Starting phenix.real_space_refine (version: dev) on Wed Dec 14 09:18:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbt_7849/12_2022/6dbt_7849_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbt_7849/12_2022/6dbt_7849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbt_7849/12_2022/6dbt_7849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbt_7849/12_2022/6dbt_7849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbt_7849/12_2022/6dbt_7849_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbt_7849/12_2022/6dbt_7849_neut.pdb" } resolution = 4.3 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= 0.006 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 490": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 101": "OE1" <-> "OE2" 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 ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C GLU 590": "OE1" <-> "OE2" Residue "C GLU 637": "OE1" <-> "OE2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C GLU 656": "OE1" <-> "OE2" Residue "C ARG 756": "NH1" <-> "NH2" Residue "C GLU 777": "OE1" <-> "OE2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C GLU 984": "OE1" <-> "OE2" 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 GLU 101": "OE1" <-> "OE2" 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 ARG 302": "NH1" <-> "NH2" 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: 19896 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4955 Classifications: {'peptide': 614} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 588} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 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: 4956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4956 Classifications: {'peptide': 614} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} 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 2636 SG CYS A 749 106.665 99.076 96.537 1.00123.70 S ATOM 2657 SG CYS A 752 108.556 101.879 97.372 1.00227.41 S ATOM 10306 SG CYS C 749 47.965 32.858 95.607 1.00 60.43 S Residues with excluded nonbonded symmetry interactions: 26 residue: pdb=" P DA E 39 " occ=0.90 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.90 residue: pdb=" P DA E 40 " occ=0.91 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.91 residue: pdb=" P DA E 41 " occ=0.97 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.97 residue: pdb=" P DA E 42 " occ=0.92 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.92 residue: pdb=" P DC E 44 " occ=0.84 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.84 residue: pdb=" P DG F 7 " occ=0.73 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.73 residue: pdb=" P DG F 8 " occ=0.76 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.76 residue: pdb=" P DT F 9 " occ=0.82 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.82 residue: pdb=" P DT F 10 " occ=0.91 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.91 residue: pdb=" P DT F 11 " occ=0.87 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.87 residue: pdb=" P DT F 12 " occ=0.82 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.82 residue: pdb=" P DT F 13 " occ=0.93 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.93 ... (remaining 14 not shown) Time building chain proxies: 11.59, per 1000 atoms: 0.58 Number of scatterers: 19896 At special positions: 0 Unit cell: (156.88, 132.5, 150.52, 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 4203 8.00 N 3553 7.00 C 11800 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: 9.98 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 ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " Number of angles added : 2 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 19 sheets defined 37.7% alpha, 19.8% beta 96 base pairs and 174 stacking pairs defined. Time for finding SS restraints: 7.02 Creating SS restraints... Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.508A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 460 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 518 through 528 removed outlier: 3.977A pdb=" N GLU A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 600 removed outlier: 5.304A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.477A 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 removed outlier: 3.717A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 3.570A 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: 3.826A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 799 Processing helix chain 'A' and resid 819 through 835 Processing helix chain 'A' and resid 846 through 863 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 895 through 912 removed outlier: 3.608A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 4.101A 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 947 removed outlier: 3.530A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.753A pdb=" N HIS A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.517A pdb=" N TRP A 978 " --> pdb=" O ILE A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.511A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 997 " --> pdb=" O PHE A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 4.559A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1025 removed outlier: 3.626A pdb=" N PHE A1024 " --> pdb=" O TYR A1020 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.797A pdb=" N LEU B 14 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 15 " --> pdb=" O GLY B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 15' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 419 through 441 removed outlier: 5.274A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 461 Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.565A pdb=" N ALA C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.626A pdb=" N SER C 511 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 527 Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 589 through 601 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.641A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix removed outlier: 3.535A 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 755 through 762 removed outlier: 3.879A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (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 819 through 835 removed outlier: 3.867A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 removed outlier: 3.692A pdb=" N ARG C 848 " --> pdb=" O SER C 844 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG C 849 " --> pdb=" O ARG C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 892 Processing helix chain 'C' and resid 895 through 917 removed outlier: 4.027A pdb=" N GLU C 899 " --> pdb=" O GLU C 895 " (cutoff:3.500A) Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 927 through 945 removed outlier: 4.638A pdb=" N SER C 932 " --> pdb=" O LEU C 928 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR C 933 " --> pdb=" O CYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 949 Processing helix chain 'C' and resid 955 through 964 removed outlier: 3.775A pdb=" N HIS C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 960 " --> pdb=" O ASN C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 972 Processing helix chain 'C' and resid 975 through 979 removed outlier: 3.625A pdb=" N TRP C 978 " --> pdb=" O ILE C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.510A pdb=" N GLU C 984 " --> pdb=" O SER C 980 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY C 986 " --> pdb=" O GLY C 982 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 991 " --> pdb=" O ASN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1017 removed outlier: 4.498A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1024 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: 6.559A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.843A 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: 6.559A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 5.934A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 22 removed outlier: 4.107A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.756A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 106 " --> pdb=" O LYS B 127 " (cutoff:3.500A) 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 161 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 537 through 539 removed outlier: 6.684A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 612 " --> pdb=" O SER C 650 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 648 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C 616 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE C 646 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER C 618 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE C 644 " --> pdb=" O SER C 618 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP C 620 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 642 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET C 622 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL C 640 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 651 " --> pdb=" O THR C 661 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR C 661 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 554 through 555 removed outlier: 6.928A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL C 640 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET C 622 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 642 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP C 620 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE C 644 " --> pdb=" O SER C 618 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER C 618 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE C 646 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C 616 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 648 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 612 " --> pdb=" O SER C 650 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY C 726 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU C 617 " --> pdb=" O GLY C 726 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 5 removed outlier: 5.650A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 22 removed outlier: 4.506A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 75 through 80 Processing sheet with id=AB6, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AC1, first strand: chain 'D' and resid 263 through 265 672 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 240 hydrogen bonds 480 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 174 stacking parallelities Total time for adding SS restraints: 10.54 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5273 1.34 - 1.46: 5875 1.46 - 1.58: 9015 1.58 - 1.71: 440 1.71 - 1.83: 168 Bond restraints: 20771 Sorted by residual: bond pdb=" C LYS A 912 " pdb=" N PRO A 913 " ideal model delta sigma weight residual 1.337 1.361 -0.024 9.80e-03 1.04e+04 5.97e+00 bond pdb=" C LYS A 840 " pdb=" N PRO A 841 " ideal model delta sigma weight residual 1.334 1.350 -0.017 8.40e-03 1.42e+04 3.99e+00 bond pdb=" CA PRO B 70 " pdb=" C PRO B 70 " ideal model delta sigma weight residual 1.514 1.504 0.010 5.50e-03 3.31e+04 3.64e+00 bond pdb=" C HIS C 482 " pdb=" N PRO C 483 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.65e+00 bond pdb=" C PRO D 17 " pdb=" N GLY D 18 " ideal model delta sigma weight residual 1.332 1.340 -0.008 5.00e-03 4.00e+04 2.49e+00 ... (remaining 20766 not shown) Histogram of bond angle deviations from ideal: 98.26 - 106.68: 1956 106.68 - 115.09: 12301 115.09 - 123.50: 13210 123.50 - 131.92: 1463 131.92 - 140.33: 81 Bond angle restraints: 29011 Sorted by residual: angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 127.00 140.33 -13.33 2.40e+00 1.74e-01 3.08e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CA PRO D 340 " ideal model delta sigma weight residual 127.00 140.21 -13.21 2.40e+00 1.74e-01 3.03e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CD PRO D 340 " ideal model delta sigma weight residual 120.60 109.10 11.50 2.20e+00 2.07e-01 2.73e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CD PRO B 340 " ideal model delta sigma weight residual 120.60 109.57 11.03 2.20e+00 2.07e-01 2.51e+01 angle pdb=" C TYR C1016 " pdb=" N THR C1017 " pdb=" CA THR C1017 " ideal model delta sigma weight residual 123.17 116.22 6.95 1.49e+00 4.50e-01 2.18e+01 ... (remaining 29006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 10427 35.28 - 70.55: 1256 70.55 - 105.83: 34 105.83 - 141.10: 0 141.10 - 176.38: 5 Dihedral angle restraints: 11722 sinusoidal: 6148 harmonic: 5574 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 180.00 142.81 37.19 0 5.00e+00 4.00e-02 5.53e+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 180.00 148.91 31.09 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA SER B 147 " pdb=" C SER B 147 " pdb=" N ARG B 148 " pdb=" CA ARG B 148 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 11719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2016 0.035 - 0.070: 839 0.070 - 0.105: 234 0.105 - 0.140: 79 0.140 - 0.175: 10 Chirality restraints: 3178 Sorted by residual: chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ASP A 624 " pdb=" N ASP A 624 " pdb=" C ASP A 624 " pdb=" CB ASP A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" C3' DA G 18 " pdb=" C4' DA G 18 " pdb=" O3' DA G 18 " pdb=" C2' DA G 18 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 3175 not shown) Planarity restraints: 2969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 197 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO D 198 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 338 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO B 339 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 34 " -0.028 2.00e-02 2.50e+03 1.22e-02 4.48e+00 pdb=" N9 DG E 34 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DG E 34 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG E 34 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG E 34 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DG E 34 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG E 34 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG E 34 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG E 34 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG E 34 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG E 34 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG E 34 " 0.002 2.00e-02 2.50e+03 ... (remaining 2966 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 152 2.47 - 3.08: 13626 3.08 - 3.68: 33277 3.68 - 4.29: 44787 4.29 - 4.90: 67298 Nonbonded interactions: 159140 Sorted by model distance: nonbonded pdb=" NZ LYS C 638 " pdb=" OD2 ASP C 683 " model vdw 1.860 2.520 nonbonded pdb=" OE2 GLU A 463 " pdb=" NZ LYS C 447 " model vdw 1.900 2.520 nonbonded pdb=" NE2 HIS D 222 " pdb=" OE2 GLU D 280 " model vdw 1.961 2.520 nonbonded pdb=" NZ LYS A 804 " pdb=" OE1 GLU B 101 " model vdw 1.976 2.520 nonbonded pdb=" NH1 ARG C 575 " pdb=" O PHE C 576 " model vdw 1.999 2.520 ... (remaining 159135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 408 through 459 or (resid 460 and (name N or name CA or na \ me C or name CB )) or resid 461 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 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 11800 2.51 5 N 3553 2.21 5 O 4203 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=0.99 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.530 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.180 Process input model: 65.700 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 0.044 20771 Z= 0.331 Angle : 0.815 13.329 29011 Z= 0.463 Chirality : 0.043 0.175 3178 Planarity : 0.005 0.060 2969 Dihedral : 24.068 176.378 8134 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.18 % Favored : 90.62 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.16 (0.15), residues: 1918 helix: -2.41 (0.16), residues: 631 sheet: -1.82 (0.27), residues: 312 loop : -3.40 (0.16), residues: 975 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 2.050 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 outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.3898 time to fit residues: 154.4287 Evaluate side-chains 149 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 109 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS A 669 ASN A 687 HIS ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 83 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN C 772 HIS C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 20771 Z= 0.230 Angle : 0.738 12.520 29011 Z= 0.400 Chirality : 0.043 0.202 3178 Planarity : 0.005 0.053 2969 Dihedral : 26.071 175.197 4336 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.51 % Favored : 92.34 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % 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: -2.75 (0.17), residues: 1918 helix: -0.86 (0.19), residues: 641 sheet: -1.62 (0.27), residues: 331 loop : -2.63 (0.17), residues: 946 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 2.035 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 outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.3840 time to fit residues: 149.3732 Evaluate side-chains 140 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 0.3980 chunk 161 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 chunk 173 optimal weight: 0.3980 chunk 193 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 HIS B 83 GLN B 146 ASN C 432 ASN ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 20771 Z= 0.252 Angle : 0.703 12.816 29011 Z= 0.380 Chirality : 0.041 0.152 3178 Planarity : 0.005 0.067 2969 Dihedral : 25.861 177.062 4336 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.09 % Favored : 92.75 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.25 (0.18), residues: 1918 helix: -0.41 (0.19), residues: 639 sheet: -1.39 (0.28), residues: 330 loop : -2.32 (0.18), residues: 949 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 2.247 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: 202 average time/residue: 0.3646 time to fit residues: 108.9985 Evaluate side-chains 128 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 2.008 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1711 time to fit residues: 2.9044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 195 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 20771 Z= 0.205 Angle : 0.672 11.507 29011 Z= 0.363 Chirality : 0.040 0.150 3178 Planarity : 0.004 0.049 2969 Dihedral : 25.673 174.705 4336 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.78 % Favored : 93.17 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1918 helix: -0.11 (0.20), residues: 641 sheet: -1.21 (0.29), residues: 328 loop : -2.10 (0.19), residues: 949 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 2.126 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: 195 average time/residue: 0.3787 time to fit residues: 109.2411 Evaluate side-chains 129 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 2.223 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2296 time to fit residues: 3.1588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 154 optimal weight: 0.0270 chunk 85 