Starting phenix.real_space_refine on Sat Oct 11 02:03:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3p_44148/10_2025/9b3p_44148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3p_44148/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b3p_44148/10_2025/9b3p_44148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3p_44148/10_2025/9b3p_44148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b3p_44148/10_2025/9b3p_44148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3p_44148/10_2025/9b3p_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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: 2.45, 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: 0.88 Conformation dependent library (CDL) restraints added in 239.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.16 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: 1.60 Time building geometry restraints manager: 1.23 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: 1.030 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.050 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:9.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00191 (11786) covalent geometry : angle 0.37357 (17012) hydrogen bonds : bond 0.36240 ( 269) hydrogen bonds : angle 9.71294 ( 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 : 0.255 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: 0.8225 time to fit residues: 133.4083 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 : 0.302 ------------------------------------------------------------------------------- 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: 0.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 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: 2.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.179092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146529 restraints weight = 13790.184| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 0.81 r_work: 0.3542 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 11786 Z= 0.186 Angle : 0.561 12.144 17012 Z= 0.323 Chirality : 0.036 0.504 1941 Planarity : 0.005 0.034 1262 Dihedral : 27.836 169.925 3621 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.52 % Favored : 98.20 % Rotamer: Outliers : 2.63 % Allowed : 13.82 % Favored : 83.55 % 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 aren not related in a simple way. whole: -2.89 (0.24), residues: 722 helix: -1.65 (0.19), residues: 481 sheet: None (None), residues: 0 loop : -2.15 (0.31), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 34 TYR 0.014 0.002 TYR C 53 PHE 0.012 0.001 PHE F 61 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00413 (11786) covalent geometry : angle 0.56061 (17012) hydrogen bonds : bond 0.04242 ( 269) hydrogen bonds : angle 3.44837 ( 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 143 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.284 Fit side-chains REVERT: C 53 TYR cc_start: 0.8880 (t80) cc_final: 0.8391 (t80) REVERT: E 48 LEU cc_start: 0.8619 (mt) cc_final: 0.8229 (mp) REVERT: G 109 VAL cc_start: 0.7479 (m) cc_final: 0.7202 (p) REVERT: H 93 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7525 (mp0) outliers start: 16 outliers final: 7 residues processed: 138 average time/residue: 0.8883 time to fit residues: 128.6280 Evaluate side-chains 113 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 54 SER 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 48 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120272 restraints weight = 13154.561| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 0.82 r_work: 0.3171 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11786 Z= 0.192 Angle : 0.558 7.382 17012 Z= 0.319 Chirality : 0.035 0.145 1941 Planarity : 0.004 0.037 1262 Dihedral : 28.574 176.852 3618 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.91 % Favored : 96.81 % Rotamer: Outliers : 3.29 % Allowed : 15.46 % 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 aren not related in a simple way. whole: -1.13 (0.29), residues: 722 helix: -0.25 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.77 (0.33), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 35 TYR 0.014 0.001 TYR A 54 PHE 0.014 0.002 PHE F 61 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00435 (11786) covalent geometry : angle 0.55807 (17012) hydrogen bonds : bond 0.04426 ( 269) hydrogen bonds : angle 3.21341 ( 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 166 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.298 Fit side-chains REVERT: B 52 GLU cc_start: 0.8036 (tp30) cc_final: 0.7776 (mp0) REVERT: C 21 GLN cc_start: 0.8040 (tt0) cc_final: 0.7839 (tt0) REVERT: C 80 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.8202 (mtm-85) REVERT: E 48 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8546 (mp) REVERT: E 52 ARG cc_start: 0.7234 (mtt-85) cc_final: 0.6803 (mtp180) REVERT: E 76 GLN cc_start: 0.8444 (tt0) cc_final: 0.8171 (tt0) REVERT: G 60 TYR cc_start: 0.8960 (t80) cc_final: 0.8634 (t80) outliers start: 20 outliers final: 6 residues processed: 156 average time/residue: 0.8466 time to fit residues: 138.8430 Evaluate side-chains 129 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.0050 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.0870 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 32 optimal weight: 0.0270 chunk 17 optimal weight: 0.5980 overall best weight: 0.2630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS G 26 