Starting phenix.real_space_refine (version: dev) on Wed Feb 22 12:11:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/02_2023/6dbx_7853.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/02_2023/6dbx_7853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/02_2023/6dbx_7853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/02_2023/6dbx_7853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/02_2023/6dbx_7853.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/02_2023/6dbx_7853.pdb" } resolution = 4.2 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= 0.007 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 Process input model Symmetric amino acids flipped Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C GLU 700": "OE1" <-> "OE2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 721": "NH1" <-> "NH2" Residue "C ARG 756": "NH1" <-> "NH2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C TYR 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 850": "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 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 300": "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-4877/modules/chem_data/mon_lib" Total number of atoms: 17436 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4966 Classifications: {'peptide': 615} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} 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: 4980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 615, 4964 Classifications: {'peptide': 615} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 615, 4964 Classifications: {'peptide': 615} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} Chain breaks: 1 bond proxies already assigned to first conformer: 5041 Chain: "D" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2720 Classifications: {'peptide': 352} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 318} 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: "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 2647 SG CYS A 749 32.932 54.101 52.515 1.00 92.47 S ATOM 10316 SG CYS C 749 105.234 99.787 56.404 1.00107.55 S Residues with excluded nonbonded symmetry interactions: 13 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=0.77 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.77 residue: pdb=" P DA E 41 " occ=0.80 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.80 residue: pdb=" P DA E 42 " occ=0.71 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.71 residue: pdb=" P DC E 44 " occ=0.64 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.64 residue: pdb=" P DG F 7 " occ=0.68 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.68 residue: pdb=" P DG F 8 " occ=0.66 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.66 residue: pdb=" P DT F 9 " occ=0.78 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.78 residue: pdb=" P DT F 10 " occ=0.72 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.72 residue: pdb=" P DT F 11 " occ=0.96 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.96 residue: pdb=" P DT F 12 " occ=0.79 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.79 residue: pdb=" P DT F 13 " occ=0.80 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.80 residue: pdb=" P DG F 14 " occ=0.51 ... (20 atoms not shown) pdb=" C4 DG F 14 " occ=0.51 Time building chain proxies: 12.04, per 1000 atoms: 0.69 Number of scatterers: 17436 At special positions: 0 Unit cell: (131.44, 156.88, 143.1, 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 100 15.00 O 3477 8.00 N 3107 7.00 C 10634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.48 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 19 sheets defined 37.2% alpha, 19.2% beta 40 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.493A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 474 removed outlier: 4.163A 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 511 removed outlier: 3.513A pdb=" N SER A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 577 through 589 Processing helix chain 'A' and resid 589 through 601 Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 707 removed outlier: 3.580A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 4.482A pdb=" N GLU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 756 through 762 removed outlier: 3.968A 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 844 through 864 removed outlier: 3.883A pdb=" N ARG A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.557A pdb=" N ALA A 876 " --> pdb=" O ASN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 894 through 916 removed outlier: 3.773A pdb=" N ARG A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 924 through 946 removed outlier: 4.135A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.974A pdb=" N HIS A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 983 removed outlier: 7.575A pdb=" N SER A 980 " --> pdb=" O ALA A 977 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLU A 981 " --> pdb=" O TRP A 978 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 982 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 removed outlier: 4.021A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 3.856A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1023 removed outlier: 3.523A pdb=" N GLN A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.810A pdb=" N LEU B 14 " --> pdb=" O CYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.694A pdb=" N LEU C 418 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 442 removed outlier: 5.708A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 460 removed outlier: 3.776A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.690A pdb=" N ALA C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 527 removed outlier: 3.817A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 589 through 600 Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.789A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR C 691 " --> pdb=" O HIS C 687 " (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 757 through 762 removed outlier: 3.751A 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 799 Processing helix chain 'C' and resid 815 through 834 Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 878 removed outlier: 3.879A pdb=" N ALA C 876 " --> pdb=" O ASN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 890 Processing helix chain 'C' and resid 895 through 910 removed