Starting phenix.real_space_refine on Mon Jul 28 22:34:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3p_44148/07_2025/9b3p_44148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3p_44148/07_2025/9b3p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3p_44148/07_2025/9b3p_44148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3p_44148/07_2025/9b3p_44148.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3p_44148/07_2025/9b3p_44148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3p_44148/07_2025/9b3p_44148.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.50, per 1000 atoms: 0.59 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: 2.63 Conformation dependent library (CDL) restraints added in 766.7 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: 3.58 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: 2.81 Time building geometry restraints manager: 3.18 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=" C3' DT I -32 " pdb=" O3' DT I -32 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CA ILE F 29 " pdb=" CB ILE F 29 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.25e-01 bond pdb=" C3' DT I -50 " pdb=" O3' DT I -50 " ideal model delta sigma weight residual 1.422 1.447 -0.025 3.00e-02 1.11e+03 6.98e-01 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.446 -0.024 3.00e-02 1.11e+03 6.62e-01 bond pdb=" C THR H 90 " pdb=" O THR H 90 " ideal model delta sigma weight residual 1.244 1.236 0.008 1.17e-02 7.31e+03 4.90e-01 ... (remaining 11781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 16595 0.99 - 1.98: 272 1.98 - 2.97: 137 2.97 - 3.96: 2 3.96 - 4.95: 6 Bond angle restraints: 17012 Sorted by residual: angle pdb=" C THR H 90 " pdb=" CA THR H 90 " pdb=" CB THR H 90 " ideal model delta sigma weight residual 114.40 110.29 4.11 1.25e+00 6.40e-01 1.08e+01 angle pdb=" C LEU C 76 " pdb=" N LYS C 77 " pdb=" CA LYS C 77 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.67e+00 angle pdb=" C3' DT I -32 " pdb=" O3' DT I -32 " pdb=" P DA I -31 " ideal model delta sigma weight residual 120.20 122.92 -2.72 1.50e+00 4.44e-01 3.29e+00 angle pdb=" C7 DT I 15 " pdb=" C5 DT I 15 " pdb=" C6 DT I 15 " ideal model delta sigma weight residual 124.00 121.74 2.26 1.50e+00 4.44e-01 2.27e+00 angle pdb=" C7 DT J 1 " pdb=" C5 DT J 1 " pdb=" C6 DT J 1 " ideal model delta sigma weight residual 124.00 121.74 2.26 1.50e+00 4.44e-01 2.27e+00 ... (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: 1510 0.025 - 0.051: 300 0.051 - 0.076: 83 0.076 - 0.101: 30 0.101 - 0.127: 18 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: 1.910 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.820 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 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 : 0.002 0.033 11786 Z= 0.102 Angle : 0.374 4.949 17012 Z= 0.250 Chirality : 0.027 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.001 0.000 HIS D 82 PHE 0.001 0.000 PHE F 100 TYR 0.001 0.000 TYR F 72 ARG 0.001 0.000 ARG G 91 Details of bonding type rmsd hydrogen bonds : bond 0.36240 ( 269) hydrogen bonds : angle 9.71294 ( 778) covalent geometry : bond 0.00191 (11786) covalent geometry : angle 0.37357 (17012) *********************** 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 : 0.877 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: 1.7186 time to fit residues: 279.5049 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 : 0.761 ------------------------------------------------------------------------------- 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 79 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 63 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 26 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.183243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151592 restraints weight = 13927.617| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 0.81 r_work: 0.3611 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 11786 Z= 0.161 Angle : 0.543 11.661 17012 Z= 0.310 Chirality : 0.033 0.129 1941 Planarity : 0.004 0.033 1262 Dihedral : 27.621 170.106 3621 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.94 % Favored : 97.78 % Rotamer: Outliers : 2.47 % Allowed : 14.97 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.24), residues: 722 helix: -1.66 (0.19), residues: 474 sheet: None (None), residues: 0 loop : -2.28 (0.30), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 113 PHE 0.011 0.001 PHE F 61 TYR 0.016 0.001 TYR C 53 ARG 0.004 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 269) hydrogen bonds : angle 3.44201 ( 778) covalent geometry : bond 0.00369 (11786) covalent geometry : angle 0.54297 (17012) *********************** 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 136 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.058 Fit side-chains REVERT: C 112 HIS cc_start: 0.7056 (m170) cc_final: 0.6687 (m170) REVERT: E 48 LEU cc_start: 0.8558 (mt) cc_final: 0.8162 (mp) REVERT: F 95 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7542 (mtt180) REVERT: H 93 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7493 (mp0) outliers start: 15 outliers final: 4 residues processed: 132 average time/residue: 2.0701 time to fit residues: 286.6358 Evaluate side-chains 109 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 0.0470 chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 85 HIS E 68 GLN F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.165879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130067 