Starting phenix.real_space_refine on Thu Jul 2 22:57:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3p_44148/07_2026/9b3p_44148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3p_44148/07_2026/9b3p_44148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b3p_44148/07_2026/9b3p_44148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3p_44148/07_2026/9b3p_44148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b3p_44148/07_2026/9b3p_44148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3p_44148/07_2026/9b3p_44148.map" } resolution = 3.0 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= 0.004 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: 5 Type Number sf(0) Gaussians P 256 5.49 5 S 10 5.16 5 C 6151 2.51 5 N 2078 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s 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: 11067 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 797 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 740 Classifications: {'peptide': 98} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 803 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 776 Classifications: {'peptide': 102} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 97} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2639 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Chain: "J" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2609 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Time building chain proxies: 2.38, per 1000 atoms: 0.22 Number of scatterers: 11067 At special positions: 0 Unit cell: (103.68, 115.56, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 256 15.00 O 2572 8.00 N 2078 7.00 C 6151 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: 0.84 Conformation dependent library (CDL) restraints added in 144.6 milliseconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 69.4% alpha, 1.1% beta 12 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.704A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.507A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.731A pdb=" N ILE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 4.164A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.681A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.772A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.967A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.533A pdb=" N ARG C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.709A pdb=" N ILE C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 39 " --> pdb=" O HIS C 35 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 74 removed outlier: 3.887A pdb=" N ALA C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 56 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.585A pdb=" N LEU C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 100 removed outlier: 3.771A pdb=" N SER C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 100' Processing helix chain 'D' and resid 40 through 49 removed outlier: 3.651A pdb=" N VAL D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 83 removed outlier: 3.564A pdb=" N SER D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.886A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.801A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 removed outlier: 3.573A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 removed outlier: 3.637A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.582A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.806A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 4.255A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 24 through 29' Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.708A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.666A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.817A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 removed outlier: 3.648A pdb=" N ARG G 22 " --> pdb=" O SER G 18 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 23 " --> pdb=" O ARG G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 removed outlier: 3.672A pdb=" N ILE G 32 " --> pdb=" O PRO G 28 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS G 37 " --> pdb=" O HIS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 73 removed outlier: 3.858A pdb=" N ALA G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE