Starting phenix.real_space_refine on Thu Aug 6 01:10:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t3t_41011/08_2026/8t3t_41011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3t_41011/08_2026/8t3t_41011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8t3t_41011/08_2026/8t3t_41011.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t3t_41011/08_2026/8t3t_41011.cif" model { file = "/net/cci-nas-00/data/ceres_data/8t3t_41011/08_2026/8t3t_41011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3t_41011/08_2026/8t3t_41011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t3t_41011/08_2026/8t3t_41011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3t_41011/08_2026/8t3t_41011.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.015 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 292 5.49 5 S 32 5.16 5 C 7243 2.51 5 N 2423 2.21 5 O 2997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12991 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "L" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12156 SG CYS K 663 99.375 75.126 80.380 1.00227.89 S ATOM 12315 SG CYS K 683 101.649 76.294 83.194 1.00249.62 S ATOM 12335 SG CYS K 686 98.552 74.224 84.036 1.00253.88 S ATOM 12039 SG CYS K 648 105.375 86.157 77.237 1.00280.67 S ATOM 12059 SG CYS K 651 107.516 88.976 76.374 1.00289.30 S ATOM 12194 SG CYS K 668 108.042 85.897 74.379 1.00267.32 S ATOM 12217 SG CYS K 671 109.223 85.686 77.834 1.00266.56 S ATOM 12699 SG CYS L 663 95.659 76.176 60.519 1.00160.31 S ATOM 12858 SG CYS L 683 92.975 77.494 58.092 1.00136.58 S ATOM 12878 SG CYS L 686 96.246 76.198 56.724 1.00148.23 S ATOM 12582 SG CYS L 648 85.727 83.231 65.188 1.00193.20 S ATOM 12602 SG CYS L 651 82.289 84.005 66.644 1.00193.10 S ATOM 12737 SG CYS L 668 83.899 80.805 67.477 1.00167.52 S ATOM 12760 SG CYS L 671 82.719 80.984 64.086 1.00156.96 S Time building chain proxies: 2.57, per 1000 atoms: 0.20 Number of scatterers: 12991 At special positions: 0 Unit cell: (129.96, 119.7, 117.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 32 16.00 P 292 15.00 O 2997 8.00 N 2423 7.00 C 7243 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 - 3.00 Amino acid : True - 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: 0.71 Conformation dependent library (CDL) restraints added in 353.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" ND1 HIS K 665 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 683 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 686 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 663 " pdb=" ZN K 802 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 668 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 651 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 648 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 671 " pdb=" ZN L 801 " pdb="ZN ZN L 801 " - pdb=" ND1 HIS L 665 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 683 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 686 " pdb="ZN ZN L 801 " - pdb=" SG CYS L 663 " pdb=" ZN L 802 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 668 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 651 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 648 " pdb="ZN ZN L 802 " - pdb=" SG CYS L 671 " Number of angles added : 18 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 66.7% alpha, 3.6% beta 133 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.684A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.574A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.786A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.940A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.816A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.887A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.581A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.607A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.509A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.834A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.781A pdb=" N SER D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.758A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.594A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.750A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.598A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.927A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.530A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.514A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.856A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.703A pdb=" N GLU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA H 77 " --> pdb=" O ILE H 73 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.608A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.756A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 633 through 647 Processing helix chain 'K' and resid 668 through 678 removed outlier: 3.893A pdb=" N CYS K 672 " --> pdb=" O CYS K 668 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS K 673 " --> pdb=" O GLU K 669 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU K 674 " --> pdb=" O ASN K 670 " (cutoff:3.500A) Processing helix chain 'L' and resid 633 through 647 removed outlier: 3.592A pdb=" N TYR L 647 " --> pdb=" O ARG L 643 " (cutoff:3.500A) Processing helix chain 'L' and resid 668 through 677 removed outlier: 3.654A pdb=" N GLU L 674 " --> pdb=" O ASN L 670 " (cutoff:3.500A) Processing helix chain 'L' and resid 691 through 693 No H-bonds generated for 'chain 'L' and resid 691 through 693' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.523A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.673A pdb=" N THR G 101 