Starting phenix.real_space_refine on Sat Feb 17 21:47:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/02_2024/6dbq_7847_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/02_2024/6dbq_7847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/02_2024/6dbq_7847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/02_2024/6dbq_7847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/02_2024/6dbq_7847_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbq_7847/02_2024/6dbq_7847_neut.pdb" } resolution = 4.22 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 3565 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 490": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A ARG 756": "NH1" <-> "NH2" 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 "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 GLU 199": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "C PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 999": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19956 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" 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: "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: 4972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4972 Classifications: {'peptide': 616} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1023 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "G" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1245 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1256 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2680 SG CYS A 749 57.331 83.908 33.106 1.00 74.96 S ATOM 10357 SG CYS C 749 61.990 61.912 113.881 1.00 62.00 S Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" P DA E 39 " occ=0.80 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.80 residue: pdb=" P DA E 40 " occ=0.71 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.71 residue: pdb=" P DA E 41 " occ=0.70 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.70 residue: pdb=" P DA E 42 " occ=0.48 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.48 residue: pdb=" P DC E 44 " occ=0.47 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.47 residue: pdb=" P DG F 7 " occ=0.62 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.62 residue: pdb=" P DG F 8 " occ=0.72 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.72 residue: pdb=" P DT F 9 " occ=0.66 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.66 residue: pdb=" P DT F 10 " occ=0.76 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.76 residue: pdb=" P DT F 11 " occ=0.70 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.70 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=0.76 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.76 ... (remaining 16 not shown) Time building chain proxies: 10.69, per 1000 atoms: 0.54 Number of scatterers: 19956 At special positions: 0 Unit cell: (154.75, 149.798, 134.942, 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 3565 7.00 C 11837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.93 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb=" ZN 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 " 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: 59 helices and 18 sheets defined 37.5% alpha, 23.0% beta 86 base pairs and 171 stacking pairs defined. Time for finding SS restraints: 7.64 Creating SS restraints... Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.510A pdb=" N SER A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.784A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 461 removed outlier: 3.511A pdb=" N VAL A 449 " --> pdb=" O ASP A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.605A 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 497 through 511 Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 577 through 601 removed outlier: 4.901A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.603A pdb=" N CYS A 607 " --> pdb=" O ASP A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 687 through 704 Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.680A pdb=" N ALA A 759 " --> pdb=" O THR A 755 " (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 819 through 835 Processing helix chain 'A' and resid 844 through 863 removed outlier: 3.919A pdb=" N ARG A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 894 through 912 Processing helix chain 'A' and resid 912 through 917 removed outlier: 4.024A pdb=" N ARG A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 946 removed outlier: 3.759A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.560A pdb=" N HIS A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.603A pdb=" N GLU A 984 " --> pdb=" O SER A 980 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1018 