Starting phenix.real_space_refine on Sat Feb 17 21:46:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/02_2024/6dbv_7851_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/02_2024/6dbv_7851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/02_2024/6dbv_7851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/02_2024/6dbv_7851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/02_2024/6dbv_7851_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbv_7851/02_2024/6dbv_7851_neut.pdb" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 222 5.49 5 S 112 5.16 5 C 11837 2.51 5 N 3567 2.21 5 O 4214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C GLU 627": "OE1" <-> "OE2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 756": "NH1" <-> "NH2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 999": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19958 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4974 Classifications: {'peptide': 616} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 591} Chain breaks: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 4999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4999 Classifications: {'peptide': 621} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 596} Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1023 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "G" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1245 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1256 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2646 SG CYS A 749 63.182 58.280 104.600 1.00 45.82 S Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" P DA E 39 " occ=0.57 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.57 residue: pdb=" P DA E 40 " occ=0.81 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.81 residue: pdb=" P DA E 41 " occ=0.63 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.63 residue: pdb=" P DA E 42 " occ=0.59 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.59 residue: pdb=" P DC E 44 " occ=0.30 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.30 residue: pdb=" P DG F 7 " occ=0.51 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.51 residue: pdb=" P DG F 8 " occ=0.47 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.47 residue: pdb=" P DT F 9 " occ=0.49 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.49 residue: pdb=" P DT F 10 " occ=0.56 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.56 residue: pdb=" P DT F 11 " occ=0.63 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.63 residue: pdb=" P DT F 12 " occ=0.74 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.74 residue: pdb=" P DT F 13 " occ=0.78 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.78 ... (remaining 16 not shown) Time building chain proxies: 10.51, per 1000 atoms: 0.53 Number of scatterers: 19958 At special positions: 0 Unit cell: (158.464, 146.084, 123.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 4 19.99 S 112 16.00 P 222 15.00 O 4214 8.00 N 3567 7.00 C 11837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.92 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 18 sheets defined 37.2% alpha, 20.7% beta 89 base pairs and 168 stacking pairs defined. Time for finding SS restraints: 7.69 Creating SS restraints... Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.614A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 460 Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.630A pdb=" N ALA A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 518 through 523 removed outlier: 4.085A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 523' Processing helix chain 'A' and resid 577 through 600 removed outlier: 5.218A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 Proline residue: A 696 - end of helix removed outlier: 3.611A pdb=" N MET A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 757 through 762 removed outlier: 4.084A pdb=" N GLN A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 815 through 835 removed outlier: 3.618A pdb=" N ASP A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 Processing helix chain 'A' and resid 872 through 879 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 