Starting phenix.real_space_refine (version: dev) on Wed Dec 14 09:23:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/12_2022/6dbv_7851_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/12_2022/6dbv_7851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/12_2022/6dbv_7851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/12_2022/6dbv_7851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/12_2022/6dbv_7851_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/12_2022/6dbv_7851_neut.pdb" } resolution = 4.29 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A ARG 848": "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 ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C GLU 627": "OE1" <-> "OE2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 756": "NH1" <-> "NH2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 999": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 114": "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 GLU 270": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 19958 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4974 Classifications: {'peptide': 616} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 591} 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: 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: "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 2646 SG CYS A 749 63.182 58.280 104.600 1.00 45.82 S Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" P DA E 39 " occ=0.57 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.57 residue: pdb=" P DA E 40 " occ=0.81 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.81 residue: pdb=" P DA E 41 " occ=0.63 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.63 residue: pdb=" P DA E 42 " occ=0.59 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.59 residue: pdb=" P DC E 44 " occ=0.30 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.30 residue: pdb=" P DG F 7 " occ=0.51 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.51 residue: pdb=" P DG F 8 " occ=0.47 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.47 residue: pdb=" P DT F 9 " occ=0.49 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.49 residue: pdb=" P DT F 10 " occ=0.56 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.56 residue: pdb=" P DT F 11 " occ=0.63 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.63 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=0.78 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.78 ... (remaining 16 not shown) Time building chain proxies: 11.59, per 1000 atoms: 0.58 Number of scatterers: 19958 At special positions: 0 Unit cell: (158.464, 146.084, 123.8, 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 3567 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: 9.01 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 959 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 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: 58 helices and 18 sheets defined 37.2% alpha, 20.7% beta 89 base pairs and 168 stacking pairs defined. Time for finding SS restraints: 6.33 Creating SS restraints... Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.614A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 460 Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.630A 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 496 through 510 Processing helix chain 'A' and resid 518 through 523 removed outlier: 4.085A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 523' Processing helix chain 'A' and resid 577 through 600 removed outlier: 5.218A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 Proline residue: A 696 - end of helix removed outlier: 3.611A pdb=" N MET A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 757 through 762 removed outlier: 4.084A 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 815 through 835 removed outlier: 3.618A pdb=" N ASP A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 Processing helix chain 'A' and resid 872 through 879 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 894 through 912 Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.593A pdb=" N ARG A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 removed outlier: 3.888A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 947 Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 removed outlier: 3.601A pdb=" N ILE A 968 " --> pdb=" O HIS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 987 removed outlier: 3.671A pdb=" N GLU A 984 " --> pdb=" O SER A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 997 removed outlier: 3.537A pdb=" N ARG A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 995 " --> pdb=" O ARG A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 4.163A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1027 removed outlier: 3.736A pdb=" N GLN A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 419 through 441 removed outlier: 5.755A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 459 removed outlier: 3.935A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 473 Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 496 through 511 Processing helix chain 'C' and resid 518 through 527 Processing helix chain 'C' and resid 577 through 600 removed outlier: 4.992A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 686 through 703 removed outlier: 3.921A 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 737 Processing helix chain 'C' and resid 755 through 762 Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 799 Processing helix chain 'C' and resid 819 through 835 removed outlier: 3.516A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 863 removed outlier: 3.618A pdb=" N ARG C 848 " --> pdb=" O SER C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 880 removed outlier: 3.710A pdb=" N ALA C 876 " --> pdb=" O ASN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 889 Processing helix chain 'C' and resid 894 through 917 Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 924 through 930 removed outlier: 4.066A 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 972 removed outlier: 3.704A pdb=" N HIS C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS C 964 " --> pdb=" O LYS C 960 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Proline residue: C 966 - end of helix Processing helix chain 'C' and resid 975 through 979 removed outlier: 3.599A pdb=" N ALA C 979 " --> pdb=" O GLY C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 998 removed outlier: 4.510A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1017 removed outlier: 4.158A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1024 Processing helix chain 'D' and resid 308 through 314 removed outlier: 3.759A pdb=" N SER D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.784A