Starting phenix.real_space_refine on Fri Jul 3 06:53:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t3t_41011/07_2026/8t3t_41011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3t_41011/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3t_41011/07_2026/8t3t_41011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3t_41011/07_2026/8t3t_41011.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3t_41011/07_2026/8t3t_41011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3t_41011/07_2026/8t3t_41011.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8t3t_41011/07_2026/8t3t_41011.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t3t_41011/07_2026/8t3t_41011.cif" } 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-dev-6108/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: 2.74, per 1000 atoms: 0.21 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: 1.01 Conformation dependent library (CDL) restraints added in 366.2 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: 1.82 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: 2.27 Time building geometry restraints manager: 1.40 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: 19018 1.82 - 3.64: 853 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.660 Find NCS groups from input model: 0.130 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- 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 : 0.755 9.090 19923 Z= 0.647 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 0.74214 / 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 : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 170 average time/residue: 0.1660 time to fit residues: 36.7742 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 : 0.310 ------------------------------------------------------------------------------- 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: 0.6980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.097926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.062706 restraints weight = 27126.719| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.74 r_work: 0.2658 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.0621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13827 Z= 0.177 Angle : 0.639 8.196 19923 Z= 0.374 Chirality : 0.047 0.221 2273 Planarity : 0.004 0.039 1505 Dihedral : 29.657 154.486 4170 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.09 % Allowed : 24.16 % Favored : 72.75 % 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 : -1.82 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 35 TYR 0.007 0.001 TYR F 51 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 0.00343 / 0.18 (13811) covalent geometry : angle 0.62478 / 0.37 (19905) hydrogen bonds : bond 0.06359 / 4.21 ( 706) hydrogen bonds : angle 2.88578 / 2.07 ( 1749) metal coordination : bond 0.00738 / 0.51 ( 16) metal coordination : angle 4.57658 / 3.24 ( 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 194 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8578 (t0) REVERT: L 675 ARG cc_start: 0.9308 (mmm160) cc_final: 0.8732 (mmm-85) REVERT: L 694 ASP cc_start: 0.8618 (m-30) cc_final: 0.8199 (m-30) outliers start: 23 outliers final: 15 residues processed: 182 average time/residue: 0.1374 time to fit residues: 32.9116 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 : 0.210 ------------------------------------------------------------------------------- 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 E residue 73 GLU 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: 3.9990 chunk 78 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.096574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.060898 restraints weight = 27610.763| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.75 r_work: 0.2607 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9233 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13827 Z= 0.246 Angle : 0.666 7.377 19923 Z= 0.381 Chirality : 0.048 0.225 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.864 154.053 4168 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.49 % Allowed : 23.76 % Favored : 72.75 % 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: 0.56 (0.28), residues: 865 helix: 1.62 (0.22), residues: 553 sheet: -1.95 (1.05), residues: 20 loop : -1.99 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 79 TYR 0.009 0.001 TYR H 121 PHE 0.015 0.002 PHE L 667 TRP 0.002 0.000 TRP K 655 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 (13811) covalent geometry : angle 0.65200 / 0.38 (19905) hydrogen bonds : bond 0.07140 / 4.75 ( 706) hydrogen bonds : angle 2.89900 / 2.08 ( 1749) metal coordination : bond 0.00931 / 0.58 ( 16) metal coordination : angle 4.56944 / 3.23 ( 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 195 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9043 (pm20) cc_final: 0.8763 (pm20) outliers start: 26 outliers final: 23 residues processed: 183 average time/residue: 0.1642 time to fit residues: 38.9736 Evaluate side-chains 192 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 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 672 CYS 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: 0.8980 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.098169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.062750 restraints weight = 27390.897| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.74 r_work: 0.2656 rms_B_bonded: 3.28 