894 through 912 Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.593A pdb=" N ARG A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 removed outlier: 3.888A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 947 Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 removed outlier: 3.601A pdb=" N ILE A 968 " --> pdb=" O HIS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 987 removed outlier: 3.671A pdb=" N GLU A 984 " --> pdb=" O SER A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 997 removed outlier: 3.537A pdb=" N ARG A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 995 " --> pdb=" O ARG A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 4.163A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1027 removed outlier: 3.736A pdb=" N GLN A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 419 through 441 removed outlier: 5.755A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 459 removed outlier: 3.935A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 473 Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 496 through 511 Processing helix chain 'C' and resid 518 through 527 Processing helix chain 'C' and resid 577 through 600 removed outlier: 4.992A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 686 through 703 removed outlier: 3.921A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 755 through 762 Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 799 Processing helix chain 'C' and resid 819 through 835 removed outlier: 3.516A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 863 removed outlier: 3.618A pdb=" N ARG C 848 " --> pdb=" O SER C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 880 removed outlier: 3.710A pdb=" N ALA C 876 " --> pdb=" O ASN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 889 Processing helix chain 'C' and resid 894 through 917 Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 924 through 930 removed outlier: 4.066A pdb=" N LEU C 928 " --> pdb=" O CYS C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 955 through 972 removed outlier: 3.704A pdb=" N HIS C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS C 964 " --> pdb=" O LYS C 960 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Proline residue: C 966 - end of helix Processing helix chain 'C' and resid 975 through 979 removed outlier: 3.599A pdb=" N ALA C 979 " --> pdb=" O GLY C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 998 removed outlier: 4.510A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1017 removed outlier: 4.158A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1024 Processing helix chain 'D' and resid 308 through 314 removed outlier: 3.759A pdb=" N SER D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.784A pdb=" N PHE A 611 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE A 722 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 613 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 724 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 615 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY A 726 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU A 617 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 728 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.784A pdb=" N PHE A 611 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE A 722 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 613 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 724 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 615 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY A 726 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU A 617 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 728 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 6.132A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 318 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 7.543A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.614A pdb=" N GLU B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.325A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.325A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.454A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 322 " --> pdb=" O THR D 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 80 removed outlier: 3.664A pdb=" N HIS D 93 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS D 89 " --> pdb=" O PHE D 80 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265 707 hydrogen bonds defined for protein. 