pdb=" N PHE A 611 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE A 722 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 613 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 724 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 615 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY A 726 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU A 617 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 728 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.729A 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: 6.784A pdb=" N PHE A 611 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE A 722 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 613 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 724 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 615 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY A 726 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU A 617 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 728 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 6.132A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 318 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 7.543A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.614A pdb=" N GLU B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.325A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.325A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.454A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 322 " --> pdb=" O THR D 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 80 removed outlier: 3.664A pdb=" N HIS D 93 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS D 89 " --> pdb=" O PHE D 80 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB7, first strand: chain 'D' and resid 159 through 160 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 265 707 hydrogen bonds defined for protein. 1953 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 222 hydrogen bonds 436 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 168 stacking parallelities Total time for adding SS restraints: 9.46 Time building geometry restraints manager: 9.68 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: 4525 1.33 - 1.46: 5954 1.46 - 1.58: 9749 1.58 - 1.71: 440 1.71 - 1.83: 168 Bond restraints: 20836 Sorted by residual: bond pdb=" CA PRO D 179 " pdb=" C PRO D 179 " ideal model delta sigma weight residual 1.514 1.496 0.019 5.50e-03 3.31e+04 1.17e+01 bond pdb=" CA ASN C 492 " pdb=" C ASN C 492 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.34e-02 5.57e+03 8.95e+00 bond pdb=" C3' DC G 55 " pdb=" O3' DC G 55 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.67e+00 bond pdb=" C THR D 97 " pdb=" N PRO D 98 " ideal model delta sigma weight residual 1.336 1.352 -0.017 1.08e-02 8.57e+03 2.36e+00 bond pdb=" CA GLN C 514 " pdb=" CB GLN C 514 " ideal model delta sigma weight residual 1.526 1.503 0.023 1.53e-02 4.27e+03 2.33e+00 ... (remaining 20831 not shown) Histogram of bond angle deviations from ideal: 97.93 - 106.46: 1871 106.46 - 114.98: 12255 114.98 - 123.50: 13404 123.50 - 132.02: 1498 132.02 - 140.55: 76 Bond angle restraints: 29104 Sorted by residual: angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CA PRO D 340 " ideal model delta sigma weight residual 127.00 140.55 -13.55 2.40e+00 1.74e-01 3.19e+01 angle pdb=" O4' DG F 34 " pdb=" C1' DG F 34 " pdb=" N9 DG F 34 " ideal model delta sigma weight residual 108.40 115.95 -7.55 1.50e+00 4.44e-01 2.53e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CD PRO D 340 " ideal model delta sigma weight residual 120.60 109.58 11.02 2.20e+00 2.07e-01 2.51e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 127.00 138.18 -11.18 2.40e+00 1.74e-01 2.17e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CD PRO B 340 " ideal model delta sigma weight residual 120.60 112.19 8.41 2.20e+00 2.07e-01 1.46e+01 ... (remaining 29099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 10649 35.45 - 70.89: 1074 70.89 - 106.34: 28 106.34 - 141.78: 3 141.78 - 177.23: 5 Dihedral angle restraints: 11759 sinusoidal: 6161 harmonic: 5598 Sorted by residual: dihedral pdb=" CA GLY A 512 " pdb=" C GLY A 512 " pdb=" N ARG A 513 " pdb=" CA ARG A 513 " ideal model delta harmonic sigma weight residual 180.00 141.74 38.26 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" CA SER C 511 " pdb=" C SER C 511 " pdb=" N GLY C 512 " pdb=" CA GLY C 512 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA PHE A 576 " pdb=" C PHE A 576 " pdb=" N ARG A 577 " pdb=" CA ARG A 577 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2808 0.074 - 0.148: 365 0.148 - 0.222: 11 0.222 - 0.297: 1 0.297 - 0.371: 2 Chirality restraints: 3187 Sorted by residual: chirality pdb=" CA GLN C1000 " pdb=" N GLN C1000 " pdb=" C GLN C1000 " pdb=" CB GLN C1000 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C1' DG F 34 " pdb=" O4' DG F 34 " pdb=" C2' DG F 34 " pdb=" N9 DG F 34 " both_signs ideal model delta sigma weight residual False 2.42 2.12 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE B 311 " pdb=" CA ILE B 311 " pdb=" CG1 ILE B 311 " pdb=" CG2 ILE B 311 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3184 not shown) Planarity restraints: 2985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG F 34 " -0.047 2.00e-02 2.50e+03 2.08e-02 1.30e+01 pdb=" N9 DG F 34 " 0.052 2.00e-02 2.50e+03 pdb=" C8 DG F 34 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG F 34 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG F 34 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG F 34 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG F 34 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG F 34 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG F 34 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG F 34 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG F 34 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG F 34 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 338 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO D 339 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 339 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 339 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC F 28 " 0.030 2.00e-02 2.50e+03 1.63e-02 5.98e+00 pdb=" N1 DC F 28 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DC F 28 " -0.022 2.00e-02 2.50e+03 pdb=" O2 DC F 28 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC F 28 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DC F 28 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC F 28 " 0.017 2.00e-02 2.50e+03 pdb=" C5 DC F 28 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC F 28 " -0.002 2.00e-02 2.50e+03 ... (remaining 2982 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 11 2.01 - 2.74: 1953 2.74 - 3.46: 29727 3.46 - 