restraints weight = 13433.285| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 0.83 r_work: 0.3309 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11786 Z= 0.146 Angle : 0.503 7.561 17012 Z= 0.291 Chirality : 0.032 0.142 1941 Planarity : 0.004 0.065 1262 Dihedral : 28.194 174.581 3618 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.22 % Favored : 97.51 % Rotamer: Outliers : 2.63 % Allowed : 16.28 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.28), residues: 722 helix: -0.05 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -2.07 (0.31), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.011 0.001 PHE F 61 TYR 0.011 0.001 TYR H 121 ARG 0.008 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 269) hydrogen bonds : angle 3.00254 ( 778) covalent geometry : bond 0.00312 (11786) covalent geometry : angle 0.50259 (17012) *********************** 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 154 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.819 Fit side-chains REVERT: A 65 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8873 (mt) REVERT: D 84 ASN cc_start: 0.8170 (m-40) cc_final: 0.7868 (m110) REVERT: E 48 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8393 (mp) REVERT: E 52 ARG cc_start: 0.7140 (mtt-85) cc_final: 0.6749 (mtp180) REVERT: E 83 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7706 (mtm180) outliers start: 16 outliers final: 4 residues processed: 144 average time/residue: 1.7822 time to fit residues: 270.1368 Evaluate side-chains 120 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 48 LEU 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 79 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN G 26 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113774 restraints weight = 12935.959| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 0.81 r_work: 0.3077 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11786 Z= 0.214 Angle : 0.600 14.764 17012 Z= 0.335 Chirality : 0.036 0.152 1941 Planarity : 0.004 0.039 1262 Dihedral : 29.159 178.148 3618 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.32 % Favored : 96.40 % Rotamer: Outliers : 4.93 % Allowed : 15.79 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.30), residues: 722 helix: 0.34 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.63 (0.34), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.011 0.002 PHE F 61 TYR 0.016 0.002 TYR E 54 ARG 0.009 0.001 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 269) hydrogen bonds : angle 3.11059 ( 778) covalent geometry : bond 0.00497 (11786) covalent geometry : angle 0.60050 (17012) *********************** 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 165 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.806 Fit side-chains REVERT: B 52 GLU cc_start: 0.8316 (tp30) cc_final: 0.8058 (mp0) REVERT: B 63 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: C 21 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: C 94 GLU cc_start: 0.7506 (tt0) cc_final: 0.7268 (mt-10) REVERT: D 57 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8349 (mmtt) REVERT: E 48 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8667 (mp) REVERT: E 52 ARG cc_start: 0.7373 (mtt-85) cc_final: 0.7086 (mtm110) REVERT: E 76 GLN cc_start: 0.8479 (tt0) cc_final: 0.8214 (tt0) REVERT: E 116 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8294 (ttp-110) REVERT: G 37 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8487 (mtpt) REVERT: G 60 TYR cc_start: 0.9048 (t80) cc_final: 0.8796 (t80) REVERT: H 33 ARG cc_start: 0.6493 (ttm170) cc_final: 0.6286 (ttp80) REVERT: H 93 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7844 (mp0) outliers start: 30 outliers final: 9 residues processed: 151 average time/residue: 1.7625 time to fit residues: 280.9067 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 : 0.858 ------------------------------------------------------------------------------- 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 63 GLU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 116 ARG 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 G residue 49 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS D 82 HIS H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111538 restraints weight = 12868.885| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.79 r_work: 0.3027 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11786 Z= 0.198 Angle : 0.543 12.279 17012 Z= 0.311 Chirality : 0.035 0.145 1941 Planarity : 0.004 0.042 1262 Dihedral : 29.149 172.341 3618 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.47 % Allowed : 20.56 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.31), residues: 722 helix: 0.83 (0.24), residues: 521 sheet: None (None), residues: 0 loop : -1.56 (0.34), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 82 PHE 0.011 0.002 PHE E 78 TYR 0.013 0.001 TYR A 54 ARG 0.010 0.001 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 269) hydrogen bonds : angle 2.93003 ( 778) covalent geometry : bond 0.00455 (11786) covalent geometry : angle 0.54287 (17012) *********************** 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 144 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.865 Fit side-chains REVERT: C 21 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: D 33 ARG cc_start: 0.5709 (ttm170) cc_final: 0.5190 (ttt180) REVERT: E 52 ARG cc_start: 0.7500 (mtt-85) cc_final: 0.7247 (mtm110) REVERT: E 76 GLN cc_start: 0.8537 (tt0) cc_final: 