1953 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 222 hydrogen bonds 436 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 168 stacking parallelities Total time for adding SS restraints: 10.61 Time building geometry restraints manager: 9.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4525 1.33 - 1.46: 5954 1.46 - 1.58: 9749 1.58 - 1.71: 440 1.71 - 1.83: 168 Bond restraints: 20836 Sorted by residual: bond pdb=" CA PRO D 179 " pdb=" C PRO D 179 " ideal model delta sigma weight residual 1.514 1.496 0.019 5.50e-03 3.31e+04 1.17e+01 bond pdb=" CA ASN C 492 " pdb=" C ASN C 492 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.34e-02 5.57e+03 8.95e+00 bond pdb=" C3' DC G 55 " pdb=" O3' DC G 55 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.67e+00 bond pdb=" C THR D 97 " pdb=" N PRO D 98 " ideal model delta sigma weight residual 1.336 1.352 -0.017 1.08e-02 8.57e+03 2.36e+00 bond pdb=" CA GLN C 514 " pdb=" CB GLN C 514 " ideal model delta sigma weight residual 1.526 1.503 0.023 1.53e-02 4.27e+03 2.33e+00 ... (remaining 20831 not shown) Histogram of bond angle deviations from ideal: 97.93 - 106.46: 1871 106.46 - 114.98: 12255 114.98 - 123.50: 13404 123.50 - 132.02: 1498 132.02 - 140.55: 76 Bond angle restraints: 29104 Sorted by residual: angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CA PRO D 340 " ideal model delta sigma weight residual 127.00 140.55 -13.55 2.40e+00 1.74e-01 3.19e+01 angle pdb=" O4' DG F 34 " pdb=" C1' DG F 34 " pdb=" N9 DG F 34 " ideal model delta sigma weight residual 108.40 115.95 -7.55 1.50e+00 4.44e-01 2.53e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CD PRO D 340 " ideal model delta sigma weight residual 120.60 109.58 11.02 2.20e+00 2.07e-01 2.51e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 127.00 138.18 -11.18 2.40e+00 1.74e-01 2.17e+01 angle pdb=" C GLY B 131 " pdb=" N ASP B 132 " pdb=" CA ASP B 132 " ideal model delta sigma weight residual 121.70 129.04 -7.34 1.80e+00 3.09e-01 1.66e+01 ... (remaining 29099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 10840 35.45 - 70.89: 1103 70.89 - 106.34: 28 106.34 - 141.78: 3 141.78 - 177.23: 5 Dihedral angle restraints: 11979 sinusoidal: 6381 harmonic: 5598 Sorted by residual: dihedral pdb=" CA GLY A 512 " pdb=" C GLY A 512 " pdb=" N ARG A 513 " pdb=" CA ARG A 513 " ideal model delta harmonic sigma weight residual 180.00 141.74 38.26 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" CA SER C 511 " pdb=" C SER C 511 " pdb=" N GLY C 512 " pdb=" CA GLY C 512 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA PHE A 576 " pdb=" C PHE A 576 " pdb=" N ARG A 577 " pdb=" CA ARG A 577 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2808 0.074 - 0.148: 365 0.148 - 0.222: 11 0.222 - 0.297: 1 0.297 - 0.371: 2 Chirality restraints: 3187 Sorted by residual: chirality pdb=" CA GLN C1000 " pdb=" N GLN C1000 " pdb=" C GLN C1000 " pdb=" CB GLN C1000 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C1' DG F 34 " pdb=" O4' DG F 34 " pdb=" C2' DG F 34 " pdb=" N9 DG F 34 " both_signs ideal model delta sigma weight residual False 2.42 2.12 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE B 311 " pdb=" CA ILE B 311 " pdb=" CG1 ILE B 311 " pdb=" CG2 ILE B 311 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3184 not shown) Planarity restraints: 2985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG F 34 " -0.047 2.00e-02 2.50e+03 2.08e-02 1.30e+01 pdb=" N9 DG F 34 " 0.052 2.00e-02 2.50e+03 pdb=" C8 DG F 34 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG F 34 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG F 34 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG F 34 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG F 34 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG F 34 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG F 34 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG F 34 