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.250A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.891A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.021A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.580A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.136A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 666 through 667 Processing sheet with id=AB3, first strand: chain 'L' and resid 666 through 667 364 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 342 hydrogen bonds 684 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3057 1.34 - 1.46: 4223 1.46 - 1.58: 5903 1.58 - 1.70: 582 1.70 - 1.82: 46 Bond restraints: 13811 Sorted by residual: bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DC I 53 " pdb=" C2' DC I 53 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.43e+00 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.12e+00 bond pdb=" C3' DC J 126 " pdb=" C2' DC J 126 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.51e+00 bond pdb=" C3' DC I 96 " pdb=" C2' DC I 96 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.27e+00 ... (remaining 13806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 19013 1.82 - 3.64: 858 3.64 - 5.45: 27 5.45 - 7.27: 5 7.27 - 9.09: 2 Bond angle restraints: 19905 Sorted by residual: angle pdb=" O4' DG J 56 " pdb=" C4' DG J 56 " pdb=" C3' DG J 56 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" O4' DT I 89 " pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 19900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.18: 5811 30.18 - 60.35: 1716 60.35 - 90.53: 35 90.53 - 120.70: 0 120.70 - 150.88: 3 Dihedral angle restraints: 7565 sinusoidal: 4988 harmonic: 2577 Sorted by residual: dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 69.12 150.88 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA CYS L 686 " pdb=" C CYS L 686 " pdb=" N ASN L 687 " pdb=" CA ASN L 687 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 2.57 -142.57 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 7562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1441 0.037 - 0.074: 621 0.074 - 0.111: 179 0.111 - 0.148: 30 0.148 - 0.185: 2 Chirality restraints: 2273 Sorted by residual: chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA ASP E 77 " pdb=" N ASP E 77 " pdb=" C ASP E 77 " pdb=" CB ASP E 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2270 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 694 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASP K 694 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP K 694 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU K 695 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 117 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ALA D 117 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA D 117 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL D 118 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU L 669 " 0.009 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" CD GLU L 669 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU L 669 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU L 669 " 0.012 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1146 2.74 - 3.28: 11111 3.28 - 3.82: 22524 3.82 - 4.36: 27629 4.36 - 4.90: 40823 Nonbonded interactions: 103233 Sorted by model distance: nonbonded pdb=" N4 DC I 11 " pdb=" N2 DG J 137 " model vdw 2.202 3.200 nonbonded pdb=" OG1 THR A 80 " pdb=" OD1 ASP A 81 " model vdw 2.229 3.040 nonbonded pdb=" O TYR K 647 " pdb=" NZ LYS K 656 " model vdw 2.254 3.120 nonbonded pdb=" N LYS K 661 " pdb=" OD1 ASP K 694 " model vdw 2.264 3.120 nonbonded pdb=" O TYR L 647 " pdb=" NZ LYS L 656 " model vdw 2.265 3.120 ... (remaining 103228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 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 0.037 13827 Z= 0.499 Angle : 0.761 9.090 19923 Z= 0.652 Chirality : 0.044 0.185 2273 Planarity : 0.004 0.033 1505 Dihedral : 27.438 150.879 5895 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.27 % Allowed : 27.52 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 865 helix: 1.24 (0.23), residues: 541 sheet: None (None), residues: 0 loop : -1.83 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.007 0.001 TYR F 51 PHE 0.012 0.001 PHE H 65 TRP 0.003 0.001 TRP K 655 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.50 (13811) covalent geometry : angle 0.74874 / 0.65 (19905) hydrogen bonds : bond 0.14052 / 8.96 ( 706) hydrogen bonds : angle 4.57560 / 3.46 ( 1749) metal coordination : bond 0.00674 / 0.41 ( 16) metal coordination : angle 4.64044 / 3.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 170 average time/residue: 0.1561 time to fit residues: 34.7034 Evaluate side-chains 171 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.097901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.062736 restraints weight = 27132.234| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.71 r_work: 0.2657 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13827 Z= 0.179 Angle : 0.653 8.351 19923 Z= 0.379 Chirality : 0.047 0.240 2273 Planarity : 0.004 0.040 1505 Dihedral : 29.624 153.796 4170 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.95 % Allowed : 24.16 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.28), residues: 865 helix: 1.59 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -1.81 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.008 0.001 TYR C 50 PHE 0.008 0.001 PHE D 65 TRP 0.001 0.000 TRP L 655 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (13811) covalent geometry : angle 0.63898 / 0.38 (19905) hydrogen bonds : bond 0.06267 / 4.15 ( 706) hydrogen bonds : angle 2.87981 / 2.07 ( 1749) metal coordination : bond 0.00758 / 0.52 ( 16) metal coordination : angle 4.59652 / 3.