outlier: 3.879A pdb=" N GLU C 899 " --> pdb=" O GLU C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 916 removed outlier: 3.769A pdb=" N TRP C 915 " --> pdb=" O MET C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 removed outlier: 3.614A pdb=" N GLN C 930 " --> pdb=" O ASP C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 945 Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 980 through 998 removed outlier: 4.615A pdb=" N GLU C 984 " --> pdb=" O SER C 980 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 985 " --> pdb=" O GLU C 981 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1016 removed outlier: 4.309A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS C1011 " --> pdb=" O GLU C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 4.950A pdb=" N PHE C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.862A pdb=" N GLU A 537 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 710 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 716 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 611 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE A 722 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL A 613 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE A 724 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 615 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLY A 726 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU A 617 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE A 644 " --> pdb=" O PRO A 676 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.862A pdb=" N GLU A 537 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 710 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 716 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 611 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE A 722 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL A 613 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE A 724 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 615 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLY A 726 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU A 617 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 660 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.507A pdb=" N SER B 2 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 346 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 329 " --> pdb=" O TYR B 346 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 330 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 318 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.507A pdb=" N SER B 2 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 346 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 329 " --> pdb=" O TYR B 346 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B 344 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.981A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 48 " --> pdb=" O VAL B 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 80 removed outlier: 3.930A pdb=" N CYS B 89 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 147 removed outlier: 3.861A pdb=" N LYS B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.565A pdb=" N VAL B 176 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 209 through 210 Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 265 removed outlier: 3.656A pdb=" N SER B 264 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 272 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.766A pdb=" N GLU C 537 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 711 " --> pdb=" O ARG C 718 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 554 through 555 removed outlier: 5.939A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 554 through 555 removed outlier: 5.939A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 24 removed outlier: 5.997A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 48 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE D 46 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER D 2 " --> pdb=" O SER D 349 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS D 344 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR D 346 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 348 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.025A pdb=" N SER D 61 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N CYS D 124 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 110 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 78 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 141 through 147 removed outlier: 3.518A pdb=" N THR D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 155 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR D 183 " --> pdb=" O LEU D 155 " (cutoff:3.500A) 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 265 654 hydrogen bonds defined for protein. 1832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 7.00 Time building geometry restraints manager: 8.09 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: 5216 1.34 - 1.47: 4918 1.47 - 1.60: 7520 1.60 - 1.72: 189 1.72 - 1.85: 168 Bond restraints: 18011 Sorted by residual: bond pdb=" CA PRO D 163 " pdb=" C PRO D 163 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.59e+01 bond pdb=" C PHE C 516 " pdb=" N GLN C 517 " ideal model delta sigma weight residual 1.327 1.289 0.037 1.71e-02 3.42e+03 4.80e+00 bond pdb=" CA VAL C 965 " pdb=" CB VAL C 965 " ideal model delta sigma weight residual 1.537 1.529 0.008 5.00e-03 4.00e+04 2.40e+00 bond pdb=" N ASP D 214 " pdb=" CA ASP D 214 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.95e-02 2.63e+03 2.30e+00 bond pdb=" C LEU C 481 " pdb=" N HIS C 482 " ideal model delta sigma weight residual 1.331 1.362 -0.031 2.07e-02 2.33e+03 2.18e+00 ... (remaining 18006 not shown) Histogram of bond angle deviations from ideal: 97.40 - 106.10: 1013 106.10 - 114.79: 10668 114.79 - 123.49: 12019 123.49 - 132.19: 1004 132.19 - 140.89: 46 Bond angle restraints: 24750 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 127.00 140.89 -13.89 2.40e+00 1.74e-01 3.35e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CA PRO D 340 " ideal model delta sigma weight residual 127.00 139.60 -12.60 2.40e+00 1.74e-01 2.76e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CD PRO B 340 " ideal model delta sigma weight residual 120.60 109.31 11.29 2.20e+00 2.07e-01 2.63e+01 angle pdb=" N ILE C 975 " pdb=" CA ILE C 975 " pdb=" C ILE C 975 " ideal model