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG F 34 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG F 34 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 338 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO D 339 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 339 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 339 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC F 28 " 0.030 2.00e-02 2.50e+03 1.63e-02 5.98e+00 pdb=" N1 DC F 28 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DC F 28 " -0.022 2.00e-02 2.50e+03 pdb=" O2 DC F 28 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC F 28 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DC F 28 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC F 28 " 0.017 2.00e-02 2.50e+03 pdb=" C5 DC F 28 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC F 28 " -0.002 2.00e-02 2.50e+03 ... (remaining 2982 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 11 2.01 - 2.74: 1953 2.74 - 3.46: 29727 3.46 - 4.18: 50931 4.18 - 4.90: 78523 Nonbonded interactions: 161145 Sorted by model distance: nonbonded pdb=" NH2 ARG C 675 " pdb=" CH2 TRP C1014 " model vdw 1.293 3.420 nonbonded pdb=" NH2 ARG C 675 " pdb=" CZ2 TRP C1014 " model vdw 1.582 3.420 nonbonded pdb=" NH2 ARG C 505 " pdb=" OP2 DT F 25 " model vdw 1.709 2.520 nonbonded pdb=" NH1 ARG A 523 " pdb=" OP2 DG G 24 " model vdw 1.808 2.520 nonbonded pdb=" OE2 GLU C 789 " pdb=" NH1 ARG C 797 " model vdw 1.894 2.520 ... (remaining 161140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 408 through 464 or resid 466 through 1028 or resid 1101 th \ rough 1103)) selection = (chain 'C' and (resid 408 through 464 or resid 466 through 628 or resid 635 thro \ ugh 1028 or resid 1101 through 1103)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.650 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 66.120 Find NCS groups from input model: 1.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20836 Z= 0.355 Angle : 0.851 16.412 29104 Z= 0.473 Chirality : 0.048 0.371 3187 Planarity : 0.005 0.066 2985 Dihedral : 22.585 177.231 8377 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.78 % Favored : 89.06 % Rotamer: Outliers : 0.06 % Allowed : 24.73 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.15), residues: 1929 helix: -2.87 (0.15), residues: 645 sheet: -1.48 (0.26), residues: 335 loop : -3.38 (0.16), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1014 HIS 0.011 0.002 HIS A 959 PHE 0.022 0.003 PHE A 724 TYR 0.028 0.003 TYR B 343 ARG 0.012 0.001 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 GLN cc_start: 0.8131 (mt0) cc_final: 0.7803 (tp40) REVERT: A 517 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8639 (mp10) REVERT: A 524 ASN cc_start: 0.8004 (p0) cc_final: 0.7681 (p0) REVERT: A 670 SER cc_start: 0.8365 (m) cc_final: 0.7404 (m) REVERT: A 704 MET cc_start: 0.6820 (tpp) cc_final: 0.6617 (tpp) REVERT: A 740 LEU cc_start: 0.8376 (mt) cc_final: 0.8061 (mt) REVERT: A 806 PHE cc_start: 0.8551 (p90) cc_final: 0.8300 (p90) REVERT: C 429 ASP cc_start: 0.7901 (m-30) cc_final: 0.7344 (p0) REVERT: C 479 PHE cc_start: 0.7864 (t80) cc_final: 0.7016 (m-80) REVERT: C 604 ASP cc_start: 0.6865 (m-30) cc_final: 0.6545 (p0) REVERT: C 680 MET cc_start: 0.7856 (mtm) cc_final: 0.7590 (mtm) REVERT: C 731 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8390 (tm-30) REVERT: C 869 MET cc_start: 0.8080 (pp-130) cc_final: 0.7742 (ppp) REVERT: C 951 ASP cc_start: 0.7999 (p0) cc_final: 0.7224 (p0) REVERT: D 129 LEU cc_start: 0.7924 (mt) cc_final: 0.7710 (pt) outliers start: 1 outliers final: 1 residues processed: 381 average time/residue: 0.3770 time to fit residues: 206.5168 Evaluate side-chains 199 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 0.0030 chunk 168 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 ASN A 937 GLN B 222 HIS ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 HIS ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 GLN ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN C1012 HIS C1028 HIS ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 20836 Z= 0.244 Angle : 0.735 11.010 29104 Z= 0.398 Chirality : 0.044 0.205 3187 Planarity : 0.005 0.059 2985 