G 57 " --> pdb=" O TYR G 53 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.533A pdb=" N LEU G 86 " --> pdb=" O THR G 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.550A pdb=" N LEU G 117 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE G 118 " --> pdb=" O LYS G 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 114 through 118' Processing helix chain 'H' and resid 40 through 49 removed outlier: 3.659A pdb=" N VAL H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.972A pdb=" N SER H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.999A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 123 removed outlier: 3.998A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 118 " --> pdb=" O GLY H 114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A 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 'C' and resid 45 through 46 removed outlier: 7.077A pdb=" N ARG C 45 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.808A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 45 through 46 removed outlier: 6.322A pdb=" N ARG G 45 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 240 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2443 1.34 - 1.45: 3593 1.45 - 1.57: 5222 1.57 - 1.69: 510 1.69 - 1.81: 18 Bond restraints: 11786 Sorted by residual: bond pdb=" C1' DT I -32 " pdb=" N1 DT I -32 " ideal model delta sigma weight residual 1.468 1.496 -0.028 1.40e-02 5.10e+03 4.14e+00 bond pdb=" C1' DT J 62 " pdb=" N1 DT J 62 " ideal model delta sigma weight residual 1.468 1.496 -0.028 1.40e-02 5.10e+03 3.92e+00 bond pdb=" C1' DC I -58 " pdb=" N1 DC I -58 " ideal model delta sigma weight residual 1.468 1.496 -0.028 1.40e-02 5.10e+03 3.91e+00 bond pdb=" C1' DC J 19 " pdb=" N1 DC J 19 " ideal model delta sigma weight residual 1.468 1.495 -0.027 1.40e-02 5.10e+03 3.80e+00 bond pdb=" C1' DC I -40 " pdb=" N1 DC I -40 " ideal model delta sigma weight residual 1.468 1.495 -0.027 1.40e-02 5.10e+03 3.72e+00 ... (remaining 11781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 15511 0.99 - 1.98: 992 1.98 - 2.97: 499 2.97 - 3.96: 4 3.96 - 4.95: 6 Bond angle restraints: 17012 Sorted by residual: angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT I -29 " pdb=" C4 DT I -29 " pdb=" O4 DT I -29 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT J -47 " pdb=" C4 DT J -47 " pdb=" O4 DT J -47 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT J 14 " pdb=" C4 DT J 14 " pdb=" O4 DT J 14 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT J -43 " pdb=" C4 DT J -43 " pdb=" O4 DT J -43 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 17007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 5475 34.64 - 69.28: 926 69.28 - 103.92: 7 103.92 - 138.55: 1 138.55 - 173.19: 2 Dihedral angle restraints: 6411 sinusoidal: 4281 harmonic: 2130 Sorted by residual: dihedral pdb=" C4' DT I -32 " pdb=" C3' DT I -32 " pdb=" O3' DT I -32 " pdb=" P DA I -31 " ideal model delta sinusoidal sigma weight residual -140.00 33.19 -173.19 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 80.29 139.71 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" C4' DT I -50 " pdb=" C3' DT I -50 " pdb=" O3' DT I -50 " pdb=" P DG I -49 " ideal model delta sinusoidal sigma weight residual 220.00 84.81 135.19 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 6408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 806 0.025 - 0.051: 748 0.051 - 0.076: 244 0.076 - 0.101: 123 0.101 - 0.127: 20 Chirality restraints: 1941 Sorted by residual: chirality pdb=" CA ILE H 54 " pdb=" N ILE H 54 " pdb=" C ILE H 54 " pdb=" CB ILE H 54 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE C 110 " pdb=" N ILE C 110 " pdb=" C ILE C 110 " pdb=" CB ILE C 110 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA ILE G 110 " pdb=" N ILE G 110 " pdb=" C ILE G 110 " pdb=" CB ILE G 110 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 1938 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 82 " -0.013 5.00e-02 4.00e+02 1.93e-02 5.99e-01 pdb=" N PRO G 83 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO G 83 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO G 83 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 82 " -0.012 5.00e-02 4.00e+02 1.82e-02 5.29e-01 pdb=" N PRO C 83 " 0.031 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.012 