Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 11:23:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/04_2023/6dbx_7853.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/04_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_7853/04_2023/6dbx_7853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/04_2023/6dbx_7853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/04_2023/6dbx_7853.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbx_7853/04_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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 11.33, per 1000 atoms: 0.65 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: 8.50 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" 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: 5.19 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: 7.45 Time building geometry restraints manager: 8.97 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 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.380 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 58.010 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.851 13.889 24750 Z= 0.475 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 : 1.886 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: 0.3355 time to fit residues: 174.3925 Evaluate side-chains 166 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6381 ------------------------------------------------------------------------------- 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: 0.0980 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: 4.8188 ------------------------------------------------------------------------------- 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 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 170 GLN ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 18011 Z= 0.397 Angle : 0.818 8.624 24750 Z= 0.438 Chirality : 0.047 0.213 2695 Planarity : 0.006 0.051 2857 Dihedral : 21.132 171.720 3131 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 21.46 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: -3.37 (0.17), residues: 1923 helix: -1.49 (0.18), residues: 632 sheet: -2.13 (0.25), residues: 352 loop : -2.82 (0.18), residues: 939 *********************** 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 273 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3227 time to fit residues: 129.1720 Evaluate side-chains 160 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4807 ------------------------------------------------------------------------------- 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: 20.0000 chunk 56 optimal weight: 0.0010 chunk 152 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 147 optimal weight: 7.9990 overall best weight: 2.4790 ------------------------------------------------------------------------------- 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 831 GLN C 930 GLN ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 HIS D 213 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 18011 Z= 0.244 Angle : 0.689 9.126 24750 Z= 0.372 Chirality : 0.043 0.167 2695 Planarity : 0.005 0.049 2857 Dihedral : 20.958 173.444 3131 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % 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: -2.48 (0.18), residues: 1923 helix: -0.50 (0.20), residues: 638 sheet: -1.76 (0.25), residues: 367 loop : -2.43 (0.19), residues: 918 *********************** 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 232 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3105 time to fit residues: 108.6279 Evaluate side-chains 152 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.043 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6061 ------------------------------------------------------------------------------- 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: 6.9990 chunk 138 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 96 optimal weight: 0.0770 chunk 174 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- 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 79 HIS B 100 ASN ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 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: 0.8208 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 18011 Z= 0.266 Angle : 0.686 8.295 24750 Z= 0.370 Chirality : 0.043 0.353 2695 Planarity : 0.004 0.046 2857 Dihedral : 20.836 173.834 3131 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.87 % Favored : 93.02 % 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: -2.07 (0.18), residues: 1923 helix: -0.15 (0.20), residues: 635 sheet: -1.39 (0.26), residues: 356 loop : -2.26 (0.19), residues: 932 *********************** 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 211 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 2.203 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: 0 residues processed: 211 average time/residue: 0.3091 time to fit residues: 100.7380 Evaluate side-chains 146 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.125 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6149 ------------------------------------------------------------------------------- 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: 3.9990 chunk 110 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN ** 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 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN ** 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: 0.8193 moved from start: 0.4883 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= 0.215 Angle : 0.646 8.452 24750 Z= 0.347 Chirality : 0.041 0.172 2695 Planarity : 0.004 0.046 2857 Dihedral : 20.667 174.352 3131 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 15.92 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: -1.77 (0.18), residues: 1923 helix: 0.13 (0.20), residues: 641 sheet: -1.18 (0.26), residues: 363 loop : -2.14 (0.19), residues: 919 *********************** 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 210 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.938 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: 210 average time/residue: 0.2962 time to fit residues: 96.2970 Evaluate side-chains 148 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.051 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7085 ------------------------------------------------------------------------------- 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: 1.9990 chunk 175 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN C 930 GLN ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 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: 0.8231 moved from start: 0.5172 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= 0.257 Angle : 0.662 10.763 24750 Z= 0.355 Chirality : 0.042 0.174 2695 Planarity : 0.004 0.046 2857 Dihedral : 20.548 174.743 3131 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.66 % Favored : 93.