Dihedral : 25.790 177.585 4567 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 0.12 % Allowed : 3.59 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.17), residues: 1929 helix: -1.03 (0.19), residues: 648 sheet: -1.20 (0.27), residues: 344 loop : -2.80 (0.17), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C1014 HIS 0.014 0.002 HIS B 237 PHE 0.016 0.002 PHE B 46 TYR 0.013 0.002 TYR B 90 ARG 0.005 0.001 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 1.916 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: A 517 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8296 (mp10) REVERT: A 594 MET cc_start: 0.8371 (mmt) cc_final: 0.8164 (mmt) REVERT: A 883 GLU cc_start: 0.9119 (pm20) cc_final: 0.8848 (pm20) REVERT: C 429 ASP cc_start: 0.7798 (m-30) cc_final: 0.7486 (p0) REVERT: C 473 MET cc_start: 0.8056 (ttp) cc_final: 0.7776 (ttt) REVERT: C 479 PHE cc_start: 0.7852 (t80) cc_final: 0.6653 (m-80) REVERT: C 700 GLU cc_start: 0.8872 (pt0) cc_final: 0.8597 (mt-10) REVERT: C 737 MET cc_start: 0.6824 (ttm) cc_final: 0.5980 (ttm) REVERT: C 951 ASP cc_start: 0.7788 (p0) cc_final: 0.7286 (p0) REVERT: D 227 ASP cc_start: 0.8706 (m-30) cc_final: 0.8249 (m-30) REVERT: D 241 LEU cc_start: 0.7527 (mm) cc_final: 0.7098 (tt) outliers start: 2 outliers final: 0 residues processed: 285 average time/residue: 0.3528 time to fit residues: 148.0123 Evaluate side-chains 167 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 195 optimal weight: 10.0000 chunk 211 optimal weight: 30.0000 chunk 174 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS B 16 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 GLN C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20836 Z= 0.197 Angle : 0.665 8.406 29104 Z= 0.363 Chirality : 0.041 0.174 3187 Planarity : 0.005 0.048 2985 Dihedral : 25.619 178.619 4567 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.64 % Favored : 93.26 % Rotamer: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.18), residues: 1929 helix: -0.23 (0.20), residues: 649 sheet: -0.79 (0.27), residues: 340 loop : -2.37 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 915 HIS 0.009 0.001 HIS B 237 PHE 0.015 0.001 PHE D 19 TYR 0.025 0.002 TYR A 578 ARG 0.009 0.001 ARG A 778 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 2.196 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: A 590 GLU cc_start: 0.8449 (tt0) cc_final: 0.8246 (tt0) REVERT: A 773 ASP cc_start: 0.8720 (p0) cc_final: 0.8298 (p0) REVERT: C 429 ASP cc_start: 0.7819 (m-30) cc_final: 0.7584 (p0) REVERT: C 474 MET cc_start: 0.5788 (mmm) cc_final: 0.5565 (mmm) REVERT: C 479 PHE cc_start: 0.7691 (t80) cc_final: 0.6564 (m-80) REVERT: C 486 CYS cc_start: 0.8703 (t) cc_final: 0.8462 (t) REVERT: C 680 MET cc_start: 0.7855 (mtm) cc_final: 0.7595 (mtm) REVERT: C 700 GLU cc_start: 0.8865 (pt0) cc_final: 0.8457 (mt-10) REVERT: C 731 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8399 (tm-30) REVERT: C 737 MET cc_start: 0.6647 (ttm) cc_final: 0.6399 (ttm) REVERT: C 869 MET cc_start: 0.8105 (ppp) cc_final: 0.7742 (ppp) REVERT: C 951 ASP cc_start: 0.7764 (p0) cc_final: 0.7267 (p0) REVERT: D 155 LEU cc_start: 0.8179 (tt) cc_final: 0.7620 (mm) REVERT: D 227 ASP cc_start: 0.8673 (m-30) cc_final: 0.8261 (m-30) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.3554 time to fit residues: 130.4918 Evaluate side-chains 168 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 10.0000 chunk 147 optimal weight: 0.7980 chunk 101 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 131 optimal weight: 0.0370 chunk 196 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 102 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 overall best weight: 3.3664 ------------------------------------------------------------------------------- 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 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 20836 Z= 0.253 Angle : 0.675 9.819 29104 Z= 0.366 Chirality : 0.041 0.198 3187 Planarity : 0.005 0.094 2985 Dihedral : 25.494 178.353 4567 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.69 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 1929 helix: 0.01 (0.20), residues: 658 sheet: -0.83 (0.27), residues: 