through 1025 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 419 through 442 removed outlier: 6.074A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 461 removed outlier: 4.021A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 526 removed outlier: 3.757A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN C 524 " --> pdb=" O HIS C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 529 No H-bonds generated for 'chain 'C' and resid 527 through 529' Processing helix chain 'C' and resid 577 through 600 removed outlier: 5.022A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 Proline residue: C 696 - end of helix removed outlier: 3.744A pdb=" N MET C 705 " --> pdb=" O ARG C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 757 through 762 removed outlier: 3.579A pdb=" N GLN C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 815 through 835 removed outlier: 4.226A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 Processing helix chain 'C' and resid 894 through 912 Processing helix chain 'C' and resid 912 through 917 removed outlier: 3.701A pdb=" N ARG C 916 " --> pdb=" O LYS C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 930 removed outlier: 4.048A 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 964 Processing helix chain 'C' and resid 964 through 972 Processing helix chain 'C' and resid 980 through 985 removed outlier: 3.578A pdb=" N GLU C 984 " --> pdb=" O SER C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 997 removed outlier: 4.004A pdb=" N PHE C 990 " --> pdb=" O GLY C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 4.665A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 3.513A pdb=" N GLN C1022 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C1027 " --> pdb=" O LYS C1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.659A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 612 " --> pdb=" O SER A 650 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE A 644 " --> pdb=" O PRO A 676 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 575 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.659A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 612 " --> pdb=" O SER A 650 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.275A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 55 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.364A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS B 89 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB1, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.589A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR C 727 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLU C 617 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 639 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.589A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR C 727 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLU C 617 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 639 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.498A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D 318 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 61 through 62 removed outlier: 6.774A pdb=" N SER D 61 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N CYS D 124 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.517A pdb=" N GLU D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 138 through 147 removed outlier: 6.830A pdb=" N GLY D 139 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 158 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 147 removed outlier: 6.830A pdb=" N GLY D 139 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 158 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY D 157 " --> pdb=" O GLN D 181 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLN D 181 " --> pdb=" O GLY D 157 " (cutoff:3.500A) 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 265 715 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 212 hydrogen bonds 408 hydrogen bond angles 0 basepair planarities 86 basepair parallelities 171 stacking parallelities Total time for adding SS restraints: 10.40 Time building geometry restraints manager: 10.58 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: 4309 1.33 - 1.45: 5718 1.45 - 1.57: 10198 1.57 - 1.70: 441 1.70 - 1.82: 168 Bond restraints: 20834 Sorted by residual: bond pdb=" CG GLN D 83 " pdb=" CD GLN D 83 " ideal model delta sigma weight residual 1.516 1.380 0.136 2.50e-02 1.60e+03 2.95e+01 bond pdb=" CG HIS C 817 " pdb=" CD2 HIS C 817 " ideal model delta sigma weight residual 1.354 1.409 -0.055 1.10e-02 8.26e+03 2.53e+01 bond pdb=" CG ASN B 10 " pdb=" OD1 ASN B 10 " ideal model delta sigma weight residual 1.231 1.321 -0.090 1.90e-02 