delta sigma weight residual 112.12 107.98 4.14 8.40e-01 1.42e+00 2.43e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CD PRO D 340 " ideal model delta sigma weight residual 120.60 110.54 10.06 2.20e+00 2.07e-01 2.09e+01 ... (remaining 24745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 9786 34.35 - 68.69: 730 68.69 - 103.04: 20 103.04 - 137.39: 1 137.39 - 171.74: 3 Dihedral angle restraints: 10540 sinusoidal: 4949 harmonic: 5591 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 180.00 150.03 29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA GLY A 623 " pdb=" C GLY A 623 " pdb=" N ASP A 624 " pdb=" CA ASP A 624 " ideal model delta harmonic sigma weight residual 180.00 152.33 27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA THR C 727 " pdb=" C THR C 727 " pdb=" N GLY C 728 " pdb=" CA GLY C 728 " ideal model delta harmonic sigma weight residual -180.00 -153.56 -26.44 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 10537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1642 0.035 - 0.071: 735 0.071 - 0.106: 220 0.106 - 0.142: 87 0.142 - 0.177: 11 Chirality restraints: 2695 Sorted by residual: chirality pdb=" CA VAL C 682 " pdb=" N VAL C 682 " pdb=" C VAL C 682 " pdb=" CB VAL C 682 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE B 262 " pdb=" N ILE B 262 " pdb=" C ILE B 262 " pdb=" CB ILE B 262 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA MET A 863 " pdb=" N MET A 863 " pdb=" C MET A 863 " pdb=" CB MET A 863 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 2692 not shown) Planarity restraints: 2857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 338 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO B 339 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 804 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO A 805 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 866 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.83e+00 pdb=" N PRO C 867 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 867 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 867 " 0.027 5.00e-02 4.00e+02 ... (remaining 2854 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 424 2.64 - 3.21: 16377 3.21 - 3.77: 28005 3.77 - 4.34: 35142 4.34 - 4.90: 54122 Nonbonded interactions: 134070 Sorted by model distance: nonbonded pdb=" OG SER B 314 " pdb=" O THR B 316 " model vdw 2.076 2.440 nonbonded pdb=" O2 DC E 31 " pdb=" N2 DG F 20 " model vdw 2.095 2.496 nonbonded pdb=" O PRO A 913 " pdb=" OG SER A 917 " model vdw 2.125 2.440 nonbonded pdb=" OD2 ASP A 566 " pdb=" OH TYR B 138 " model vdw 2.151 2.440 nonbonded pdb=" OG1 THR B 97 " pdb=" O ASN B 99 " model vdw 2.156 2.440 ... (remaining 134065 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 512 or resid 514 through 627 or resid 636 thro \ ugh 849 or resid 851 through 1028 or resid 1101 through 1103)) selection = (chain 'C' and (resid 408 through 512 or resid 514 through 849 or resid 851 thro \ ugh 1028 or resid 1101 through 1103)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 1 through 351) } 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 100 5.49 5 S 112 5.16 5 C 10634 2.51 5 N 3107 2.21 5 O 3477 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: 0.850 Set stop_for_unknowns flag: 0.010 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: 5.160 Check model and map are aligned: 0.250 Process input model: 55.730 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 0.077 18011 Z= 0.313 Angle : 0.849 13.889 24750 Z= 0.473 Chirality : 0.046 0.177 2695 Planarity : 0.005 0.061 2857 Dihedral : 20.211 171.736 6942 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.87 % Favored : 87.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.15), residues: 1923 helix: -2.79 (0.15), residues: 613 sheet: -2.66 (0.25), residues: 314 loop : -3.53 (0.15), residues: 996 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 1.976 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 outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.3214 time to fit residues: 166.9571 Evaluate side-chains 166 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.949 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 158 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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** A 822 ASN A 934 ASN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 170 GLN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN C 930 GLN ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN D 83 GLN D 170 GLN D 195 HIS ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 18011 Z= 0.405 Angle : 0.843 11.987 24750 Z= 0.445 Chirality : 0.047 0.222 2695 Planarity : 0.006 0.052 2857 Dihedral : 21.149 171.626 3131 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.50 % Favored : 92.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.17), residues: 1923 helix: -1.51 (0.18), residues: 633 sheet: -2.13 (0.25), residues: 345 loop : -2.83 (0.18), residues: 945 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.3214 time to fit residues: 128.5204 Evaluate side-chains 164 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.0470 chunk 152 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 overall best weight: 2.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN A1013 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN C 687 HIS ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN C 959 HIS C 983 ASN C1013 HIS D 213 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 18011 Z= 0.229 Angle : 0.690 11.754 24750 Z= 0.366 Chirality : 0.042 0.171 2695 Planarity : 0.005 0.053 2857 Dihedral : 20.940 173.485 3131 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.83 % Favored : 94.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.18), residues: 1923 helix: -0.45 (0.20), residues: 636 sheet: -1.81 (0.25), residues: 376 loop : -2.42 (0.19), residues: 911 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.772 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: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2981 time to fit residues: 105.2351 Evaluate side-chains 161 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.781 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 87 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 195 optimal weight: 20.0000 chunk 96 optimal weight: 0.0070 chunk 174 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN D 16 GLN D 100 ASN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 18011 Z= 0.306 Angle : 0.721 11.858 24750 Z= 0.379 Chirality : 0.043 0.295 2695 Planarity : 0.005 0.044 2857 Dihedral : 20.821 174.040 3131 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.39 % Favored : 92.