5.00e-02 4.00e+02 1.75e-02 4.88e-01 pdb=" N PRO A 121 " -0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.010 5.00e-02 4.00e+02 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2628 2.81 - 3.34: 8621 3.34 - 3.86: 18528 3.86 - 4.38: 22781 4.38 - 4.90: 33678 Nonbonded interactions: 86236 Sorted by model distance: nonbonded pdb=" OG1 THR C 41 " pdb=" N SER C 42 " model vdw 2.292 3.120 nonbonded pdb=" OG1 THR G 41 " pdb=" N SER G 42 " model vdw 2.311 3.120 nonbonded pdb=" OH TYR D 40 " pdb=" OP1 DG I 48 " model vdw 2.337 3.040 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.376 3.120 nonbonded pdb=" O HIS G 43 " pdb=" OG SER H 87 " model vdw 2.377 3.040 ... (remaining 86231 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' and resid 38 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = (chain 'C' and resid 17 through 113) selection = (chain 'G' and resid 17 through 113) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.490 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.570 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 11786 Z= 0.428 Angle : 0.591 4.949 17012 Z= 0.553 Chirality : 0.040 0.127 1941 Planarity : 0.002 0.019 1262 Dihedral : 24.092 173.192 5039 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.57 % Favored : 94.88 % Rotamer: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -5.86 (0.18), residues: 722 helix: -4.69 (0.06), residues: 424 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 91 TYR 0.001 0.000 TYR F 72 PHE 0.001 0.000 PHE F 100 HIS 0.001 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.43 (11786) covalent geometry : angle 0.59082 / 0.55 (17012) hydrogen bonds : bond 0.36240 / 23.76 ( 269) hydrogen bonds : angle 9.71294 / 6.71 ( 778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.289 Fit side-chains REVERT: G 64 GLU cc_start: 0.7722 (tp30) cc_final: 0.7507 (mm-30) REVERT: G 87 GLN cc_start: 0.8141 (tp40) cc_final: 0.7869 (tp40) outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.7445 time to fit residues: 121.3258 Evaluate side-chains 93 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 63 ASN E 68 GLN F 25 ASN G 26 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.189446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159948 restraints weight = 14231.249| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 0.82 r_work: 0.3712 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11786 Z= 0.181 Angle : 0.660 13.198 17012 Z= 0.360 Chirality : 0.045 0.344 1941 Planarity : 0.006 0.039 1262 Dihedral : 27.547 167.655 3621 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.94 % Favored : 97.78 % Rotamer: Outliers : 3.29 % Allowed : 12.99 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.27 (0.24), residues: 722 helix: -1.96 (0.19), residues: 462 sheet: None (None), residues: 0 loop : -2.29 (0.29), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 86 TYR 0.019 0.001 TYR C 53 PHE 0.012 0.002 PHE F 61 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (11786) covalent geometry : angle 0.66024 / 0.36 (17012) hydrogen bonds : bond 0.08762 / 5.91 ( 269) hydrogen bonds : angle 3.96389 / 2.76 ( 778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.228 Fit side-chains REVERT: E 48 LEU cc_start: 0.8458 (mt) cc_final: 0.8065 (mp) REVERT: E 83 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7388 (mtm180) REVERT: G 64 GLU cc_start: 0.8383 (tp30) cc_final: 0.8128 (mm-30) outliers start: 20 outliers final: 9 residues processed: 126 average time/residue: 0.8400 time to fit residues: 111.4751 Evaluate side-chains 102 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 54 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 48 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.168213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132934 restraints weight = 13480.250| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 0.82 r_work: 0.3358 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11786 Z= 0.178 Angle : 0.596 9.743 17012 Z= 0.338 Chirality : 0.041 0.176 1941 Planarity : 0.005 0.041 1262 Dihedral : 28.353 168.640 3618 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.35 % Favored : 97.37 % Rotamer: Outliers : 3.62 % Allowed : 15.13 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -1.42 (0.28), residues: 722 helix: -0.54 (0.22), residues: 