328 loop : -2.13 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1014 HIS 0.008 0.001 HIS B 237 PHE 0.017 0.002 PHE C 938 TYR 0.020 0.002 TYR A 578 ARG 0.016 0.001 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.040 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: A 606 MET cc_start: 0.6773 (ppp) cc_final: 0.6305 (ppp) REVERT: B 285 MET cc_start: 0.8150 (tpt) cc_final: 0.7897 (tpp) REVERT: C 429 ASP cc_start: 0.7824 (m-30) cc_final: 0.7526 (p0) REVERT: C 479 PHE cc_start: 0.7676 (t80) cc_final: 0.6757 (m-80) REVERT: C 688 GLU cc_start: 0.8589 (pm20) cc_final: 0.8324 (mp0) REVERT: C 951 ASP cc_start: 0.7774 (p0) cc_final: 0.7200 (p0) REVERT: D 241 LEU cc_start: 0.7760 (mm) cc_final: 0.7260 (tp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3124 time to fit residues: 112.6181 Evaluate side-chains 154 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 3 optimal weight: 50.0000 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 177 optimal weight: 0.0770 chunk 143 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 106 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20836 Z= 0.237 Angle : 0.657 11.932 29104 Z= 0.357 Chirality : 0.040 0.168 3187 Planarity : 0.005 0.094 2985 Dihedral : 25.400 177.045 4567 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.84 % Favored : 93.05 % Rotamer: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 1929 helix: 0.20 (0.20), residues: 658 sheet: -0.73 (0.28), residues: 328 loop : -2.02 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 317 HIS 0.009 0.001 HIS B 237 PHE 0.016 0.002 PHE C 806 TYR 0.023 0.002 TYR A 578 ARG 0.006 0.001 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 2.101 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: A 523 ARG cc_start: 0.8705 (mmp80) cc_final: 0.8427 (mmp80) REVERT: A 526 GLU cc_start: 0.9148 (pm20) cc_final: 0.8459 (pm20) REVERT: A 606 MET cc_start: 0.7199 (ppp) cc_final: 0.6675 (ppp) REVERT: A 704 MET cc_start: 0.7013 (mmm) cc_final: 0.6793 (tpt) REVERT: B 285 MET cc_start: 0.8269 (tpt) cc_final: 0.8035 (mmt) REVERT: C 479 PHE cc_start: 0.7575 (t80) cc_final: 0.6664 (m-80) REVERT: C 705 MET cc_start: 0.8687 (mmm) cc_final: 0.8469 (mpp) REVERT: C 733 MET cc_start: 0.8266 (tpp) cc_final: 0.7376 (tpp) REVERT: C 951 ASP cc_start: 0.7835 (p0) cc_final: 0.7293 (p0) REVERT: D 155 LEU cc_start: 0.8528 (tt) cc_final: 0.8002 (mm) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.3001 time to fit residues: 105.6074 Evaluate side-chains 158 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 208 optimal weight: 30.0000 chunk 172 optimal weight: 6.9990 chunk 96 optimal weight: 50.0000 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 20836 Z= 0.316 Angle : 0.702 13.477 29104 Z= 0.380 Chirality : 0.041 0.242 3187 Planarity : 0.005 0.083 2985 Dihedral : 25.437 175.026 4567 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.52 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.18), residues: 1929 helix: 0.16 (0.20), residues: 658 sheet: -0.77 (0.28), residues: 322 loop : -1.96 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 915 HIS 0.006 0.001 HIS B 207 PHE 0.017 0.002 PHE C 681 TYR 0.019 0.002 TYR A 578 ARG 0.008 0.001 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.075 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: A 517 GLN cc_start: 0.8691 (mm110) cc_final: 0.8397 (mm110) REVERT: A 523 ARG cc_start: 0.8727 (mmp80) cc_final: 0.8426 (mmp80) REVERT: A 524 ASN cc_start: 0.8528 (t0) cc_final: 0.8251 (t0) REVERT: A 526 GLU cc_start: 0.9217 (pm20) cc_final: 0.8917 (pm20) REVERT: A 606 MET cc_start: 0.7364 (ppp) cc_final: 0.6776 (ppp) REVERT: B 253 HIS cc_start: 0.7670 (t70) cc_final: 0.7440 (t70) REVERT: B 285 MET cc_start: 0.8236 (tpt) cc_final: 0.7964 (mmt) REVERT: C 474 MET cc_start: 0.5676 (mmm) cc_final: 0.5065 (mmm) REVERT: C 479 PHE cc_start: 0.7536 (t80) cc_final: 0.6407 (m-80) REVERT: D 155 LEU cc_start: 0.8529 (tt) cc_final: 0.8048 (mm) REVERT: D 241 LEU cc_start: 0.7902 (mm) cc_final: 0.7403 (tp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3046 time to fit residues: 93.7734 Evaluate side-chains 147 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 207 optimal