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.69 (0.19), residues: 1923 helix: 0.16 (0.20), residues: 642 sheet: -1.20 (0.27), residues: 361 loop : -2.04 (0.19), residues: 920 *********************** 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 209 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.033 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: 209 average time/residue: 0.2914 time to fit residues: 94.6012 Evaluate side-chains 144 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.040 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7228 ------------------------------------------------------------------------------- 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: 2.9990 chunk 111 optimal weight: 0.0470 chunk 142 optimal weight: 0.0040 chunk 110 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 930 GLN ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5419 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= 0.183 Angle : 0.627 8.855 24750 Z= 0.335 Chirality : 0.041 0.196 2695 Planarity : 0.004 0.047 2857 Dihedral : 20.392 175.102 3131 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.62 % Favored : 94.33 % 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: -1.46 (0.19), residues: 1923 helix: 0.33 (0.20), residues: 646 sheet: -0.96 (0.27), residues: 355 loop : -1.93 (0.19), residues: 922 *********************** 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 221 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.151 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: 221 average time/residue: 0.2879 time to fit residues: 98.5132 Evaluate side-chains 146 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5358 ------------------------------------------------------------------------------- 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: 1.9990 chunk 77 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 96 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN D 347 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 18011 Z= 0.281 Angle : 0.693 9.318 24750 Z= 0.367 Chirality : 0.042 0.188 2695 Planarity : 0.004 0.049 2857 Dihedral : 20.407 175.410 3131 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.82 % Favored : 93.08 % 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: -1.42 (0.19), residues: 1923 helix: 0.35 (0.20), residues: 642 sheet: -0.96 (0.28), residues: 352 loop : -1.89 (0.19), residues: 929 *********************** 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 202 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.094 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: 202 average time/residue: 0.2910 time to fit residues: 92.7925 Evaluate side-chains 139 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5793 ------------------------------------------------------------------------------- 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: 4.9990 chunk 186 optimal weight: 2.9990 chunk 170 optimal weight: 0.1980 chunk 181 optimal weight: 20.0000 chunk 109 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 163 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 964 HIS ** A 987 ASN ** 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 930 GLN ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN D 195 HIS ** 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: 0.8158 moved from start: 0.5830 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= 0.169 Angle : 0.645 7.900 24750 Z= 0.339 Chirality : 0.041 0.181 2695 Planarity : 0.004 0.049 2857 Dihedral : 20.303 175.571 3131 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.69 % 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: -1.20 (0.19), residues: 1923 helix: 0.59 (0.21), residues: 639 sheet: -0.77 (0.28), residues: 339 loop : -1.80 (0.19), residues: 945 *********************** 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 210 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2933 time to fit residues: 96.3498 Evaluate side-chains 147 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8027 ------------------------------------------------------------------------------- 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: 0.5980 chunk 191 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 987 ASN ** 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 930 GLN C 959 HIS C 997 ASN D 195 HIS ** 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: 0.8228 moved from start: 0.5947 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= 0.259 Angle : 0.675 8.351 24750 Z= 0.356 Chirality : 0.042 0.180 2695 Planarity : 0.004 0.048 2857 Dihedral : 20.308 175.906 3131 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.45 % Favored : 93.44 % 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: -1.19 (0.19), residues: 1923 helix: 0.56 (0.21), residues: 640 sheet: -0.74 (0.28), residues: 348 loop : -1.79 (0.19), residues: 935 ********************** 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 193 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.894 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: 193 average time/residue: 0.2961 time to fit residues: 89.7768 Evaluate side-chains 137 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6629 ------------------------------------------------------------------------------- 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: 0.0040 chunk 170 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- 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 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN C 983 ASN D 195 HIS ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.083838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058725 restraints weight = 187705.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.061861 restraints weight = 72208.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.063045 restraints weight = 32073.193| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 18011 Z= 0.207 Angle : 0.652 8.549 24750 Z= 0.343 Chirality : 0.042 0.172 2695 Planarity : 0.004 0.047 2857 Dihedral : 20.262 176.055 3131 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.69 % 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: -1.09 (0.19), residues: 1923 helix: 0.64 (0.21), residues: 639 sheet: -0.70 (0.28), residues: 356 loop : -1.73 (0.19), residues: 928 =============================================================================== Job complete usr+sys time: 3264.19 seconds wall clock time: 60 minutes 40.16 seconds (3640.16 seconds total)