486 sheet: None (None), residues: 0 loop : -1.56 (0.34), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 84 TYR 0.024 0.002 TYR C 53 PHE 0.013 0.002 PHE D 70 HIS 0.014 0.002 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (11786) covalent geometry : angle 0.59558 / 0.34 (17012) hydrogen bonds : bond 0.06099 / 4.07 ( 269) hydrogen bonds : angle 3.48897 / 2.44 ( 778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.295 Fit side-chains REVERT: B 93 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: C 53 TYR cc_start: 0.9044 (t80) cc_final: 0.8486 (t80) REVERT: C 80 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.8154 (mtm-85) REVERT: E 52 ARG cc_start: 0.7141 (mtt-85) cc_final: 0.6620 (mtt90) REVERT: G 34 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8774 (ttp-170) REVERT: G 60 TYR cc_start: 0.8853 (t80) cc_final: 0.8642 (t80) REVERT: G 64 GLU cc_start: 0.8342 (tp30) cc_final: 0.8134 (mm-30) outliers start: 22 outliers final: 8 residues processed: 145 average time/residue: 0.8461 time to fit residues: 129.1921 Evaluate side-chains 122 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 34 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.162283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126595 restraints weight = 13436.910| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 0.82 r_work: 0.3239 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11786 Z= 0.158 Angle : 0.542 8.340 17012 Z= 0.313 Chirality : 0.038 0.167 1941 Planarity : 0.004 0.051 1262 Dihedral : 28.500 171.381 3618 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.25 % Favored : 98.48 % Rotamer: Outliers : 3.29 % Allowed : 17.60 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.40 (0.30), residues: 722 helix: 0.31 (0.23), residues: 501 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 86 TYR 0.011 0.001 TYR H 121 PHE 0.010 0.001 PHE F 61 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (11786) covalent geometry : angle 0.54198 / 0.31 (17012) hydrogen bonds : bond 0.04424 / 2.94 ( 269) hydrogen bonds : angle 3.03418 / 2.14 ( 778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.269 Fit side-chains REVERT: C 37 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8360 (mtpp) REVERT: C 80 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.8213 (mtm-85) REVERT: E 48 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8542 (mp) REVERT: E 52 ARG cc_start: 0.7506 (mtt-85) cc_final: 0.7208 (mtm110) REVERT: E 120 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8109 (mtm) REVERT: E 133 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7892 (mt-10) REVERT: G 60 TYR cc_start: 0.8927 (t80) cc_final: 0.8569 (t80) REVERT: G 64 GLU cc_start: 0.8422 (tp30) cc_final: 0.8143 (mm-30) outliers start: 20 outliers final: 7 residues processed: 142 average time/residue: 0.7949 time to fit residues: 119.1643 Evaluate side-chains 128 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 0.0070 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122415 restraints weight = 13184.769| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 0.82 r_work: 0.3207 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11786 Z= 0.138 Angle : 0.513 7.054 17012 Z= 0.297 Chirality : 0.037 0.173 1941 Planarity : 0.004 0.041 1262 Dihedral : 28.685 172.540 3618 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.63 % Allowed : 19.90 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.31 (0.31), residues: 722 helix: 0.87 (0.24), residues: 504 sheet: None (None), residues: 0 loop : -1.29 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.007 0.001 TYR E 54 PHE 0.010 0.001 PHE F 61 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (11786) covalent geometry : angle 0.51267 / 0.30 (17012) hydrogen bonds : bond 0.04037 / 2.68 ( 269) hydrogen bonds : angle 2.91070 / 2.04 ( 778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.305 Fit side-chains REVERT: A 45 THR cc_start: 0.8422 (p) cc_final: 0.8207 (t) REVERT: C 37 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8330 (mtpp) REVERT: E 48 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8610 (mp) REVERT: E 52 ARG cc_start: 0.7562 (mtt-85) cc_final: 0.7224 (mtm110) REVERT: E 63 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8166 (mmp80) REVERT: E 115 