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8557 (t0) REVERT: L 675 ARG cc_start: 0.9308 (mmm160) cc_final: 0.8729 (mmm-85) REVERT: L 694 ASP cc_start: 0.8623 (m-30) cc_final: 0.8206 (m-30) outliers start: 22 outliers final: 14 residues processed: 183 average time/residue: 0.1429 time to fit residues: 34.4891 Evaluate side-chains 185 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 672 CYS Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 102 optimal weight: 40.0000 chunk 49 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 27 GLN K 687 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.061342 restraints weight = 27551.015| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.75 r_work: 0.2618 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9225 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13827 Z= 0.221 Angle : 0.660 7.298 19923 Z= 0.376 Chirality : 0.048 0.245 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.818 153.052 4168 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.36 % Allowed : 24.30 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.29), residues: 865 helix: 1.66 (0.22), residues: 555 sheet: -1.93 (1.05), residues: 20 loop : -1.96 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.008 0.001 TYR F 51 PHE 0.015 0.002 PHE L 667 TRP 0.002 0.000 TRP K 655 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (13811) covalent geometry : angle 0.64545 / 0.38 (19905) hydrogen bonds : bond 0.06778 / 4.50 ( 706) hydrogen bonds : angle 2.83960 / 2.04 ( 1749) metal coordination : bond 0.00827 / 0.53 ( 16) metal coordination : angle 4.62706 / 3.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 669 GLU cc_start: 0.8707 (tp30) cc_final: 0.8448 (tm-30) REVERT: L 673 LYS cc_start: 0.8974 (ptpp) cc_final: 0.8021 (pttp) REVERT: L 694 ASP cc_start: 0.8648 (m-30) cc_final: 0.8196 (m-30) outliers start: 25 outliers final: 21 residues processed: 183 average time/residue: 0.1492 time to fit residues: 35.4379 Evaluate side-chains 190 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain K residue 687 ASN Chi-restraints excluded: chain K residue 698 VAL Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 13 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 654 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.063885 restraints weight = 27530.080| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.75 r_work: 0.2689 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13827 Z= 0.139 Angle : 0.598 10.138 19923 Z= 0.348 Chirality : 0.044 0.239 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.800 155.239 4168 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.09 % Allowed : 25.23 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.28), residues: 865 helix: 1.90 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.80 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.008 0.001 TYR C 50 PHE 0.007 0.001 PHE D 70 TRP 0.001 0.000 TRP L 655 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.14 (13811) covalent geometry : angle 0.58640 / 0.35 (19905) hydrogen bonds : bond 0.05015 / 3.34 ( 706) hydrogen bonds : angle 2.58568 / 1.86 ( 1749) metal coordination : bond 0.01069 / 0.59 ( 16) metal coordination : angle 3.89988 / 2.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 42 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.7985 (ptm160) REVERT: G 73 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8560 (t0) REVERT: H 95 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: L 668 CYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6481 (p) REVERT: L 694 ASP cc_start: 0.8629 (m-30) cc_final: 0.8145 (m-30) outliers start: 23 outliers final: 12 residues processed: 186 average time/residue: 0.1542 time to fit residues: 37.4729 Evaluate side-chains 186 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 687 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 668 CYS Chi-restraints excluded: chain L residue 672 CYS Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.060806 restraints weight = 27136.330| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.72 r_work: 0.2607 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9234 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13827 Z= 0.283 Angle : 0.692 7.791 19923 Z= 0.388 Chirality : 0.050 0.243 2273 Planarity : 0.004 0.034 1505 Dihedral : 29.908 152.675 4168 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.10 % Allowed : 22.42 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.28), residues: 865 helix: 1.74 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.82 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.010 0.002 TYR H 121 PHE 0.015 0.002 PHE H 65 TRP 0.002 0.000 TRP K 655 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.28 (13811) covalent geometry : angle 0.67952 / 0.39 (19905) hydrogen bonds : bond 0.07240 / 4.83 ( 706) hydrogen bonds : angle 2.86765 / 2.06 ( 1749) metal coordination : bond 0.01137 / 0.70 ( 16) metal coordination : angle 4.36146 / 2.