2.77e+03 2.25e+01 bond pdb=" CB ILE D 234 " pdb=" CG1 ILE D 234 " ideal model delta sigma weight residual 1.530 1.444 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CB GLN A 423 " pdb=" CG GLN A 423 " ideal model delta sigma weight residual 1.520 1.398 0.122 3.00e-02 1.11e+03 1.66e+01 ... (remaining 20829 not shown) Histogram of bond angle deviations from ideal: 66.60 - 87.52: 2 87.52 - 108.44: 3073 108.44 - 129.36: 25799 129.36 - 150.29: 225 150.29 - 171.21: 2 Bond angle restraints: 29101 Sorted by residual: angle pdb=" CB ASN C 432 " pdb=" CG ASN C 432 " pdb=" ND2 ASN C 432 " ideal model delta sigma weight residual 116.40 66.60 49.80 1.50e+00 4.44e-01 1.10e+03 angle pdb=" CB ASN C 432 " pdb=" CG ASN C 432 " pdb=" OD1 ASN C 432 " ideal model delta sigma weight residual 120.80 171.21 -50.41 2.00e+00 2.50e-01 6.35e+02 angle pdb=" CG GLN A 423 " pdb=" CD GLN A 423 " pdb=" NE2 GLN A 423 " ideal model delta sigma weight residual 116.40 79.13 37.27 1.50e+00 4.44e-01 6.17e+02 angle pdb=" CG GLN A 423 " pdb=" CD GLN A 423 " pdb=" OE1 GLN A 423 " ideal model delta sigma weight residual 120.80 157.58 -36.78 2.00e+00 2.50e-01 3.38e+02 angle pdb=" OD1 ASN C 432 " pdb=" CG ASN C 432 " pdb=" ND2 ASN C 432 " ideal model delta sigma weight residual 122.60 106.78 15.82 1.00e+00 1.00e+00 2.50e+02 ... (remaining 29096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 10739 35.53 - 71.05: 1202 71.05 - 106.58: 30 106.58 - 142.10: 2 142.10 - 177.63: 5 Dihedral angle restraints: 11978 sinusoidal: 6380 harmonic: 5598 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 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" N HIS B 344 " pdb=" C HIS B 344 " pdb=" CA HIS B 344 " pdb=" CB HIS B 344 " ideal model delta harmonic sigma weight residual 122.80 109.89 12.91 0 2.50e+00 1.60e-01 2.67e+01 dihedral pdb=" CA PRO D 98 " pdb=" C PRO D 98 " pdb=" N ASN D 99 " pdb=" CA ASN D 99 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 11975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2690 0.060 - 0.120: 449 0.120 - 0.180: 41 0.180 - 0.240: 5 0.240 - 0.300: 2 Chirality restraints: 3187 Sorted by residual: chirality pdb=" CA HIS C 817 " pdb=" N HIS C 817 " pdb=" C HIS C 817 " pdb=" CB HIS C 817 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA GLN D 83 " pdb=" N GLN D 83 " pdb=" C GLN D 83 " pdb=" CB GLN D 83 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA HIS B 344 " pdb=" N HIS B 344 " pdb=" C HIS B 344 " pdb=" CB HIS B 344 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3184 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 817 " 0.149 2.00e-02 2.50e+03 1.49e-01 3.33e+02 pdb=" CG HIS C 817 " -0.313 2.00e-02 2.50e+03 pdb=" ND1 HIS C 817 " 0.088 2.00e-02 2.50e+03 pdb=" CD2 HIS C 817 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS C 817 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS C 817 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 344 " 0.085 2.00e-02 2.50e+03 1.12e-01 1.88e+02 pdb=" CG HIS B 344 " -0.237 2.00e-02 2.50e+03 pdb=" ND1 HIS B 344 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS B 344 " 0.080 2.00e-02 2.50e+03 pdb=" CE1 HIS B 344 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 344 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 10 " 0.058 2.00e-02 2.50e+03 1.18e-01 1.40e+02 pdb=" CG ASN B 10 " -0.204 2.00e-02 2.50e+03 pdb=" OD1 ASN B 10 " 0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN B 10 " 0.069 2.00e-02 2.50e+03 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 118 2.34 - 2.98: 10527 2.98 - 3.62: 32798 3.62 - 4.26: 48285 4.26 - 4.90: 72855 Nonbonded interactions: 164583 Sorted by model distance: nonbonded pdb=" NH1 ARG D 123 " pdb=" OE2 GLU D 125 " model vdw 1.700 2.520 nonbonded pdb=" OD1 ASN B 99 " pdb=" OE2 GLU B 101 " model vdw 1.806 3.040 nonbonded pdb=" NZ LYS C 435 " pdb=" OE2 GLU C 439 " model vdw 1.807 2.520 nonbonded pdb=" OE2 GLU A 789 " pdb=" NH1 ARG A 797 " model vdw 1.837 2.520 nonbonded pdb=" OG1 THR B 97 " pdb=" OE2 GLU B 101 " model vdw 1.856 2.440 ... (remaining 164578 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 628 or resid 635 through 1028 or resid 1101 th \ rough 1103)) selection = (chain 'C' and (resid 408 through 1028 or resid 1101 through 1103)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 2.750 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 67.930 Find NCS groups from input model: 1.130 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 0.136 20834 Z= 0.339 Angle : 1.053 50.410 29101 Z= 0.618 Chirality : 0.044 0.300 3187 Planarity : 0.007 0.149 2984 Dihedral : 23.407 177.626 8376 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 28.