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 105 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.5844 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** 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: 0.8234 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 20771 Z= 0.232 Angle : 0.678 11.210 29011 Z= 0.367 Chirality : 0.040 0.171 3178 Planarity : 0.004 0.075 2969 Dihedral : 25.601 174.863 4336 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.73 % Favored : 93.17 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % 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: -1.71 (0.18), residues: 1918 helix: -0.03 (0.20), residues: 641 sheet: -0.88 (0.30), residues: 306 loop : -2.02 (0.19), residues: 971 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 2.241 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: 1 outliers final: 0 residues processed: 182 average time/residue: 0.3734 time to fit residues: 100.9906 Evaluate side-chains 124 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 20.0000 chunk 186 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 0.0870 chunk 108 optimal weight: 6.9990 overall best weight: 4.7764 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 20771 Z= 0.333 Angle : 0.731 11.201 29011 Z= 0.392 Chirality : 0.041 0.167 3178 Planarity : 0.005 0.049 2969 Dihedral : 25.592 173.493 4336 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.82 % Favored : 92.08 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.69 (0.18), residues: 1918 helix: -0.10 (0.20), residues: 651 sheet: -0.89 (0.30), residues: 318 loop : -1.96 (0.19), residues: 949 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 2.188 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: 1 outliers final: 0 residues processed: 171 average time/residue: 0.3682 time to fit residues: 93.8116 Evaluate side-chains 121 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 129 optimal weight: 0.4980 chunk 125 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 514 GLN ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 20771 Z= 0.190 Angle : 0.669 11.482 29011 Z= 0.359 Chirality : 0.040 0.203 3178 Planarity : 0.004 0.049 2969 Dihedral : 25.491 173.583 4336 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % 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: -1.44 (0.19), residues: 1918 helix: 0.05 (0.20), residues: 654 sheet: -0.80 (0.29), residues: 327 loop : -1.74 (0.19), residues: 937 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.985 Fit side-chains 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: 185 average time/residue: 0.3651 time to fit residues: 99.9869 Evaluate side-chains 125 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.953 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1739 time to fit residues: 2.9059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 20771 Z= 0.229 Angle : 0.680 12.696 29011 Z= 0.362 Chirality : 0.040 0.162 3178 Planarity : 0.004 0.048 2969 Dihedral : 25.442 174.105 4336 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.04 % Favored : 92.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 1918 helix: 0.17 (0.20), residues: 653 sheet: -0.70 (0.29), residues: 327 loop : -1.74 (0.19), residues: 938 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.915 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: 166 average time/residue: 0.3345 time to fit residues: 84.1399 Evaluate side-chains 124 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 20.0000 chunk 180 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 chunk 150 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 181 optimal weight: 30.0000 chunk 191 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN B 16 GLN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 20771 Z= 0.318 Angle : 0.731 11.774 29011 Z= 0.390 Chirality : 0.041 0.161 3178 Planarity : 0.005 0.049 2969 Dihedral : 25.503 173.120 4336 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.08 % Favored : 91.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.46 (0.19), residues: 1918 helix: 0.10 (0.20), residues: 651 sheet: -0.93 (0.29), residues: 332 loop : -1.75 (0.19), residues: 935 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.052 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: 163 average time/residue: 0.3559 time to fit residues: 88.3340 Evaluate side-chains 119 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 96 optimal weight: 0.0370 chunk 141 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 169 optimal weight: 0.0070 chunk 17 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 overall best weight: 0.9878 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20771 Z= 0.185 Angle : 0.678 13.511 29011 Z= 0.360 Chirality : 0.040 0.157 3178 Planarity : 0.004 0.050 2969 Dihedral : 25.436 173.876 4336 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.88 % Favored : 93.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % 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: -1.22 (0.19), residues: 1918 helix: 0.33 (0.20), residues: 653 sheet: -0.70 (0.29), residues: 319 loop : -1.67 (0.19), residues: 946 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3343 time to fit residues: 86.1385 Evaluate side-chains 119 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 HIS ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.068931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.049505 restraints weight = 111485.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050660 restraints weight = 62847.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.051380 restraints weight = 43418.131| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 103 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 20771 Z= 0.179 Angle : 0.676 11.438 29011 Z= 0.358 Chirality : 0.039 0.153 3178 Planarity : 0.004 0.067 2969 Dihedral : 25.301 175.451 4336 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.88 % Favored : 93.01 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % 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: -1.10 (0.19), residues: 1918 helix: 0.38 (0.20), residues: 655 sheet: -0.40 (0.29), residues: 318 loop : -1.67 (0.19), residues: 945 =============================================================================== Job complete usr+sys time: 3176.69 seconds wall clock time: 59 minutes 15.94 seconds (3555.94 seconds total)