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8136 (mmpt) REVERT: E 120 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7990 (mmm) REVERT: G 34 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8871 (ttp-170) REVERT: G 60 TYR cc_start: 0.8904 (t80) cc_final: 0.8549 (t80) REVERT: G 64 GLU cc_start: 0.8441 (tp30) cc_final: 0.8159 (mm-30) REVERT: G 91 ARG cc_start: 0.9031 (mmp80) cc_final: 0.8728 (mmt180) outliers start: 16 outliers final: 9 residues processed: 126 average time/residue: 0.8343 time to fit residues: 110.8322 Evaluate side-chains 127 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 chunk 71 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN H 47 GLN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121705 restraints weight = 13237.609| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 0.81 r_work: 0.3185 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11786 Z= 0.127 Angle : 0.503 16.958 17012 Z= 0.289 Chirality : 0.036 0.178 1941 Planarity : 0.004 0.040 1262 Dihedral : 28.722 174.211 3618 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.63 % Allowed : 20.07 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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 (0.31), residues: 722 helix: 1.31 (0.24), residues: 504 sheet: None (None), residues: 0 loop : -1.31 (0.35), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.008 0.001 TYR H 121 PHE 0.007 0.001 PHE F 61 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (11786) covalent geometry : angle 0.50294 / 0.29 (17012) hydrogen bonds : bond 0.03452 / 2.29 ( 269) hydrogen bonds : angle 2.78935 / 1.94 ( 778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.309 Fit side-chains REVERT: A 45 THR cc_start: 0.8441 (p) cc_final: 0.8204 (t) REVERT: A 56 LYS cc_start: 0.8095 (mtpm) cc_final: 0.7679 (mttt) REVERT: A 65 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8831 (mt) REVERT: C 37 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8331 (mtpp) REVERT: C 94 GLU cc_start: 0.7384 (tt0) cc_final: 0.7113 (mt-10) REVERT: E 48 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8616 (mp) REVERT: E 52 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.7273 (mtm110) REVERT: E 63 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8010 (mmp80) REVERT: E 76 GLN cc_start: 0.8435 (tt0) cc_final: 0.8173 (tt0) REVERT: E 115 LYS cc_start: 0.8326 (mmtm) cc_final: 0.8105 (mmpt) REVERT: E 120 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8001 (mmm) REVERT: G 34 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8876 (ptt-90) REVERT: G 60 TYR cc_start: 0.8923 (t80) cc_final: 0.8540 (t80) REVERT: G 64 GLU cc_start: 0.8420 (tp30) cc_final: 0.8176 (mm-30) REVERT: G 91 ARG cc_start: 0.9008 (mmp80) cc_final: 0.8757 (mmt-90) REVERT: H 106 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7657 (mt) outliers start: 16 outliers final: 5 residues processed: 130 average time/residue: 0.8494 time to fit residues: 116.2456 Evaluate side-chains 127 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.0030 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.157365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120223 restraints weight = 13079.825| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 0.80 r_work: 0.3175 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11786 Z= 0.127 Angle : 0.496 14.649 17012 Z= 0.287 Chirality : 0.036 0.180 1941 Planarity : 0.004 0.032 1262 Dihedral : 28.798 174.600 3618 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.96 % Allowed : 20.23 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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 (0.31), residues: 722 helix: 1.40 (0.24), residues: 517 sheet: None (None), residues: 0 loop : -1.40 (0.35), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 92 TYR 0.007 0.001 TYR C 60 PHE 0.007 0.001 PHE G 27 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (11786) covalent geometry : angle 0.49637 / 0.29 (17012) hydrogen bonds : bond 0.03369 / 2.25 ( 269) hydrogen bonds : angle 2.77224 / 1.92 ( 778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.198 Fit side-chains REVERT: A 45 THR cc_start: 0.8446 (p) cc_final: 0.8238 (t) REVERT: A 65 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8790 (mt) REVERT: B 52 GLU cc_start: 0.8275 (tp30) cc_final: 0.7947 (mp0) REVERT: C 94 