weight: 30.0000 chunk 129 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20836 Z= 0.220 Angle : 0.665 12.417 29104 Z= 0.360 Chirality : 0.040 0.176 3187 Planarity : 0.005 0.106 2985 Dihedral : 25.378 175.980 4567 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.38 % Favored : 93.52 % Rotamer: Outliers : 0.06 % Allowed : 1.77 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 1929 helix: 0.31 (0.20), residues: 656 sheet: -0.67 (0.29), residues: 312 loop : -1.85 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 915 HIS 0.007 0.001 HIS C 520 PHE 0.023 0.001 PHE D 62 TYR 0.025 0.002 TYR A 578 ARG 0.014 0.000 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 2.059 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: A 523 ARG cc_start: 0.8503 (mmp80) cc_final: 0.8159 (mmp80) REVERT: A 524 ASN cc_start: 0.8542 (t0) cc_final: 0.8207 (t0) REVERT: A 526 GLU cc_start: 0.9080 (pm20) cc_final: 0.8492 (pm20) REVERT: A 606 MET cc_start: 0.7284 (ppp) cc_final: 0.6680 (ppp) REVERT: A 773 ASP cc_start: 0.9008 (p0) cc_final: 0.8462 (p0) REVERT: B 200 LEU cc_start: 0.9096 (mm) cc_final: 0.8635 (mm) REVERT: B 253 HIS cc_start: 0.7560 (t70) cc_final: 0.7316 (t70) REVERT: B 285 MET cc_start: 0.8286 (tpt) cc_final: 0.7986 (tpp) REVERT: C 474 MET cc_start: 0.5537 (mmm) cc_final: 0.5116 (mmm) REVERT: C 479 PHE cc_start: 0.7484 (t80) cc_final: 0.6310 (m-80) REVERT: C 700 GLU cc_start: 0.8847 (pm20) cc_final: 0.8633 (mp0) REVERT: C 705 MET cc_start: 0.8656 (mmm) cc_final: 0.8420 (mpp) REVERT: C 945 MET cc_start: 0.8322 (mmm) cc_final: 0.8087 (mmm) REVERT: D 155 LEU cc_start: 0.8541 (tt) cc_final: 0.7992 (mm) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.3122 time to fit residues: 106.9458 Evaluate side-chains 159 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 131 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20836 Z= 0.199 Angle : 0.658 11.598 29104 Z= 0.356 Chirality : 0.040 0.180 3187 Planarity : 0.005 0.068 2985 Dihedral : 25.294 176.976 4567 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.19), residues: 1929 helix: 0.46 (0.20), residues: 658 sheet: -0.63 (0.29), residues: 318 loop : -1.74 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 915 HIS 0.004 0.001 HIS C 520 PHE 0.014 0.001 PHE C 681 TYR 0.028 0.001 TYR C1020 ARG 0.005 0.000 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.933 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: A 517 GLN cc_start: 0.8717 (mm110) cc_final: 0.8494 (mm-40) REVERT: A 523 ARG cc_start: 0.8637 (mmp80) cc_final: 0.8347 (mmp80) REVERT: A 526 GLU cc_start: 0.9002 (pm20) cc_final: 0.8559 (pm20) REVERT: A 606 MET cc_start: 0.7253 (ppp) cc_final: 0.6605 (ppp) REVERT: A 688 GLU cc_start: 0.8783 (pm20) cc_final: 0.8571 (pm20) REVERT: B 200 LEU cc_start: 0.8937 (mm) cc_final: 0.8573 (mm) REVERT: B 285 MET cc_start: 0.8311 (tpt) cc_final: 0.7984 (tpp) REVERT: C 473 MET cc_start: 0.7603 (ttt) cc_final: 0.7231 (ttt) REVERT: C 479 PHE cc_start: 0.7350 (t80) cc_final: 0.6286 (m-80) REVERT: C 503 MET cc_start: 0.7874 (ppp) cc_final: 0.7507 (tmm) REVERT: C 557 LEU cc_start: 0.8631 (mp) cc_final: 0.8415 (mt) REVERT: C 594 MET cc_start: 0.8260 (mtt) cc_final: 0.7977 (mtt) REVERT: C 945 MET cc_start: 0.8324 (mmm) cc_final: 0.8072 (mmm) REVERT: D 155 LEU cc_start: 0.8538 (tt) cc_final: 0.7942 (mm) REVERT: D 241 LEU cc_start: 0.7922 (mm) cc_final: 0.7410 (tp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2989 time to fit residues: 104.1028 Evaluate side-chains 158 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 40.0000 chunk 181 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 174 optimal weight: 0.4980 chunk 182 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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 524 ASN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 20836 Z= 0.322 Angle : 0.721 14.595 29104 Z= 0.387 Chirality : 0.041 0.161 3187 Planarity : 0.005 0.102 2985 Dihedral : 25.334 177.823 4567 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 0.06 % Allowed : 1.00 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 1929 helix: 0.24 (0.20), residues: 657 sheet: -0.75 (0.28), residues: 312 loop : -1.74 