0.8250 (tt0) REVERT: H 33 ARG cc_start: 0.6277 (ttm170) cc_final: 0.6073 (ttp80) outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 1.8022 time to fit residues: 260.6527 Evaluate side-chains 134 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 C residue 21 GLN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR 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 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.0170 chunk 3 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112489 restraints weight = 12991.185| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 0.79 r_work: 0.3054 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.7535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11786 Z= 0.148 Angle : 0.506 13.201 17012 Z= 0.292 Chirality : 0.032 0.157 1941 Planarity : 0.003 0.038 1262 Dihedral : 29.077 170.666 3618 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.96 % Allowed : 19.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.31), residues: 722 helix: 1.33 (0.24), residues: 521 sheet: None (None), residues: 0 loop : -1.46 (0.35), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 82 PHE 0.007 0.001 PHE F 61 TYR 0.008 0.001 TYR C 60 ARG 0.007 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 269) hydrogen bonds : angle 2.77048 ( 778) covalent geometry : bond 0.00334 (11786) covalent geometry : angle 0.50567 (17012) *********************** 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 143 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.902 Fit side-chains REVERT: A 65 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8810 (mt) REVERT: A 79 LYS cc_start: 0.7616 (tttm) cc_final: 0.7310 (tttm) REVERT: C 21 GLN cc_start: 0.7976 (tt0) cc_final: 0.7398 (tt0) REVERT: D 33 ARG cc_start: 0.5632 (ttm170) cc_final: 0.5100 (ttt180) REVERT: E 48 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8656 (mp) REVERT: E 52 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.7257 (mtm110) REVERT: E 76 GLN cc_start: 0.8482 (tt0) cc_final: 0.8197 (tt0) REVERT: E 116 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8173 (ttp-170) REVERT: H 33 ARG cc_start: 0.6249 (ttm170) cc_final: 0.6033 (ttp80) outliers start: 18 outliers final: 11 residues processed: 134 average time/residue: 2.2707 time to fit residues: 320.9283 Evaluate side-chains 136 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 91 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108748 restraints weight = 13076.745| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 0.80 r_work: 0.2976 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.7881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11786 Z= 0.185 Angle : 0.545 14.339 17012 Z= 0.311 Chirality : 0.034 0.154 1941 Planarity : 0.004 0.039 1262 Dihedral : 29.270 164.913 3618 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.80 % Allowed : 20.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 722 helix: 1.42 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS H 82 PHE 0.008 0.002 PHE E 78 TYR 0.011 0.001 TYR G 60 ARG 0.007 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 269) hydrogen bonds : angle 2.87007 ( 778) covalent geometry : bond 0.00428 (11786) covalent geometry : angle 0.54534 (17012) *********************** 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 141 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.900 Fit side-chains REVERT: A 79 LYS cc_start: 0.7644 (tttm) cc_final: 0.7371 (tttm) REVERT: E 48 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8665 (mp) REVERT: E 52 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7339 (mtm110) REVERT: E 76 GLN cc_start: 0.8525 (tt0) cc_final: 0.8232 (tt0) REVERT: E 116 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8252 (ttp-170) REVERT: G 37 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8437 (mtpt) REVERT: H 33 ARG cc_start: 0.6245 (ttm170) cc_final: 0.6037 (ttp80) REVERT: H 93 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7920 (mp0) outliers start: 17 outliers final: 11 residues processed: 134 average time/residue: 1.8257 time to fit residues: 258.5634 Evaluate side-chains 135 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 116 ARG 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 G residue 49 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110379 restraints weight = 12961.010| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 0.79 r_work: 0.2996 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.7903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11786 Z= 0.154 Angle : 0.526 14.200 17012 Z= 0.301 Chirality : 0.032 0.151 1941 Planarity : 0.004 0.037 1262 Dihedral : 29.201 164.836 3618 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.12 % Allowed : 20.