4.18: 50931 4.18 - 4.90: 78523 Nonbonded interactions: 161145 Sorted by model distance: nonbonded pdb=" NH2 ARG C 675 " pdb=" CH2 TRP C1014 " model vdw 1.293 3.420 nonbonded pdb=" NH2 ARG C 675 " pdb=" CZ2 TRP C1014 " model vdw 1.582 3.420 nonbonded pdb=" NH2 ARG C 505 " pdb=" OP2 DT F 25 " model vdw 1.709 2.520 nonbonded pdb=" NH1 ARG A 523 " pdb=" OP2 DG G 24 " model vdw 1.808 2.520 nonbonded pdb=" OE2 GLU C 789 " pdb=" NH1 ARG C 797 " model vdw 1.894 2.520 ... (remaining 161140 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 464 or resid 466 through 1028 or resid 1101 th \ rough 1103)) selection = (chain 'C' and (resid 408 through 464 or resid 466 through 628 or resid 635 thro \ ugh 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 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 3567 2.21 5 O 4214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 0.010 Normalize map: mean=0, sd=1: 0.300 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: 3.560 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.170 Process input model: 62.830 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 0.006 0.073 20836 Z= 0.355 Angle : 0.849 16.412 29104 Z= 0.471 Chirality : 0.048 0.371 3187 Planarity : 0.005 0.066 2985 Dihedral : 22.470 177.231 8157 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.78 % Favored : 89.06 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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: -4.29 (0.15), residues: 1929 helix: -2.87 (0.15), residues: 645 sheet: -1.48 (0.26), residues: 335 loop : -3.38 (0.16), residues: 949 *********************** 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 382 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 2.173 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 381 average time/residue: 0.3551 time to fit residues: 196.1047 Evaluate side-chains 194 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 2.586 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3992 time to fit residues: 4.3294 ------------------------------------------------------------------------------- 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: 8.9990 chunk 162 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 0.0030 chunk 168 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 ASN A 937 GLN B 222 HIS ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 HIS ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 GLN ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN C1000 GLN C1012 HIS C1028 HIS ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 20836 Z= 0.272 Angle : 0.751 11.865 29104 Z= 0.401 Chirality : 0.044 0.212 3187 Planarity : 0.006 0.058 2985 Dihedral : 25.786 176.048 4347 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.95 % Favored : 93.00 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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: -2.89 (0.17), residues: 1929 helix: -1.12 (0.18), residues: 648 sheet: -1.21 (0.27), residues: 344 loop : -2.82 (0.17), residues: 937 *********************** 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 271 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 268 time to evaluate : 2.108 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: 3 outliers final: 0 residues processed: 270 average time/residue: 0.3605 time to fit residues: 144.1868 Evaluate side-chains 163 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.190 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7449 ------------------------------------------------------------------------------- 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: 0.8980 chunk 60 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 211 optimal weight: 30.0000 chunk 174 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 20836 Z= 0.298 Angle : 0.725 12.846 29104 Z= 0.388 Chirality : 0.042 0.191 3187 Planarity : 0.005 0.050 2985 Dihedral : 25.698 173.081 4347 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.09 % Favored : 91.76 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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: -2.18 (0.18), residues: 1929 helix: -0.50 (0.19), residues: 650 sheet: -0.97 (0.27), residues: 348 loop : -2.36 (0.19), residues: 931 *********************** 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 215 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 2.169 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 outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.3262 time to fit residues: 107.1072 Evaluate side-chains 148 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6271 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 858 GLN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 20836 Z= 0.309 Angle : 0.721 12.273 29104 Z= 0.385 Chirality : 0.042 0.175 3187 Planarity : 0.005 0.090 2985 Dihedral : 25.676 173.188 4347 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.04 % Favored : 91.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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: -1.88 (0.18), residues: 1929 helix: -0.23 (0.20), residues: 657 sheet: -0.94 (0.27), residues: 353 loop : -2.15 (0.19), residues: 919 *********************** 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 208 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.071 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: 208 average time/residue: 0.3032 time to fit residues: 98.5244 Evaluate side-chains 146 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0311 ------------------------------------------------------------------------------- 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: 8.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 0.0770 chunk 177 optimal weight: 30.0000 chunk 143 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 106 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 GLN C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 20836 Z= 0.191 Angle : 0.656 11.130 29104 Z= 0.352 Chirality : 0.040 0.162 3187 Planarity : 0.005 0.079 2985 Dihedral : 25.491 175.596 4347 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.17 % Favored : 93.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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: -1.48 (0.18), residues: 1929 helix: 0.20 (0.20), residues: 658 sheet: -0.71 (0.28), residues: 343 loop : -1.99 (0.19), residues: 928 *********************** 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 231 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.147 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: 231 average time/residue: 0.3104 time to fit residues: 112.3110 Evaluate side-chains 157 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4321 ------------------------------------------------------------------------------- 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: 7.9990 chunk 187 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 30.0000 chunk 172 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 17 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 20836 Z= 0.231 Angle : 0.673 10.932 29104 Z= 0.360 Chirality : 0.040 0.166 3187 Planarity : 0.005 0.069 2985 Dihedral : 25.407 175.601 4347 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.05 % Favored : 92.