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.37 % Favored : 89.53 % Rotamer: Outliers : 0.12 % Allowed : 27.39 % Favored : 72.50 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 6.59 % 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: -4.19 (0.15), residues: 1929 helix: -2.72 (0.14), residues: 660 sheet: -1.82 (0.26), residues: 323 loop : -3.19 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 538 HIS 0.151 0.005 HIS C 817 PHE 0.023 0.003 PHE B 62 TYR 0.036 0.003 TYR D 29 ARG 0.015 0.001 ARG D 123 *********************** 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 378 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 376 time to evaluate : 1.935 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: A 477 ARG cc_start: 0.6533 (mtt-85) cc_final: 0.6297 (mpt180) REVERT: A 705 MET cc_start: 0.7386 (mmm) cc_final: 0.6833 (mtp) REVERT: B 23 ASP cc_start: 0.7779 (t0) cc_final: 0.7317 (t0) REVERT: B 39 ARG cc_start: 0.8394 (tpt-90) cc_final: 0.7873 (ttp-170) REVERT: B 270 GLU cc_start: 0.8275 (mp0) cc_final: 0.8042 (mm-30) REVERT: B 285 MET cc_start: 0.8313 (mmm) cc_final: 0.8057 (mpp) REVERT: C 466 GLN cc_start: 0.8628 (mt0) cc_final: 0.7634 (mp10) REVERT: C 617 GLU cc_start: 0.9009 (pt0) cc_final: 0.8716 (pt0) REVERT: C 691 THR cc_start: 0.9251 (p) cc_final: 0.9014 (p) REVERT: C 898 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7481 (ttm-80) REVERT: C 909 LEU cc_start: 0.9069 (mt) cc_final: 0.8699 (mt) REVERT: C 945 MET cc_start: 0.8637 (mtp) cc_final: 0.8424 (mmm) REVERT: C 1028 HIS cc_start: 0.8657 (t70) cc_final: 0.8169 (t-170) REVERT: D 1 MET cc_start: 0.6785 (pmt) cc_final: 0.6291 (pmt) REVERT: D 51 LYS cc_start: 0.8564 (mttt) cc_final: 0.8196 (mmmt) REVERT: D 86 LYS cc_start: 0.8133 (tptp) cc_final: 0.7901 (tptp) outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.3845 time to fit residues: 208.7323 Evaluate side-chains 198 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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: 20.0000 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 109 optimal weight: 0.0370 chunk 87 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 195 optimal weight: 7.9990 overall best weight: 1.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 HIS A 775 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS B 344 HIS ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS C 761 GLN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 ASN ** C 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN C1012 HIS D 33 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20834 Z= 0.239 Angle : 0.743 8.965 29101 Z= 0.408 Chirality : 0.044 0.179 3187 Planarity : 0.006 0.069 2984 Dihedral : 26.233 176.694 4566 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.36 % Rotamer: Outliers : 0.12 % Allowed : 4.18 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -2.93 (0.17), residues: 1929 helix: -1.32 (0.17), residues: 672 sheet: -1.34 (0.28), residues: 301 loop : -2.64 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 560 HIS 0.016 0.002 HIS B 237 PHE 0.018 0.002 PHE B 62 TYR 0.024 0.002 TYR D 268 ARG 0.010 0.001 ARG C 708 *********************** 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 311 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 309 time to evaluate : 1.811 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: A 477 ARG cc_start: 0.6468 (mtt-85) cc_final: 0.6230 (mpt180) REVERT: A 579 ASP cc_start: 0.9335 (p0) cc_final: 0.8791 (t70) REVERT: A 629 HIS cc_start: 0.5820 (t-90) cc_final: 0.5536 (t-90) REVERT: A 704 MET cc_start: 0.8817 (ptp) cc_final: 0.8532 (ptp) REVERT: A 738 GLU cc_start: 0.9575 (pp20) cc_final: 0.9341 (tm-30) REVERT: A 914 VAL cc_start: 0.8857 (m) cc_final: 0.8253 (p) REVERT: B 23 ASP cc_start: 0.8141 (t0) cc_final: 0.7619 (t0) REVERT: B 39 ARG cc_start: 0.8245 (tpt-90) cc_final: 0.7614 (ttp-170) REVERT: C 871 MET cc_start: 0.9164 (tmm) cc_final: 0.8943 (tmm) REVERT: C 880 MET cc_start: 0.8648 (mmp) cc_final: 0.8381 (ppp) REVERT: C 898 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7532 (ttm110) REVERT: C 945 MET cc_start: 0.8593 (mtp) cc_final: 0.8385 (mmm) REVERT: C 951 ASP cc_start: 0.9135 (p0) cc_final: 0.8928 (p0) REVERT: D 51 LYS cc_start: 0.8530 (mttt) cc_final: 0.8182 (mmmt) REVERT: D 93 HIS cc_start: 0.8324 (t70) cc_final: 0.7393 (t70) REVERT: D 187 LEU cc_start: 0.9028 (tt) cc_final: 0.8805 (tt) REVERT: D 306 GLN cc_start: 0.8772 (pm20) cc_final: 0.8447 (tp40) outliers start: 2 outliers final: 1 residues processed: 311 average time/residue: 0.3451 time to fit residues: 158.6594 Evaluate side-chains 191 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 2.092 ------------------------------------------------------------------------------- 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: 