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: 0.9195 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 13827 Z= 0.142 Angle : 0.619 7.834 19923 Z= 0.361 Chirality : 0.046 0.219 2273 Planarity : 0.004 0.040 1505 Dihedral : 29.859 155.843 4168 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.22 % Allowed : 24.70 % Favored : 72.08 % 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: 0.80 (0.29), residues: 865 helix: 1.87 (0.22), residues: 549 sheet: -2.16 (1.03), residues: 20 loop : -1.96 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 643 TYR 0.011 0.001 TYR C 50 PHE 0.007 0.001 PHE D 65 TRP 0.002 0.000 TRP L 655 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (13811) covalent geometry : angle 0.60718 / 0.36 (19905) hydrogen bonds : bond 0.05609 / 3.72 ( 706) hydrogen bonds : angle 2.70348 / 1.94 ( 1749) metal coordination : bond 0.01293 / 0.76 ( 16) metal coordination : angle 4.11043 / 2.91 ( 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 195 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 42 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.7985 (ptm160) REVERT: G 73 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8561 (t0) REVERT: H 95 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: L 668 CYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6527 (p) REVERT: L 675 ARG cc_start: 0.9315 (mmm160) cc_final: 0.8534 (mmm160) REVERT: L 694 ASP cc_start: 0.8433 (m-30) cc_final: 0.8013 (m-30) outliers start: 24 outliers final: 14 residues processed: 186 average time/residue: 0.1471 time to fit residues: 35.8244 Evaluate side-chains 188 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 D residue 122 THR 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 95 GLN Chi-restraints excluded: chain L residue 666 VAL Chi-restraints excluded: chain L residue 668 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: 0.9990 chunk 86 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.096191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.060693 restraints weight = 27147.012| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.73 r_work: 0.2609 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9238 moved from start: 0.1154 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= 0.268 Angle : 0.681 8.540 19923 Z= 0.384 Chirality : 0.049 0.227 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.969 154.389 4168 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.37 % Allowed : 22.28 % 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: 0.63 (0.28), residues: 865 helix: 1.68 (0.22), residues: 555 sheet: -2.19 (1.02), residues: 20 loop : -1.98 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 92 TYR 0.009 0.001 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 0.00583 / 0.27 (13811) covalent geometry : angle 0.66544 / 0.38 (19905) hydrogen bonds : bond 0.07308 / 4.87 ( 706) hydrogen bonds : angle 2.91040 / 2.09 ( 1749) metal coordination : bond 0.01193 / 0.71 ( 16) metal coordination : angle 4.82067 / 3.18 ( 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 212 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9026 (pm20) cc_final: 0.8767 (pm20) REVERT: A 133 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6414 (mp0) REVERT: G 42 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7919 (ptm160) REVERT: G 73 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8626 (t0) REVERT: L 658 MET cc_start: 0.8613 (tpp) cc_final: 0.8409 (tpp) REVERT: L 668 CYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6582 (p) REVERT: L 694 ASP cc_start: 0.8547 (m-30) cc_final: 0.8132 (m-30) outliers start: 40 outliers final: 30 residues processed: 199 average time/residue: 0.1523 time to fit residues: 39.6680 Evaluate side-chains 206 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 78 SER Chi-restraints excluded: chain D residue 91 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 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 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 657 ASN Chi-restraints excluded: chain K residue 698 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 50.0000 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.097681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.062243 restraints weight = 27187.444| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.74 r_work: 0.2644 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13827 Z= 0.142 Angle : 0.629 8.760 19923 Z= 0.361 Chirality : 0.046 0.221 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.953 156.252 4168 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.89 % Allowed : 24.16 % Favored : 71.95 % 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: 0.93 (0.28), residues: 865 helix: 1.87 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.83 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 33 TYR 0.011 0.001 TYR C 50 PHE 0.014 0.001 PHE L 667 TRP 0.001 0.000 TRP L 655 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (13811) covalent geometry : angle 0.61519 / 0.36 (19905) hydrogen bonds : bond 0.05729 / 3.80 ( 706) hydrogen bonds : angle 2.70911 / 1.94 ( 1749) metal coordination : bond 0.01167 / 0.73 ( 16) metal coordination : angle 4.34313 / 2.95 ( 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 202 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: G 42 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7924 (ptm160) REVERT: G 73 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8599 (t0) REVERT: H 95 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: L 694 ASP cc_start: 0.8556 (m-30) cc_final: 0.8071 (m-30) outliers start: 29 outliers final: 19 residues processed: 192 average time/residue: 0.1485 time to fit residues: 37.2112 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 : 0.228 ------------------------------------------------------------------------------- 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 56 SER Chi-restraints excluded: chain D residue 122 THR 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 42 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR 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 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: 9.9990 chunk 78 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 30.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.097844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.062615 restraints weight = 26898.113| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.73 r_work: 0.2663 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9195 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13827 Z= 0.153 Angle : 0.624 8.871 19923 Z= 0.358 Chirality : 0.045 0.221 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.950 156.382 4168 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.56 % Allowed : 23.22 % 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: 1.03 (0.28), residues: 865 helix: 1.96 (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 F 51 PHE 0.007 0.001 PHE H 65 TRP 0.001 0.000 TRP L 655 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (13811) covalent geometry : angle 0.60870 / 0.36 (19905) hydrogen bonds : bond 0.05509 / 3.67 ( 706) hydrogen bonds : angle 2.65477 / 1.91 ( 1749) metal coordination : bond 0.01001 / 0.71 ( 16) metal coordination : angle 4.63705 / 3.11 ( 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 206 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8970 (pm20) cc_final: 0.8757 (pm20) REVERT: A 133 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6376 (mp0) REVERT: G 42 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8003 (ptm160) REVERT: G 73 ASN cc_start: 0.9209 (OUTLIER) cc_final: 0.8624 (t0) REVERT: H 95 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8587 (tt0) REVERT: K 658 MET cc_start: 0.7009 (tpp) cc_final: 0.6708 (tpt) REVERT: K 694 ASP cc_start: 0.8620 (t0) cc_final: 0.8387 (t0) REVERT: L 668 CYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6455 (p) REVERT: L 673 LYS cc_start: 0.8993 (mtmm) cc_final: 0.8760 (mtmt) REVERT: L 694 ASP cc_start: 0.8559 (m-30) cc_final: 0.8057 (m-30) outliers start: 34 outliers final: 25 residues processed: 194 average time/residue: 0.1451 time to fit residues: 36.6714 Evaluate side-chains 202 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 43 VAL 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 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 122 THR 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 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 668 CYS 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: 0.6980 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 63 optimal weight: 0.0020 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.098078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.063010 restraints weight = 26653.898| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.69 r_work: 0.2669 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13827 Z= 0.159 Angle : 0.604 9.298 19923 Z= 0.349 Chirality : 0.044 0.214 2273 Planarity : 0.004 0.033 1505 Dihedral : 29.954 155.942 4168 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.16 % Allowed : 23.36 % 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: 1.11 (0.28), residues: 865 helix: 2.02 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.76 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 33 TYR 0.007 0.001 TYR C 50 PHE 0.008 0.001 PHE H 65 TRP 0.002 0.000 TRP K 655 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (13811) covalent geometry : angle 0.59069 / 0.35 (19905) hydrogen bonds : bond 0.05347 / 3.56 ( 706) hydrogen bonds : angle 2.58514 / 1.86 ( 1749) metal coordination : bond 0.00875 / 0.62 ( 16) metal coordination : angle 4.25767 / 2.91 ( 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 201 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6366 (mp0) REVERT: G 42 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.7996 (ptm160) REVERT: G 73 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8644 (t0) REVERT: H 95 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8646 (tt0) REVERT: L 669 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8322 (tm-30) REVERT: L 673 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8575 (mtmm) REVERT: L 687 ASN cc_start: 0.9183 (t0) cc_final: 0.8972 (t0) REVERT: L 694 ASP cc_start: 0.8595 (m-30) cc_final: 0.8088 (m-30) outliers start: 31 outliers final: 25 residues processed: 190 average time/residue: 0.1566 time to fit residues: 38.7832 Evaluate side-chains 197 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 56 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 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 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: 9.9990 chunk 73 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 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: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.059339 