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 915 HIS 0.006 0.001 HIS C 520 PHE 0.019 0.002 PHE A 993 TYR 0.023 0.002 TYR C1020 ARG 0.010 0.001 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.992 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: A 517 GLN cc_start: 0.8883 (mm110) cc_final: 0.8336 (mp10) REVERT: A 523 ARG cc_start: 0.8676 (mmp80) cc_final: 0.8457 (mmp80) REVERT: A 524 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8190 (t0) REVERT: A 526 GLU cc_start: 0.9140 (pm20) cc_final: 0.8728 (pm20) REVERT: A 606 MET cc_start: 0.7481 (ppp) cc_final: 0.7255 (ppp) REVERT: B 200 LEU cc_start: 0.9006 (mm) cc_final: 0.8627 (mm) REVERT: B 285 MET cc_start: 0.8314 (tpt) cc_final: 0.7987 (tpp) REVERT: C 473 MET cc_start: 0.7583 (ttt) cc_final: 0.7060 (ttt) REVERT: C 474 MET cc_start: 0.5571 (mmm) cc_final: 0.4823 (mmm) REVERT: C 479 PHE cc_start: 0.7347 (t80) cc_final: 0.6329 (m-80) REVERT: C 594 MET cc_start: 0.8261 (mtt) cc_final: 0.8050 (mtt) REVERT: C 945 MET cc_start: 0.8445 (mmm) cc_final: 0.8188 (mmm) REVERT: D 223 ILE cc_start: 0.8919 (mt) cc_final: 0.8614 (tt) REVERT: D 241 LEU cc_start: 0.7963 (mm) cc_final: 0.7728 (mm) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.3088 time to fit residues: 95.9633 Evaluate side-chains 141 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 10.0000 chunk 124 optimal weight: 0.2980 chunk 96 optimal weight: 40.0000 chunk 141 optimal weight: 0.3980 chunk 214 optimal weight: 10.0000 chunk 197 optimal weight: 30.0000 chunk 170 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20836 Z= 0.186 Angle : 0.669 11.246 29104 Z= 0.359 Chirality : 0.041 0.169 3187 Planarity : 0.004 0.062 2985 Dihedral : 25.235 178.918 4567 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.19), residues: 1929 helix: 0.49 (0.20), residues: 653 sheet: -0.53 (0.29), residues: 321 loop : -1.67 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 915 HIS 0.006 0.001 HIS C 687 PHE 0.017 0.002 PHE B 274 TYR 0.031 0.002 TYR C1020 ARG 0.006 0.000 ARG C 870 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.937 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: A 517 GLN cc_start: 0.8748 (mm110) cc_final: 0.8377 (mp10) REVERT: A 523 ARG cc_start: 0.8715 (mmp80) cc_final: 0.8387 (mmp80) REVERT: A 526 GLU cc_start: 0.8989 (pm20) cc_final: 0.8506 (pm20) REVERT: A 606 MET cc_start: 0.7569 (ppp) cc_final: 0.6863 (ppp) REVERT: A 883 GLU cc_start: 0.9106 (pm20) cc_final: 0.8881 (pm20) REVERT: B 285 MET cc_start: 0.8284 (tpt) cc_final: 0.7955 (tpp) REVERT: C 473 MET cc_start: 0.7438 (ttt) cc_final: 0.6933 (ttt) REVERT: C 474 MET cc_start: 0.5541 (mmm) cc_final: 0.4870 (mmm) REVERT: C 479 PHE cc_start: 0.7253 (t80) cc_final: 0.6206 (m-80) REVERT: C 503 MET cc_start: 0.7960 (ppp) cc_final: 0.7563 (tmm) REVERT: C 594 MET cc_start: 0.8220 (mtt) cc_final: 0.8007 (mtt) REVERT: C 705 MET cc_start: 0.8349 (mmm) cc_final: 0.7877 (mpp) REVERT: D 155 LEU cc_start: 0.8469 (tt) cc_final: 0.8006 (mm) REVERT: D 223 ILE cc_start: 0.8822 (mt) cc_final: 0.8479 (tt) REVERT: D 241 LEU cc_start: 0.7916 (mm) cc_final: 0.7429 (tp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3033 time to fit residues: 97.1138 Evaluate side-chains 150 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.082212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.058788 restraints weight = 94270.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.060335 restraints weight = 53229.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061306 restraints weight = 36939.812| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20836 Z= 0.199 Angle : 0.657 11.435 29104 Z= 0.353 Chirality : 0.040 0.174 3187 Planarity : 0.004 0.063 2985 Dihedral : 25.156 178.709 4567 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.65 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1929 helix: 0.59 (0.20), residues: 657 sheet: -0.54 (0.29), residues: 325 loop : -1.64 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 915 HIS 0.004 0.001 HIS B 237 PHE 0.021 0.001 PHE A 681 TYR 0.024 0.001 TYR C1020 ARG 0.006 0.000 ARG A 505 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3468.13 seconds wall clock time: 64 minutes 46.45 seconds (3886.45 seconds total)