0.0870 chunk 60 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 211 optimal weight: 20.0000 chunk 174 optimal weight: 0.3980 chunk 193 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN A 817 HIS A 822 ASN A 831 GLN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS C 761 GLN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN C1012 HIS D 64 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20834 Z= 0.197 Angle : 0.674 7.886 29101 Z= 0.374 Chirality : 0.042 0.169 3187 Planarity : 0.005 0.060 2984 Dihedral : 25.998 177.779 4566 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 0.24 % Allowed : 3.18 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -2.22 (0.17), residues: 1929 helix: -0.52 (0.18), residues: 665 sheet: -1.17 (0.27), residues: 321 loop : -2.32 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 538 HIS 0.010 0.001 HIS B 237 PHE 0.017 0.002 PHE B 62 TYR 0.015 0.002 TYR C1020 ARG 0.007 0.000 ARG C 735 *********************** 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 267 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 263 time to evaluate : 2.087 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: A 477 ARG cc_start: 0.6438 (mtt-85) cc_final: 0.6136 (mpt180) REVERT: A 738 GLU cc_start: 0.9563 (pp20) cc_final: 0.9191 (tm-30) REVERT: A 911 MET cc_start: 0.9286 (ptm) cc_final: 0.8915 (mmm) REVERT: A 950 TYR cc_start: 0.7960 (m-80) cc_final: 0.7745 (m-80) REVERT: B 1 MET cc_start: 0.7151 (mmp) cc_final: 0.6203 (ppp) REVERT: B 23 ASP cc_start: 0.8091 (t0) cc_final: 0.7381 (t0) REVERT: B 33 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7669 (pp30) REVERT: B 39 ARG cc_start: 0.8245 (tpt-90) cc_final: 0.7545 (ttp-170) REVERT: B 65 ASN cc_start: 0.8810 (p0) cc_final: 0.8586 (p0) REVERT: B 202 ASP cc_start: 0.8052 (t0) cc_final: 0.7828 (m-30) REVERT: C 647 MET cc_start: 0.9206 (mmm) cc_final: 0.8935 (mmm) REVERT: C 733 MET cc_start: 0.9046 (tpp) cc_final: 0.8797 (tpp) REVERT: C 737 MET cc_start: 0.8760 (ttm) cc_final: 0.8239 (mtp) REVERT: C 898 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7567 (ttm110) REVERT: C 945 MET cc_start: 0.8630 (mtp) cc_final: 0.8106 (tmm) REVERT: C 951 ASP cc_start: 0.9174 (p0) cc_final: 0.8764 (p0) REVERT: D 51 LYS cc_start: 0.8547 (mttt) cc_final: 0.8162 (mmmt) REVERT: D 93 HIS cc_start: 0.8177 (t70) cc_final: 0.7188 (t70) outliers start: 4 outliers final: 2 residues processed: 267 average time/residue: 0.3253 time to fit residues: 132.5341 Evaluate side-chains 184 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 1.921 ------------------------------------------------------------------------------- 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: 0.0970 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 186 optimal weight: 5.9990 chunk 56 optimal weight: 0.0870 overall best weight: 2.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS A 775 ASN A 817 HIS A 822 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 535 GLN C 761 GLN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8251 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20834 Z= 0.228 Angle : 0.669 7.745 29101 Z= 0.370 Chirality : 0.041 0.212 3187 Planarity : 0.004 0.056 2984 Dihedral : 25.878 178.287 4566 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.07 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -1.82 (0.18), residues: 1929 helix: -0.09 (0.19), residues: 669 sheet: -1.01 (0.27), residues: 321 loop : -2.13 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 538 HIS 0.011 0.001 HIS D 269 PHE 0.030 0.002 PHE A 993 TYR 0.014 0.002 TYR D 268 ARG 0.024 0.001 ARG C 870 *********************** 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 232 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.032 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 477 ARG cc_start: 0.6184 (mtt-85) cc_final: 0.5921 (mpt180) REVERT: A 594 MET cc_start: 0.8657 (mmt) cc_final: 0.8403 (mmt) REVERT: A 629 HIS cc_start: 0.5633 (t70) cc_final: 0.5382 (t70) REVERT: A 704 MET cc_start: 0.8825 (ptm) cc_final: 0.8346 (ptm) REVERT: A 738 GLU cc_start: 0.9581 (pp20) cc_final: 0.9274 (tm-30) REVERT: A 911 MET cc_start: 0.9319 (ptm) cc_final: 0.9080 (mmm) REVERT: A 989 LEU cc_start: 0.9330 (mp) cc_final: 0.9119 (mm) REVERT: A 1000 GLN cc_start: 0.8824 (tp40) cc_final: 0.8067 (tp-100) REVERT: B 39 ARG cc_start: 0.8302 (tpt-90) cc_final: 0.7551 (ttp-170) REVERT: B 65 ASN cc_start: 0.8929 (p0) cc_final: 0.8705 (p0) REVERT: B 202 ASP cc_start: 0.8142 (t0) cc_final: 0.7940 (m-30) REVERT: C 898 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7361 (ttm-80) REVERT: C 945 MET cc_start: 0.8606 (mtp) cc_final: 0.8397 (mmm) REVERT: C 951 ASP cc_start: 0.9181 (p0) cc_final: 0.8769 (p0) REVERT: D 51 LYS cc_start: 0.8593 (mttt) cc_final: 0.8289 (mmmt) REVERT: D 93 HIS cc_start: 0.8182 (t70) cc_final: 0.7328 (t70) REVERT: D 341 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7994 (pp20) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3209 time to fit residues: 114.3961 Evaluate side-chains 172 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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: 20.0000 chunk 117 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 106 optimal weight: 0.8980 chunk 186 optimal weight: 0.0020 chunk 52 optimal weight: 10.0000 overall best weight: 3.