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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: -1.33 (0.19), residues: 1929 helix: 0.31 (0.20), residues: 656 sheet: -0.60 (0.28), residues: 332 loop : -1.89 (0.19), residues: 941 *********************** 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 210 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.860 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 outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3223 time to fit residues: 105.6238 Evaluate side-chains 151 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8115 ------------------------------------------------------------------------------- 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: 0.0030 chunk 151 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 175 optimal weight: 0.4980 chunk 116 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 129 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 overall best weight: 4.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 20836 Z= 0.291 Angle : 0.713 10.995 29104 Z= 0.380 Chirality : 0.041 0.179 3187 Planarity : 0.005 0.078 2985 Dihedral : 25.408 176.569 4347 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.10 % Favored : 92.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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: -1.37 (0.18), residues: 1929 helix: 0.21 (0.20), residues: 659 sheet: -0.63 (0.28), residues: 332 loop : -1.84 (0.19), residues: 938 *********************** 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 190 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.051 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: 190 average time/residue: 0.3141 time to fit residues: 94.9109 Evaluate side-chains 139 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8805 ------------------------------------------------------------------------------- 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: 5.9990 chunk 82 optimal weight: 30.0000 chunk 123 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 40 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 188 optimal weight: 0.4980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 20836 Z= 0.220 Angle : 0.676 11.913 29104 Z= 0.360 Chirality : 0.040 0.166 3187 Planarity : 0.005 0.063 2985 Dihedral : 25.333 177.749 4347 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 18.85 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 : 1.25 % 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: -1.17 (0.19), residues: 1929 helix: 0.42 (0.20), residues: 656 sheet: -0.56 (0.28), residues: 337 loop : -1.75 (0.19), residues: 936 *********************** 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 195 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3046 time to fit residues: 93.3822 Evaluate side-chains 147 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.904 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4966 ------------------------------------------------------------------------------- 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: 6.9990 chunk 193 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 20836 Z= 0.248 Angle : 0.691 10.908 29104 Z= 0.370 Chirality : 0.041 0.160 3187 Planarity : 0.005 0.062 2985 Dihedral : 25.309 178.916 4347 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.95 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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: -1.20 (0.19), residues: 1929 helix: 0.37 (0.20), residues: 658 sheet: -0.61 (0.28), residues: 339 loop : -1.73 (0.19), residues: 932 *********************** 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 187 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.3187 time to fit residues: 93.8994 Evaluate side-chains 136 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6990 ------------------------------------------------------------------------------- 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: 0.9990 chunk 96 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 197 optimal weight: 30.0000 chunk 170 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 20836 Z= 0.220 Angle : 0.693 11.023 29104 Z= 0.371 Chirality : 0.041 0.180 3187 Planarity : 0.005 0.058 2985 Dihedral : 25.283 179.401 4347 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.43 % Favored : 93.47 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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: -1.13 (0.19), residues: 1929 helix: 0.41 (0.20), residues: 657 sheet: -0.54 (0.28), residues: 345 loop : -1.69 (0.20), residues: 927 ********************** 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: 1 poor density : 189 time to evaluate : 2.141 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: 190 average time/residue: 0.2953 time to fit residues: 91.1989 Evaluate side-chains 141 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5803 ------------------------------------------------------------------------------- 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: 20.0000 chunk 52 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 47 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** 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 = 0.3666 r_free = 0.3666 target = 0.081662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.057859 restraints weight = 94983.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059410 restraints weight = 53872.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060401 restraints weight = 37615.156| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 97 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 20836 Z= 0.212 Angle : 0.695 11.118 29104 Z= 0.368 Chirality : 0.041 0.192 3187 Planarity : 0.005 0.057 2985 Dihedral : 25.257 179.374 4347 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.32 % Favored : 93.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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: -1.05 (0.19), residues: 1929 helix: 0.48 (0.20), residues: 657 sheet: -0.44 (0.28), residues: 340 loop : -1.68 (0.19), residues: 932 =============================================================================== Job complete usr+sys time: 3167.77 seconds wall clock time: 59 minutes 22.97 seconds (3562.97 seconds total)