restraints weight = 26870.484| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.76 r_work: 0.2572 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9260 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 13827 Z= 0.367 Angle : 0.762 10.594 19923 Z= 0.419 Chirality : 0.053 0.241 2273 Planarity : 0.005 0.046 1505 Dihedral : 30.108 154.196 4168 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.70 % Allowed : 23.09 % 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: 0.61 (0.28), residues: 865 helix: 1.62 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -1.93 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 99 TYR 0.013 0.002 TYR H 121 PHE 0.019 0.002 PHE D 70 TRP 0.007 0.001 TRP K 655 HIS 0.007 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.37 (13811) covalent geometry : angle 0.74887 / 0.42 (19905) hydrogen bonds : bond 0.08427 / 5.63 ( 706) hydrogen bonds : angle 3.04964 / 2.18 ( 1749) metal coordination : bond 0.01459 / 0.86 ( 16) metal coordination : angle 4.68322 / 2.98 ( 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 200 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: G 42 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.7959 (ptm160) REVERT: G 73 ASN cc_start: 0.9255 (OUTLIER) cc_final: 0.8702 (t0) REVERT: K 658 MET cc_start: 0.6873 (tpp) cc_final: 0.6582 (tpt) REVERT: K 694 ASP cc_start: 0.8514 (t0) cc_final: 0.8307 (t0) REVERT: L 658 MET cc_start: 0.8341 (mmt) cc_final: 0.7960 (tpp) REVERT: L 669 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8148 (tm-30) REVERT: L 673 LYS cc_start: 0.8881 (mtmm) cc_final: 0.8607 (mtmt) REVERT: L 694 ASP cc_start: 0.8614 (m-30) cc_final: 0.8132 (m-30) outliers start: 35 outliers final: 28 residues processed: 187 average time/residue: 0.1403 time to fit residues: 34.4659 Evaluate side-chains 196 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 78 SER 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 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 K residue 657 ASN Chi-restraints excluded: chain K residue 662 THR Chi-restraints excluded: chain K residue 673 LYS 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: 0.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.096622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.061308 restraints weight = 26820.248| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.72 r_work: 0.2626 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9226 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13827 Z= 0.169 Angle : 0.679 11.560 19923 Z= 0.381 Chirality : 0.049 0.228 2273 Planarity : 0.004 0.038 1505 Dihedral : 30.075 156.263 4168 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.76 % Allowed : 24.16 % Favored : 72.08 % 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: 0.83 (0.28), residues: 865 helix: 1.79 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -1.85 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 33 TYR 0.012 0.001 TYR F 51 PHE 0.009 0.001 PHE H 65 TRP 0.004 0.001 TRP K 655 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (13811) covalent geometry : angle 0.66188 / 0.38 (19905) hydrogen bonds : bond 0.06517 / 4.33 ( 706) hydrogen bonds : angle 2.83674 / 2.04 ( 1749) metal coordination : bond 0.01421 / 1.06 ( 16) metal coordination : angle 5.04988 / 3.23 ( 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 196 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: G 42 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8054 (ptm160) REVERT: G 73 ASN cc_start: 0.9235 (OUTLIER) cc_final: 0.8679 (t0) REVERT: K 658 MET cc_start: 0.6912 (tpp) cc_final: 0.6598 (tpt) REVERT: L 658 MET cc_start: 0.8285 (mmt) cc_final: 0.7867 (tpp) REVERT: L 694 ASP cc_start: 0.8600 (m-30) cc_final: 0.8081 (m-30) outliers start: 28 outliers final: 24 residues processed: 184 average time/residue: 0.1634 time to fit residues: 39.2292 Evaluate side-chains 195 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 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 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 K residue 657 ASN Chi-restraints excluded: chain K residue 673 LYS 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: 0.1980 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 ASN L 687 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.061795 restraints weight = 26702.306| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.70 r_work: 0.2638 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9217 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13827 Z= 0.163 Angle : 0.658 9.578 19923 Z= 0.372 Chirality : 0.047 0.229 2273 Planarity : 0.004 0.032 1505 Dihedral : 30.068 156.891 4168 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.43 % Allowed : 23.89 % 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: 0.92 (0.28), residues: 865 helix: 1.88 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -1.86 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE H 65 TRP 0.003 0.000 TRP K 655 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (13811) covalent geometry : angle 0.64378 / 0.37 (19905) hydrogen bonds : bond 0.06098 / 4.07 ( 706) hydrogen bonds : angle 2.77300 / 1.99 ( 1749) metal coordination : bond 0.00986 / 0.69 ( 16) metal coordination : angle 4.60554 / 3.06 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3462.94 seconds wall clock time: 59 minutes 36.99 seconds (3576.99 seconds total)