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN A 817 HIS A 822 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 HIS ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 HIS ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20834 Z= 0.241 Angle : 0.667 7.849 29101 Z= 0.368 Chirality : 0.041 0.177 3187 Planarity : 0.004 0.055 2984 Dihedral : 25.786 178.278 4566 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -1.57 (0.18), residues: 1929 helix: 0.09 (0.19), residues: 661 sheet: -0.87 (0.27), residues: 332 loop : -1.96 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 307 HIS 0.010 0.001 HIS D 269 PHE 0.027 0.002 PHE A 993 TYR 0.023 0.002 TYR C 578 ARG 0.005 0.000 ARG C 735 *********************** 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 238 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.891 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 477 ARG cc_start: 0.6096 (mtt-85) cc_final: 0.5792 (mpt180) REVERT: A 594 MET cc_start: 0.8631 (mmt) cc_final: 0.8411 (mmt) REVERT: A 704 MET cc_start: 0.8837 (ptm) cc_final: 0.8426 (ptm) REVERT: A 911 MET cc_start: 0.9289 (ptm) cc_final: 0.9050 (mmm) REVERT: A 989 LEU cc_start: 0.9332 (mp) cc_final: 0.9103 (mm) REVERT: A 1000 GLN cc_start: 0.8886 (tp40) cc_final: 0.8206 (tp-100) REVERT: B 39 ARG cc_start: 0.8325 (tpt-90) cc_final: 0.7519 (ttp-170) REVERT: B 65 ASN cc_start: 0.8979 (p0) cc_final: 0.8759 (p0) REVERT: C 737 MET cc_start: 0.8801 (ttm) cc_final: 0.8594 (mtp) REVERT: C 898 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7509 (ttm-80) REVERT: C 945 MET cc_start: 0.8652 (mtp) cc_final: 0.8235 (tmm) REVERT: C 951 ASP cc_start: 0.9182 (p0) cc_final: 0.8633 (p0) REVERT: C 1017 THR cc_start: 0.9428 (m) cc_final: 0.9141 (p) REVERT: D 51 LYS cc_start: 0.8597 (mttt) cc_final: 0.8252 (mmmt) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3275 time to fit residues: 117.6717 Evaluate side-chains 168 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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: 0.7980 chunk 187 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 208 optimal weight: 30.0000 chunk 172 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 ASN ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** 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: 0.8299 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20834 Z= 0.243 Angle : 0.667 8.185 29101 Z= 0.371 Chirality : 0.041 0.182 3187 Planarity : 0.005 0.070 2984 Dihedral : 25.695 177.757 4566 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.96 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -1.49 (0.18), residues: 1929 helix: 0.07 (0.19), residues: 662 sheet: -0.84 (0.27), residues: 339 loop : -1.84 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 307 HIS 0.009 0.001 HIS D 269 PHE 0.026 0.002 PHE A 993 TYR 0.017 0.002 TYR C 504 ARG 0.010 0.001 ARG C 860 *********************** 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 225 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.004 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 477 ARG cc_start: 0.6161 (mtt-85) cc_final: 0.5757 (mpt180) REVERT: A 704 MET cc_start: 0.8851 (ptm) cc_final: 0.8410 (ptm) REVERT: A 738 GLU cc_start: 0.9525 (tp30) cc_final: 0.9291 (tp30) REVERT: A 869 MET cc_start: 0.7989 (ppp) cc_final: 0.7455 (ppp) REVERT: A 871 MET cc_start: 0.9273 (mpp) cc_final: 0.9024 (mpp) REVERT: A 911 MET cc_start: 0.9326 (ptm) cc_final: 0.9046 (mmm) REVERT: A 1000 GLN cc_start: 0.8845 (tp40) cc_final: 0.8287 (tp-100) REVERT: B 39 ARG cc_start: 0.8370 (tpt-90) cc_final: 0.7564 (ttp-170) REVERT: B 65 ASN cc_start: 0.9082 (p0) cc_final: 0.8854 (p0) REVERT: C 898 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7878 (ttm110) REVERT: C 945 MET cc_start: 0.8718 (mtp) cc_final: 0.8261 (tmm) REVERT: C 951 ASP cc_start: 0.9180 (p0) cc_final: 0.8613 (p0) REVERT: C 1017 THR cc_start: 0.9411 (m) cc_final: 0.9156 (p) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3386 time to fit residues: 116.6935 Evaluate side-chains 154 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.989 ------------------------------------------------------------------------------- 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: 5.9990 chunk 151 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 207 optimal weight: 40.0000 chunk 129 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 GLN ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8418 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 20834 Z= 0.428 Angle : 0.814 9.917 29101 Z= 0.444 Chirality : 0.044 0.209 3187 Planarity : 0.006 0.065 2984 Dihedral : 25.798 176.527 4566 Min Nonbonded Distance : 1.480 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.62 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -1.87 (0.18), residues: 1929 helix: -0.40 (0.19), residues: 670 sheet: -1.00 (0.28), residues: 331 loop : -1.96 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 782 HIS 0.014 0.002 HIS D 269 PHE 0.021 0.003 PHE A 993 TYR 0.025 0.003 TYR B 29 ARG 0.010 0.001 ARG D 39 *********************** 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 195 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.858 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: A 477 ARG cc_start: 0.6284 (mtt-85) cc_final: 0.6052 (ttt180) REVERT: A 704 MET cc_start: 0.8910 (ptm) cc_final: 0.8571 (ptm) REVERT: A 738 GLU cc_start: 0.9453 (tp30) cc_final: 0.9172 (tp30) REVERT: A 911 MET cc_start: 0.9360 (ptm) cc_final: 0.9124 (mmm) REVERT: A 950 TYR cc_start: 0.8332 (m-80) cc_final: 0.8101 (m-80) REVERT: A 989 LEU cc_start: 0.9439 (mp) cc_final: 0.9102 (mp) REVERT: A 1000 GLN cc_start: 0.8867 (tp40) cc_final: 0.8456 (tm-30) REVERT: B 65 ASN cc_start: 0.9207 (p0) cc_final: 0.8887 (p0) REVERT: B 285 MET cc_start: 0.8017 (mmm) cc_final: 0.7702 (mmp) REVERT: C 898 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8152 (ttm110) REVERT: C 945 MET cc_start: 0.8818 (mtp) cc_final: 0.8399 (tmm) REVERT: C 1017 THR cc_start: 0.9519 (m) cc_final: 0.9313 (p) REVERT: D 299 MET cc_start: 0.8783 (mpp) cc_final: 0.8478 (mpp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3174 time to fit residues: 96.8151 Evaluate side-chains 143 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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: 0.3980 chunk 82 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 102 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** 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: 0.8352 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20834 Z= 0.254 Angle : 0.696 10.485 29101 Z= 0.383 Chirality : 0.042 0.200 3187 Planarity : 0.005 0.058 2984 Dihedral : 25.728 175.701 4566 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.96 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -1.51 (0.18), residues: 1929 helix: 0.01 (0.20), residues: 655 sheet: -0.75 (0.29), residues: 299 loop : -1.81 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 782 HIS 0.009 0.001 HIS D 269 PHE 0.026 0.002 PHE C 806 TYR 0.022 0.002 TYR C 578 ARG 0.005 0.001 ARG C 735 *********************** 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 207 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.084 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 477 ARG cc_start: 0.6126 (mtt-85) cc_final: 0.5836 (ttt180) REVERT: A 704 MET cc_start: 0.8833 (ptm) cc_final: 0.8407 (ptm) REVERT: A 737 MET cc_start: 0.8227 (mtp) cc_final: 0.7746 (mtp) REVERT: A 738 GLU cc_start: 0.9400 (tp30) cc_final: 0.9149 (tp30) REVERT: A 1000 GLN cc_start: 0.8922 (tp40) cc_final: 0.8684 (tp-100) REVERT: B 39 ARG cc_start: 0.8564 (tpt-90) cc_final: 0.7689 (ttp-170) REVERT: B 65 ASN cc_start: 0.9194 (p0) cc_final: 0.8929 (p0) REVERT: B 285 MET cc_start: 0.8225 (mmm) cc_final: 0.7982 (mmm) REVERT: C 898 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7848 (ttm110) REVERT: C 945 MET cc_start: 0.9071 (mtt) cc_final: 0.8645 (tmm) REVERT: C 1013 HIS cc_start: 0.8511 (t-90) cc_final: 0.8198 (t-170) REVERT: C 1017 THR cc_start: 0.9465 (m) cc_final: 0.9131 (p) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.3347 time to fit residues: 108.2708 Evaluate side-chains 157 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.106 ------------------------------------------------------------------------------- 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: 20.0000 chunk 181 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 174 optimal weight: 0.1980 chunk 182 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 ASN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 ASN ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1012 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20834 Z= 0.194 Angle : 0.675 8.864 29101 Z= 0.371 Chirality : 0.041 0.183 3187 Planarity : 0.004 0.051 2984 Dihedral : 25.564 175.412 4566 