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.18), residues: 1923 helix: -0.23 (0.20), residues: 634 sheet: -1.55 (0.26), residues: 362 loop : -2.27 (0.19), residues: 927 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.875 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: 210 average time/residue: 0.3063 time to fit residues: 97.6722 Evaluate side-chains 143 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 0.0010 chunk 110 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 99 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 937 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN C 930 GLN C 983 ASN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 18011 Z= 0.332 Angle : 0.718 11.230 24750 Z= 0.379 Chirality : 0.043 0.189 2695 Planarity : 0.005 0.048 2857 Dihedral : 20.712 174.879 3131 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.76 % Favored : 92.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.18), residues: 1923 helix: -0.19 (0.20), residues: 634 sheet: -1.50 (0.27), residues: 354 loop : -2.21 (0.19), residues: 935 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.898 Fit side-chains 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: 204 average time/residue: 0.2982 time to fit residues: 93.4581 Evaluate side-chains 146 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 195 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN C 930 GLN C 983 ASN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 18011 Z= 0.332 Angle : 0.716 11.184 24750 Z= 0.377 Chirality : 0.043 0.168 2695 Planarity : 0.005 0.045 2857 Dihedral : 20.592 175.579 3131 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.65 % Favored : 92.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.18), residues: 1923 helix: -0.18 (0.20), residues: 636 sheet: -1.28 (0.28), residues: 345 loop : -2.18 (0.19), residues: 942 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.004 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: 198 average time/residue: 0.3001 time to fit residues: 92.6731 Evaluate side-chains 141 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 18011 Z= 0.230 Angle : 0.668 10.918 24750 Z= 0.349 Chirality : 0.042 0.210 2695 Planarity : 0.004 0.045 2857 Dihedral : 20.460 175.699 3131 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.19), residues: 1923 helix: 0.03 (0.20), residues: 639 sheet: -1.22 (0.27), residues: 360 loop : -2.02 (0.19), residues: 924 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.999 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: 205 average time/residue: 0.3051 time to fit residues: 96.5434 Evaluate side-chains 145 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.933 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 123 optimal weight: 0.0770 chunk 132 optimal weight: 6.9990 chunk 96 optimal weight: 0.0570 chunk 18 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN D 195 HIS D 347 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 18011 Z= 0.174 Angle : 0.666 11.017 24750 Z= 0.344 Chirality : 0.042 0.198 2695 Planarity : 0.004 0.047 2857 Dihedral : 20.326 175.887 3131 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 1923 helix: 0.33 (0.21), residues: 634 sheet: -0.86 (0.28), residues: 349 loop : -1.91 (0.19), residues: 940 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.201 Fit side-chains 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: 216 average time/residue: 0.2781 time to fit residues: 94.7580 Evaluate side-chains 162 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 10.0000 chunk 186 optimal weight: 0.4980 chunk 170 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 109 optimal weight: 0.0070 chunk 79 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 180 optimal weight: 0.0980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 18011 Z= 0.176 Angle : 0.653 11.088 24750 Z= 0.336 Chirality : 0.041 0.185 2695 Planarity : 0.004 0.048 2857 Dihedral : 20.262 176.084 3131 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 1923 helix: 0.43 (0.21), residues: 636 sheet: -0.73 (0.28), residues: 345 loop : -1.84 (0.19), residues: 942 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.948 Fit side-chains 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: 215 average time/residue: 0.2776 time to fit residues: 94.7709 Evaluate side-chains 148 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 133 optimal weight: 0.6980 chunk 201 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 18011 Z= 0.205 Angle : 0.667 11.010 24750 Z= 0.342 Chirality : 0.041 0.179 2695 Planarity : 0.004 0.048 2857 Dihedral : 20.237 176.297 3131 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.78 % Favored : 94.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.19), residues: 1923 helix: 0.49 (0.21), residues: 640 sheet: -0.71 (0.28), residues: 342 loop : -1.79 (0.19), residues: 941 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.176 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: 207 average time/residue: 0.2814 time to fit residues: 93.3246 Evaluate side-chains 140 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.131 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN D 195 HIS ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.082599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056551 restraints weight = 199766.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059518 restraints weight = 78693.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060648 restraints weight = 37958.836| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 18011 Z= 0.273 Angle : 0.688 10.854 24750 Z= 0.356 Chirality : 0.042 0.190 2695 Planarity : 0.004 0.048 2857 Dihedral : 20.243 176.577 3131 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.30 % Favored : 93.60 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.18), residues: 1923 helix: 0.36 (0.20), residues: 645 sheet: -0.75 (0.28), residues: 347 loop : -1.80 (0.19), residues: 931 =============================================================================== Job complete usr+sys time: 3122.68 seconds wall clock time: 57 minutes 51.65 seconds (3471.65 seconds total)