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9015 (pm20) cc_final: 0.8755 (pm20) REVERT: A 133 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: G 42 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7906 (ptm160) REVERT: G 73 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8645 (t0) REVERT: L 694 ASP cc_start: 0.8661 (m-30) cc_final: 0.8176 (m-30) outliers start: 38 outliers final: 29 residues processed: 196 average time/residue: 0.1692 time to fit residues: 43.2248 Evaluate side-chains 205 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 662 THR Chi-restraints excluded: chain K residue 687 ASN Chi-restraints excluded: chain K residue 698 VAL Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 672 CYS Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 50.0000 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.062206 restraints weight = 26810.507| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.71 r_work: 0.2650 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13827 Z= 0.152 Angle : 0.650 9.419 19923 Z= 0.368 Chirality : 0.047 0.239 2273 Planarity : 0.004 0.034 1505 Dihedral : 29.896 154.055 4168 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.30 % Allowed : 24.16 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.28), residues: 865 helix: 1.89 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.77 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.009 0.001 TYR F 51 PHE 0.011 0.001 PHE L 667 TRP 0.001 0.000 TRP K 655 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (13811) covalent geometry : angle 0.63462 / 0.37 (19905) hydrogen bonds : bond 0.05987 / 3.98 ( 706) hydrogen bonds : angle 2.76136 / 1.98 ( 1749) metal coordination : bond 0.00871 / 0.53 ( 16) metal coordination : angle 4.64982 / 3.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: G 42 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.7934 (ptm160) REVERT: G 73 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8604 (t0) REVERT: K 658 MET cc_start: 0.7016 (tpp) cc_final: 0.6633 (tpt) REVERT: K 694 ASP cc_start: 0.8434 (t0) cc_final: 0.8177 (t0) REVERT: L 673 LYS cc_start: 0.9050 (mtmm) cc_final: 0.8800 (mmtt) REVERT: L 694 ASP cc_start: 0.8633 (m-30) cc_final: 0.8121 (m-30) outliers start: 32 outliers final: 25 residues processed: 192 average time/residue: 0.1571 time to fit residues: 39.3310 Evaluate side-chains 200 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain K residue 662 THR Chi-restraints excluded: chain K residue 687 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.061975 restraints weight = 26841.075| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.72 r_work: 0.2642 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13827 Z= 0.183 Angle : 0.644 8.966 19923 Z= 0.365 Chirality : 0.046 0.242 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.914 154.488 4168 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.83 % Allowed : 22.95 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.28), residues: 865 helix: 1.91 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.76 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.008 0.001 TYR F 51 PHE 0.010 0.001 PHE H 65 TRP 0.001 0.000 TRP K 655 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (13811) covalent geometry : angle 0.63073 / 0.36 (19905) hydrogen bonds : bond 0.05956 / 3.97 ( 706) hydrogen bonds : angle 2.72857 / 1.96 ( 1749) metal coordination : bond 0.00932 / 0.61 ( 16) metal coordination : angle 4.43036 / 2.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8965 (pm20) cc_final: 0.8750 (pm20) REVERT: A 133 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: G 42 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.7940 (ptm160) REVERT: G 73 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8626 (t0) REVERT: H 95 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: K 694 ASP cc_start: 0.8345 (t0) cc_final: 0.8104 (t0) REVERT: L 694 ASP cc_start: 0.8651 (m-30) cc_final: 0.8136 (m-30) outliers start: 36 outliers final: 29 residues processed: 194 average time/residue: 0.1473 time to fit residues: 37.4918 Evaluate side-chains 204 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain K residue 662 THR Chi-restraints excluded: chain K residue 687 ASN Chi-restraints excluded: chain K residue 697 THR Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 654 ASN ** 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 = 0.3525 r_free = 0.3525 target = 0.097409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.062225 restraints weight = 26596.547| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.69 r_work: 0.2647 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9203 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13827 Z= 0.188 Angle : 0.635 8.846 19923 Z= 0.361 Chirality : 0.046 0.240 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.934 154.533 4168 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.97 % Allowed : 22.68 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.29), residues: 865 helix: 1.92 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.73 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.008 0.001 TYR F 51 PHE 0.010 0.001 PHE H 65 TRP 0.003 0.001 TRP K 655 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (13811) covalent geometry : angle 0.62277 / 0.36 (19905) hydrogen bonds : bond 0.05852 / 3.91 ( 706) hydrogen bonds : angle 2.67728 / 1.93 ( 1749) metal coordination : bond 0.00805 / 0.53 ( 16) metal coordination : angle 4.21912 / 2.