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.32), residues: 722 helix: 1.63 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.32 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 82 PHE 0.007 0.001 PHE E 78 TYR 0.009 0.001 TYR H 121 ARG 0.007 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 269) hydrogen bonds : angle 2.84533 ( 778) covalent geometry : bond 0.00349 (11786) covalent geometry : angle 0.52609 (17012) *********************** 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 143 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.836 Fit side-chains REVERT: A 79 LYS cc_start: 0.7626 (tttm) cc_final: 0.7355 (tttm) REVERT: C 21 GLN cc_start: 0.8050 (tt0) cc_final: 0.7375 (tt0) REVERT: E 52 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7351 (mtm110) REVERT: E 76 GLN cc_start: 0.8516 (tt0) cc_final: 0.8229 (tt0) REVERT: G 37 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8413 (mtpt) REVERT: H 93 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7866 (mp0) outliers start: 19 outliers final: 14 residues processed: 133 average time/residue: 1.6870 time to fit residues: 236.8969 Evaluate side-chains 138 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 2 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 0.0050 chunk 4 optimal weight: 0.0050 chunk 49 optimal weight: 0.8980 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110300 restraints weight = 13004.695| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 0.79 r_work: 0.3000 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.7913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11786 Z= 0.146 Angle : 0.523 13.959 17012 Z= 0.299 Chirality : 0.032 0.147 1941 Planarity : 0.003 0.035 1262 Dihedral : 29.168 164.754 3618 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.96 % Allowed : 21.38 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.32), residues: 722 helix: 1.74 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.27 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 82 PHE 0.005 0.001 PHE F 61 TYR 0.008 0.001 TYR H 121 ARG 0.007 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 269) hydrogen bonds : angle 2.82996 ( 778) covalent geometry : bond 0.00330 (11786) covalent geometry : angle 0.52258 (17012) *********************** 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 143 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.096 Fit side-chains REVERT: A 65 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8898 (mt) REVERT: A 79 LYS cc_start: 0.7650 (tttm) cc_final: 0.7352 (tttm) REVERT: C 21 GLN cc_start: 0.8064 (tt0) cc_final: 0.7364 (tt0) REVERT: E 52 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.7351 (mtm110) REVERT: E 76 GLN cc_start: 0.8499 (tt0) cc_final: 0.8205 (tt0) REVERT: E 116 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8091 (ttp-170) REVERT: G 37 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8430 (mtpt) REVERT: H 93 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7862 (mp0) outliers start: 18 outliers final: 13 residues processed: 133 average time/residue: 2.3668 time to fit residues: 331.4174 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 : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 70 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111941 restraints weight = 12971.495| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 0.79 r_work: 0.3013 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.7913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11786 Z= 0.137 Angle : 0.517 14.105 17012 Z= 0.296 Chirality : 0.031 0.148 1941 Planarity : 0.003 0.034 1262 Dihedral : 29.127 164.493 3618 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.63 % Allowed : 21.38 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.32), residues: 722 helix: 1.86 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.23 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 82 PHE 0.004 0.001 PHE F 61 TYR 0.008 0.001 TYR H 121 ARG 0.008 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 269) hydrogen bonds : angle 2.81384 ( 778) covalent geometry : bond 0.00305 (11786) covalent geometry : angle 0.51744 (17012) ********************** 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 141 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.007 Fit side-chains REVERT: A 65 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8876 (mt) REVERT: A 79 LYS cc_start: 0.7630 (tttm) cc_final: 0.7331 (tttm) REVERT: C 21 GLN cc_start: 0.8046 (tt0) cc_final: 0.7348 (tt0) REVERT: E 52 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7345 (mtm110) REVERT: E 76 GLN cc_start: 0.8493 (tt0) cc_final: 0.8211 (tt0) REVERT: E 116 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8063 (ttp-170) REVERT: G 37 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8425 (mtpt) REVERT: H 93 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7853 (mp0) outliers start: 16 outliers final: 11 residues processed: 131 average time/residue: 1.9766 time to fit residues: 273.0333 Evaluate side-chains 138 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 78 SER 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 69 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.104640 restraints weight = 13223.682| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 0.87 r_work: 0.2961 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.8241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11786 Z= 0.248 Angle : 0.610 15.260 17012 Z= 0.343 Chirality : 0.038 0.142 1941 Planarity : 0.005 0.041 1262 Dihedral : 29.640 166.121 3618 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.80 % Allowed : 21.71 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.32), residues: 722 helix: 1.51 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.34 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 82 PHE 0.012 0.002 PHE E 78 TYR 0.016 0.002 TYR G 60 ARG 0.009 0.001 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 269) hydrogen bonds : angle 3.08190 ( 778) covalent geometry : bond 0.00577 (11786) covalent geometry : angle 0.61021 (17012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10033.21 seconds wall clock time: 182 minutes 47.77 seconds (10967.77 seconds total)