GLU cc_start: 0.7442 (tt0) cc_final: 0.7202 (mt-10) REVERT: E 48 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8608 (mp) REVERT: E 52 ARG cc_start: 0.7635 (mtt-85) cc_final: 0.7312 (mtm110) REVERT: E 76 GLN cc_start: 0.8434 (tt0) cc_final: 0.8163 (tt0) REVERT: E 120 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7921 (mmm) REVERT: G 60 TYR cc_start: 0.8956 (t80) cc_final: 0.8577 (t80) REVERT: G 64 GLU cc_start: 0.8398 (tp30) cc_final: 0.8150 (mm-30) REVERT: G 91 ARG cc_start: 0.8989 (mmt90) cc_final: 0.8735 (mmt-90) REVERT: H 33 ARG cc_start: 0.6631 (ttm170) cc_final: 0.6400 (ttp80) REVERT: H 106 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7787 (mt) outliers start: 18 outliers final: 9 residues processed: 134 average time/residue: 0.7122 time to fit residues: 100.8367 Evaluate side-chains 131 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.0010 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS H 47 GLN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.152636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115245 restraints weight = 13025.278| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 0.78 r_work: 0.3118 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.6789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 11786 Z= 0.149 Angle : 0.556 17.039 17012 Z= 0.314 Chirality : 0.038 0.187 1941 Planarity : 0.005 0.043 1262 Dihedral : 29.088 179.340 3618 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.96 % Allowed : 20.39 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 1.13 (0.31), residues: 722 helix: 1.55 (0.24), residues: 519 sheet: None (None), residues: 0 loop : -1.35 (0.35), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 86 TYR 0.010 0.001 TYR A 54 PHE 0.009 0.002 PHE E 78 HIS 0.019 0.002 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (11786) covalent geometry : angle 0.55594 / 0.31 (17012) hydrogen bonds : bond 0.03772 / 2.51 ( 269) hydrogen bonds : angle 2.91994 / 2.04 ( 778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.280 Fit side-chains REVERT: A 45 THR cc_start: 0.8417 (p) cc_final: 0.8190 (t) REVERT: A 65 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8878 (mt) REVERT: C 94 GLU cc_start: 0.7513 (tt0) cc_final: 0.7298 (mt-10) REVERT: D 33 ARG cc_start: 0.5667 (ttm170) cc_final: 0.5262 (ttm170) REVERT: D 57 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8225 (mmtm) REVERT: E 48 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8619 (mp) REVERT: E 52 ARG cc_start: 0.7695 (mtt-85) cc_final: 0.7359 (mtm110) REVERT: E 76 GLN cc_start: 0.8501 (tt0) cc_final: 0.8185 (tt0) REVERT: E 120 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8213 (mtm) REVERT: F 93 GLN cc_start: 0.8087 (mt0) cc_final: 0.7836 (mt0) REVERT: G 60 TYR cc_start: 0.9013 (t80) cc_final: 0.8637 (t80) REVERT: G 64 GLU cc_start: 0.8362 (tp30) cc_final: 0.8107 (mm-30) REVERT: G 91 ARG cc_start: 0.8954 (mmt90) cc_final: 0.8691 (mmt180) REVERT: H 33 ARG cc_start: 0.6433 (ttm170) cc_final: 0.6216 (ttp80) REVERT: H 76 GLU cc_start: 0.8631 (tp30) cc_final: 0.8374 (tp30) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 0.8155 time to fit residues: 112.7614 Evaluate side-chains 130 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 53 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115658 restraints weight = 12895.085| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 0.80 r_work: 0.3074 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11786 Z= 0.128 Angle : 0.517 16.073 17012 Z= 0.296 Chirality : 0.036 0.190 1941 Planarity : 0.003 0.034 1262 Dihedral : 29.062 179.452 3618 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.14 % Allowed : 22.04 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 1.36 (0.31), residues: 722 helix: 1.74 (0.24), residues: 519 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 92 TYR 0.011 0.001 TYR E 54 PHE 0.007 0.001 PHE F 61 HIS 0.012 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (11786) covalent geometry : angle 0.51737 / 0.30 (17012) hydrogen bonds : bond 0.03288 / 2.22 ( 269) hydrogen bonds : angle 2.82767 / 1.96 ( 778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.312 Fit side-chains REVERT: A 45 THR cc_start: 0.8299 (p) cc_final: 0.8090 (t) REVERT: A 65 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8779 (mt) REVERT: C 94 GLU cc_start: 0.7456 (tt0) cc_final: 0.7237 (mt-10) REVERT: D 33 ARG cc_start: 0.5595 (ttm170) cc_final: 0.5174 (ttm170) REVERT: E 48 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8587 (mp) REVERT: E 52 ARG cc_start: 0.7596 (mtt-85) cc_final: 0.7294 (mtm110) REVERT: E 76 GLN cc_start: 0.8476 (tt0) cc_final: 0.8173 (tt0) REVERT: F 93 GLN cc_start: 0.8121 (mt0) cc_final: 0.7883 (mt0) REVERT: G 64 GLU cc_start: 0.8348 (tp30) cc_final: 0.8084 (mm-30) REVERT: G 91 ARG cc_start: 0.8961 (mmt90) cc_final: 0.8753 (mmt180) REVERT: H 33 ARG cc_start: 0.6468 (ttm170) cc_final: 0.6262 (ttp80) REVERT: H 76 GLU cc_start: 0.8614 (tp30) cc_final: 0.8370 (tp30) REVERT: H 93 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7918 (mp0) outliers start: 13 outliers final: 6 residues processed: 127 average time/residue: 0.8437 time to fit residues: 112.9177 Evaluate side-chains 127 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 0.0670 chunk 19 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS F 93 GLN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115839 restraints weight = 13060.912| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 0.80 r_work: 0.3073 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.6950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11786 Z= 0.126 Angle : 0.520 15.685 17012 Z= 0.297 Chirality : 0.036 0.197 1941 Planarity : 0.004 0.045 1262 Dihedral : 29.084 179.529 3618 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.30 % Allowed : 21.55 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 1.52 (0.32), residues: 722 helix: 1.83 (0.24), residues: 521 sheet: None (None), residues: 0 loop : -1.23 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 35 TYR 0.011 0.001 TYR E 54 PHE 0.006 0.001 PHE F 61 HIS 0.009 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (11786) covalent geometry : angle 0.52029 / 0.30 (17012) hydrogen bonds : bond 0.03183 / 2.15 ( 269) hydrogen bonds : angle 2.80360 / 1.95 ( 778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.304 Fit side-chains REVERT: A 45 THR cc_start: 0.8392 (p) cc_final: 0.8166 (t) REVERT: A 65 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8785 (mt) REVERT: A 79 LYS cc_start: 0.7617 (tttm) cc_final: 0.7372 (tttm) REVERT: B 79 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8348 (mttm) REVERT: C 94 GLU cc_start: 0.7456 (tt0) cc_final: 0.7231 (mt-10) REVERT: D 33 ARG cc_start: 0.5610 (ttm170) cc_final: 0.5160 (ttm170) REVERT: D 57 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8383 (mmtt) REVERT: E 52 ARG cc_start: 0.7618 (mtt-85) cc_final: 0.7314 (mtm110) REVERT: E 76 GLN cc_start: 0.8495 (tt0) cc_final: 0.8203 (tt0) REVERT: F 93 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7796 (mt0) REVERT: G 34 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8975 (ttp-170) REVERT: G 60 TYR cc_start: 0.9062 (t80) cc_final: 0.8785 (t80) REVERT: G 64 GLU cc_start: 0.8391 (tp30) cc_final: 0.8124 (mm-30) REVERT: H 76 GLU cc_start: 0.8598 (tp30) cc_final: 0.8314 (tp30) outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 0.8438 time to fit residues: 111.2646 Evaluate side-chains 131 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 85 optimal weight: 10.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS D 82 HIS H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115889 restraints weight = 13007.541| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.80 r_work: 0.3126 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 11786 Z= 0.166 Angle : 0.798 59.163 17012 Z= 0.477 Chirality : 0.036 0.353 1941 Planarity : 0.004 0.044 1262 Dihedral : 29.085 179.523 3618 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.14 % Allowed : 22.04 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 1.52 (0.32), residues: 722 helix: 1.83 (0.24), residues: 521 sheet: None (None), residues: 0 loop : -1.23 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.009 0.001 TYR E 54 PHE 0.006 0.001 PHE F 61 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.17 (11786) covalent geometry : angle 0.79835 / 0.48 (17012) hydrogen bonds : bond 0.03185 / 2.15 ( 269) hydrogen bonds : angle 2.80431 / 1.95 ( 778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3946.77 seconds wall clock time: 67 minutes 47.28 seconds (4067.28 seconds total)