 " pdb=" OE2 GLU B 101 " model vdw 1.806 3.040 nonbonded pdb=" NZ LYS C 435 " pdb=" OE2 GLU C 439 " model vdw 1.807 2.520 nonbonded pdb=" OE2 GLU A 789 " pdb=" NH1 ARG A 797 " model vdw 1.837 2.520 nonbonded pdb=" OG1 THR B 97 " pdb=" OE2 GLU B 101 " model vdw 1.856 2.440 ... (remaining 164578 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' and (resid 408 through 628 or resid 635 through 1028 or resid 1101 th \ rough 1103)) selection = (chain 'C' and (resid 408 through 1028 or resid 1101 through 1103)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.360 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 63.740 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.136 20834 Z= 0.339 Angle : 1.053 50.410 29101 Z= 0.618 Chirality : 0.044 0.300 3187 Planarity : 0.007 0.149 2984 Dihedral : 23.250 177.626 8156 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 28.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.37 % Favored : 89.53 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % 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: -4.19 (0.15), residues: 1929 helix: -2.72 (0.14), residues: 660 sheet: -1.82 (0.26), residues: 323 loop : -3.19 (0.17), residues: 946 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 376 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.3825 time to fit residues: 208.5383 Evaluate side-chains 194 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 109 optimal weight: 0.0370 chunk 87 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 65 optimal weight: 0.0870 chunk 102 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 overall best weight: 3.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 HIS A 687 HIS A 775 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS B 344 HIS ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS C 761 GLN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 ASN ** C 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN C1012 HIS D 33 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 20834 Z= 0.276 Angle : 0.750 8.453 29101 Z= 0.412 Chirality : 0.044 0.202 3187 Planarity : 0.006 0.072 2984 Dihedral : 26.158 175.460 4346 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.79 % Favored : 93.11 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % 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: -3.01 (0.17), residues: 1929 helix: -1.40 (0.17), residues: 672 sheet: -1.39 (0.27), residues: 313 loop : -2.68 (0.18), residues: 944 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 2.083 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 outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.3681 time to fit residues: 163.7280 Evaluate side-chains 176 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 211 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN A 964 HIS B 33 GLN C 432 ASN C 501 HIS C 761 GLN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN C1012 HIS ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 20834 Z= 0.257 Angle : 0.692 8.026 29101 Z= 0.385 Chirality : 0.042 0.178 3187 Planarity : 0.005 0.063 2984 Dihedral : 26.010 175.433 4346 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.69 % Favored : 93.21 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.34 (0.17), residues: 1929 helix: -0.66 (0.18), residues: 670 sheet: -1.24 (0.26), residues: 331 loop : -2.37 (0.18), residues: 928 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 242 time to evaluate : 2.019 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 outliers start: 3 outliers final: 1 residues processed: 245 average time/residue: 0.3292 time to fit residues: 123.8657 Evaluate side-chains 169 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 2.000 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2255 time to fit residues: 3.0673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 10.0000 chunk 147 optimal weight: 0.0470 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 207 optimal weight: 40.0000 chunk 102 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 HIS A 817 HIS A 822 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 GLN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 20834 Z= 0.260 Angle : 0.687 7.923 29101 Z= 0.380 Chirality : 0.042 0.214 3187 Planarity : 0.005 0.070 2984 Dihedral : 25.952 178.720 4346 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.22 % Favored : 93.73 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % 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: -1.98 (0.18), residues: 1929 helix: -0.33 (0.19), residues: 671 sheet: -1.10 (0.27), residues: 331 loop : -2.16 (0.19), residues: 927 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 2.121 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 outliers start: 2 outliers final: 1 residues processed: 231 average time/residue: 0.3281 time to fit residues: 116.9346 Evaluate side-chains 163 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 2.037 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2293 time to fit residues: 3.0235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 106 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS A 822 ASN A 831 GLN A 936 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 20834 Z= 0.321 Angle : 0.723 8.209 29101 Z= 0.399 Chirality : 0.042 0.197 3187 Planarity : 0.005 0.115 2984 Dihedral : 25.948 178.785 4346 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.95 % Favored : 92.95 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % 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: -1.94 (0.18), residues: 1929 helix: -0.38 (0.19), residues: 672 sheet: -1.06 (0.27), residues: 323 loop : -2.05 (0.19), residues: 934 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 2.073 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 outliers start: 1 outliers final: 1 residues processed: 212 average time/residue: 0.3327 time to fit residues: 109.6936 Evaluate side-chains 155 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 1.898 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2341 time to fit residues: 3.0673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 208 optimal weight: 30.0000 chunk 172 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN A 822 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 GLN ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 20834 Z= 0.300 Angle : 0.703 9.787 29101 Z= 0.389 Chirality : 0.042 0.201 3187 Planarity : 0.005 0.055 2984 Dihedral : 25.927 177.243 4346 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.69 % Favored : 93.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % 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: -1.71 (0.18), residues: 1929 helix: -0.19 (0.19), residues: 671 sheet: -0.89 (0.28), residues: 305 loop : -1.93 (0.19), residues: 953 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.061 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 outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.3293 time to fit residues: 104.6389 Evaluate side-chains 148 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.049 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 207 optimal weight: 40.0000 chunk 129 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 20834 Z= 0.319 Angle : 0.720 9.679 29101 Z= 0.397 Chirality : 0.042 0.200 3187 Planarity : 0.005 0.055 2984 Dihedral : 25.921 176.556 4346 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.78 % Favored : 92.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % 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: -1.71 (0.18), residues: 1929 helix: -0.27 (0.19), residues: 668 sheet: -1.01 (0.28), residues: 312 loop : -1.81 (0.19), residues: 949 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.205 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 outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.3311 time to fit residues: 106.9178 Evaluate side-chains 153 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 102 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 20834 Z= 0.277 Angle : 0.692 9.012 29101 Z= 0.384 Chirality : 0.041 0.195 3187 Planarity : 0.005 0.054 2984 Dihedral : 25.890 175.481 4346 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.69 % Favored : 93.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % 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: -1.57 (0.18), residues: 1929 helix: -0.09 (0.19), residues: 661 sheet: -1.02 (0.28), residues: 314 loop : -1.73 (0.19), residues: 954 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.999 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 outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.3084 time to fit residues: 98.5268 Evaluate side-chains 149 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 30.0000 chunk 181 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 HIS B 33 GLN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 20834 Z= 0.245 Angle : 0.690 12.639 29101 Z= 0.380 Chirality : 0.041 0.188 3187 Planarity : 0.005 0.057 2984 Dihedral : 25.854 174.409 4346 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.74 % Favored : 93.16 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % 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: -1.44 (0.18), residues: 1929 helix: 0.02 (0.19), residues: 658 sheet: -0.95 (0.28), residues: 314 loop : -1.65 (0.19), residues: 957 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.951 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 outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.3108 time to fit residues: 98.3663 Evaluate side-chains 150 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 20834 Z= 0.326 Angle : 0.730 11.383 29101 Z= 0.399 Chirality : 0.042 0.237 3187 Planarity : 0.005 0.070 2984 Dihedral : 25.820 174.010 4346 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.41 % Favored : 92.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % 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: -1.45 (0.18), residues: 1929 helix: -0.04 (0.19), residues: 656 sheet: -1.00 (0.28), residues: 314 loop : -1.59 (0.19), residues: 959 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.144 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 outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3232 time to fit residues: 98.2865 Evaluate side-chains 140 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.091351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.063962 restraints weight = 85116.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065657 restraints weight = 45708.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066676 restraints weight = 31263.602| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 20834 Z= 0.245 Angle : 0.688 10.328 29101 Z= 0.377 Chirality : 0.041 0.185 3187 Planarity : 0.005 0.056 2984 Dihedral : 25.766 175.066 4346 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 1929 helix: 0.10 (0.19), residues: 658 sheet: -0.95 (0.27), residues: 330 loop : -1.58 (0.20), residues: 941 =============================================================================== Job complete usr+sys time: 3362.21 seconds wall clock time: 63 minutes 0.44 seconds (3780.44 seconds total)