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9044 (pm20) cc_final: 0.8802 (pm20) REVERT: A 133 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6369 (mp0) REVERT: G 42 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8013 (ptm160) REVERT: G 73 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8663 (t0) REVERT: H 95 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8689 (tt0) REVERT: K 694 ASP cc_start: 0.8401 (t0) cc_final: 0.8157 (t0) REVERT: L 658 MET cc_start: 0.7791 (tpp) cc_final: 0.7543 (tpp) REVERT: L 694 ASP cc_start: 0.8654 (m-30) cc_final: 0.8139 (m-30) outliers start: 37 outliers final: 30 residues processed: 194 average time/residue: 0.1515 time to fit residues: 38.5506 Evaluate side-chains 204 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain K residue 662 THR Chi-restraints excluded: chain K residue 687 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 82 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 107 optimal weight: 0.0050 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 654 ASN ** 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 = 0.3504 r_free = 0.3504 target = 0.096279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.060852 restraints weight = 26919.448| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 1.71 r_work: 0.2608 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9234 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13827 Z= 0.261 Angle : 0.690 10.096 19923 Z= 0.385 Chirality : 0.050 0.247 2273 Planarity : 0.004 0.035 1505 Dihedral : 29.996 153.699 4168 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.10 % Allowed : 22.68 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.29), residues: 865 helix: 1.75 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.79 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.009 0.001 TYR H 121 PHE 0.014 0.002 PHE D 70 TRP 0.005 0.001 TRP K 655 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.26 (13811) covalent geometry : angle 0.67697 / 0.38 (19905) hydrogen bonds : bond 0.07008 / 4.68 ( 706) hydrogen bonds : angle 2.85416 / 2.05 ( 1749) metal coordination : bond 0.01202 / 0.72 ( 16) metal coordination : angle 4.43729 / 2.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9083 (pm20) cc_final: 0.8816 (pm20) REVERT: A 133 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: G 42 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7969 (ptm160) REVERT: G 73 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8677 (t0) REVERT: H 95 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: K 694 ASP cc_start: 0.8508 (t0) cc_final: 0.8198 (t0) REVERT: L 694 ASP cc_start: 0.8666 (m-30) cc_final: 0.8170 (m-30) outliers start: 38 outliers final: 30 residues processed: 194 average time/residue: 0.1624 time to fit residues: 41.1184 Evaluate side-chains 202 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain K residue 662 THR Chi-restraints excluded: chain K residue 687 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.0010 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 106 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.5346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062375 restraints weight = 26918.736| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.72 r_work: 0.2658 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9202 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13827 Z= 0.142 Angle : 0.658 11.829 19923 Z= 0.370 Chirality : 0.047 0.239 2273 Planarity : 0.004 0.034 1505 Dihedral : 29.965 155.227 4168 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.03 % Allowed : 24.56 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.29), residues: 865 helix: 1.91 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.76 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 33 TYR 0.013 0.001 TYR C 50 PHE 0.007 0.001 PHE A 67 TRP 0.003 0.001 TRP K 655 HIS 0.002 0.001 HIS K 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (13811) covalent geometry : angle 0.64258 / 0.37 (19905) hydrogen bonds : bond 0.05678 / 3.77 ( 706) hydrogen bonds : angle 2.70416 / 1.95 ( 1749) metal coordination : bond 0.01340 / 1.02 ( 16) metal coordination : angle 4.77883 / 3.11 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9053 (pm20) cc_final: 0.8781 (pm20) REVERT: A 133 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: G 42 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7988 (ptm160) REVERT: G 73 ASN cc_start: 0.9219 (OUTLIER) cc_final: 0.8648 (t0) REVERT: H 95 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8599 (tt0) REVERT: K 658 MET cc_start: 0.6966 (tpp) cc_final: 0.6652 (tpt) REVERT: K 694 ASP cc_start: 0.8482 (t0) cc_final: 0.8193 (t0) REVERT: L 673 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8409 (ptpp) REVERT: L 694 ASP cc_start: 0.8641 (m-30) cc_final: 0.8139 (m-30) outliers start: 30 outliers final: 23 residues processed: 188 average time/residue: 0.1591 time to fit residues: 38.9460 Evaluate side-chains 196 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 662 THR Chi-restraints excluded: chain K residue 687 ASN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 676 LEU Chi-restraints excluded: chain L residue 697 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 99 optimal weight: 0.0570 chunk 2 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** L 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 687 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.062645 restraints weight = 26859.559| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.71 r_work: 0.2657 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13827 Z= 0.140 Angle : 0.638 10.726 19923 Z= 0.360 Chirality : 0.046 0.241 2273 Planarity : 0.004 0.048 1505 Dihedral : 29.959 155.504 4168 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.49 % Allowed : 24.97 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.29), residues: 865 helix: 1.97 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.78 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.010 0.001 TYR C 50 PHE 0.008 0.001 PHE D 70 TRP 0.003 0.000 TRP K 655 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (13811) covalent geometry : angle 0.62387 / 0.36 (19905) hydrogen bonds : bond 0.05505 / 3.67 ( 706) hydrogen bonds : angle 2.66282 / 1.92 ( 1749) metal coordination : bond 0.00898 / 0.64 ( 16) metal coordination : angle 4.53069 / 3.00 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3591.90 seconds wall clock time: 61 minutes 44.40 seconds (3704.40 seconds total)