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -1.27 (0.18), residues: 1929 helix: 0.20 (0.20), residues: 656 sheet: -0.73 (0.28), residues: 316 loop : -1.63 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 307 HIS 0.012 0.001 HIS A 964 PHE 0.024 0.002 PHE C 494 TYR 0.017 0.002 TYR C1020 ARG 0.004 0.000 ARG C 718 *********************** 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 220 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.026 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 477 ARG cc_start: 0.5982 (mtt-85) cc_final: 0.5699 (ttt180) REVERT: A 486 CYS cc_start: 0.8439 (t) cc_final: 0.8209 (t) REVERT: A 704 MET cc_start: 0.8813 (ptm) cc_final: 0.8361 (ptm) REVERT: A 738 GLU cc_start: 0.9358 (tp30) cc_final: 0.9109 (tp30) REVERT: A 967 GLU cc_start: 0.9336 (pm20) cc_final: 0.9016 (tm-30) REVERT: A 1000 GLN cc_start: 0.8967 (tp40) cc_final: 0.8560 (tp-100) REVERT: B 39 ARG cc_start: 0.8455 (tpt-90) cc_final: 0.7672 (ttp80) REVERT: B 65 ASN cc_start: 0.9150 (p0) cc_final: 0.8922 (p0) REVERT: C 590 GLU cc_start: 0.9214 (tt0) cc_final: 0.8690 (tm-30) REVERT: C 671 GLU cc_start: 0.9237 (pm20) cc_final: 0.9014 (pm20) REVERT: C 711 ILE cc_start: 0.7675 (mm) cc_final: 0.7394 (mm) REVERT: C 898 ARG cc_start: 0.8199 (ttm170) cc_final: 0.7843 (ttm110) REVERT: C 1013 HIS cc_start: 0.8414 (t-90) cc_final: 0.8080 (t-170) REVERT: C 1017 THR cc_start: 0.9401 (m) cc_final: 0.9043 (p) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.3113 time to fit residues: 105.7249 Evaluate side-chains 164 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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: 10.0000 chunk 96 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 135 optimal weight: 4.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20834 Z= 0.279 Angle : 0.705 9.943 29101 Z= 0.387 Chirality : 0.042 0.189 3187 Planarity : 0.005 0.084 2984 Dihedral : 25.544 174.412 4566 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.18), residues: 1929 helix: 0.19 (0.20), residues: 654 sheet: -0.87 (0.28), residues: 332 loop : -1.59 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 782 HIS 0.009 0.001 HIS D 269 PHE 0.020 0.002 PHE C 494 TYR 0.018 0.002 TYR C1020 ARG 0.007 0.001 ARG C 860 ********************** 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 205 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.882 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 477 ARG cc_start: 0.6112 (mtt-85) cc_final: 0.5797 (ttt180) REVERT: A 704 MET cc_start: 0.8871 (ptm) cc_final: 0.8515 (ptm) REVERT: A 738 GLU cc_start: 0.9368 (tp30) cc_final: 0.9152 (tp30) REVERT: B 65 ASN cc_start: 0.9231 (p0) cc_final: 0.8987 (p0) REVERT: C 590 GLU cc_start: 0.9197 (tt0) cc_final: 0.8643 (tm-30) REVERT: C 671 GLU cc_start: 0.9256 (pm20) cc_final: 0.9023 (pm20) REVERT: C 871 MET cc_start: 0.9231 (tmm) cc_final: 0.9003 (tmm) REVERT: C 898 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7901 (ttm110) REVERT: C 945 MET cc_start: 0.9071 (mtt) cc_final: 0.8853 (ttt) REVERT: C 1005 GLU cc_start: 0.9461 (tt0) cc_final: 0.9241 (tm-30) REVERT: C 1013 HIS cc_start: 0.8629 (t-90) cc_final: 0.8239 (t-170) REVERT: C 1017 THR cc_start: 0.9455 (m) cc_final: 0.9139 (p) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3123 time to fit residues: 100.1146 Evaluate side-chains 159 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.038 ------------------------------------------------------------------------------- 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: 10.0000 chunk 52 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 175 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** 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 = 0.3765 r_free = 0.3765 target = 0.092089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.064984 restraints weight = 84519.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066701 restraints weight = 45229.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.067747 restraints weight = 30695.228| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20834 Z= 0.237 Angle : 0.684 8.792 29101 Z= 0.376 Chirality : 0.041 0.186 3187 Planarity : 0.004 0.055 2984 Dihedral : 25.485 175.279 4566 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.17 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -1.23 (0.18), residues: 1929 helix: 0.20 (0.20), residues: 655 sheet: -0.87 (0.27), residues: 346 loop : -1.51 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 782 HIS 0.008 0.001 HIS D 269 PHE 0.024 0.002 PHE B 62 TYR 0.018 0.002 TYR C1020 ARG 0.010 0.001 ARG C 922 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3618.64 seconds wall clock time: 67 minutes 13.27 seconds (4033.27 seconds total)