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.159964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123373 restraints weight = 13265.236| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 0.82 r_work: 0.3229 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11786 Z= 0.119 Angle : 0.460 6.282 17012 Z= 0.272 Chirality : 0.031 0.133 1941 Planarity : 0.003 0.035 1262 Dihedral : 28.508 177.279 3618 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.06 % Rotamer: Outliers : 2.47 % Allowed : 19.41 % Favored : 78.12 % 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 aren not related in a simple way. whole: 0.04 (0.30), residues: 722 helix: 0.72 (0.24), residues: 508 sheet: None (None), residues: 0 loop : -1.57 (0.34), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 35 TYR 0.010 0.001 TYR H 121 PHE 0.008 0.001 PHE F 61 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00254 (11786) covalent geometry : angle 0.46009 (17012) hydrogen bonds : bond 0.02539 ( 269) hydrogen bonds : angle 2.74535 ( 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: 15 poor density : 139 time to evaluate : 0.296 Fit side-chains REVERT: A 56 LYS cc_start: 0.7909 (mtpm) cc_final: 0.7694 (mttp) REVERT: A 65 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8757 (mt) REVERT: C 80 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8188 (mtm-85) REVERT: D 57 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8377 (mmtt) REVERT: E 52 ARG cc_start: 0.7175 (mtt-85) cc_final: 0.6770 (mtp180) REVERT: E 76 GLN cc_start: 0.8427 (tt0) cc_final: 0.8170 (tt0) REVERT: F 95 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7827 (mtt180) REVERT: G 60 TYR cc_start: 0.8908 (t80) cc_final: 0.8624 (t80) REVERT: H 78 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8743 (m) REVERT: H 106 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7617 (mt) outliers start: 15 outliers final: 5 residues processed: 145 average time/residue: 0.8690 time to fit residues: 132.3925 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 : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 E 68 GLN F 75 HIS H 47 GLN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116515 restraints weight = 13003.839| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 0.81 r_work: 0.3102 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.6709 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= 0.149 Angle : 0.494 6.345 17012 Z= 0.287 Chirality : 0.032 0.137 1941 Planarity : 0.004 0.035 1262 Dihedral : 28.820 178.547 3618 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.95 % Allowed : 18.42 % Favored : 77.63 % 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 aren not related in a simple way. whole: 0.57 (0.31), residues: 722 helix: 1.12 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -1.54 (0.34), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.009 0.001 TYR A 54 PHE 0.008 0.002 PHE F 61 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00335 (11786) covalent geometry : angle 0.49354 (17012) hydrogen bonds : bond 0.03298 ( 269) hydrogen bonds : angle 2.73969 ( 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 151 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.322 Fit side-chains REVERT: A 79 LYS cc_start: 0.7612 (tttm) cc_final: 0.7353 (tttm) REVERT: C 80 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8256 (mtm-85) REVERT: D 57 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8408 (mmtt) REVERT: E 52 ARG cc_start: 0.7438 (mtt-85) cc_final: 0.7209 (mtm110) REVERT: E 76 GLN cc_start: 0.8486 (tt0) cc_final: 0.8192 (tt0) REVERT: E 120 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7978 (mmm) REVERT: G 60 TYR cc_start: 0.8979 (t80) cc_final: 0.8630 (t80) REVERT: H 106 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8149 (mt) outliers start: 24 outliers final: 12 residues processed: 139 average time/residue: 0.8469 time to fit residues: 124.0974 Evaluate side-chains 132 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER 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 40 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 0.0030 chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 0.0050 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116923 restraints weight = 13114.749| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 0.82 r_work: 0.3131 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11786 Z= 0.138 Angle : 0.474 7.764 17012 Z= 0.277 Chirality : 0.031 0.144 1941 Planarity : 0.003 0.034 1262 Dihedral : 28.798 178.086 3618 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.96 % Allowed : 19.57 % 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 aren not related in a simple way. whole: 1.16 (0.32), residues: 722 helix: 1.55 (0.24), residues: 519 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 35 TYR 0.008 0.001 TYR D 83 PHE 0.007 0.001 PHE F 61 HIS 0.009 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00308 (11786) covalent geometry : angle 0.47356 (17012) hydrogen bonds : bond 0.02843 ( 269) hydrogen bonds : angle 2.68980 ( 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 137 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.316 Fit side-chains REVERT: A 59 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: A 65 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8708 (mt) REVERT: A 79 LYS cc_start: 0.7578 (tttm) cc_final: 0.7321 (tttm) REVERT: B 91 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8744 (ttpp) REVERT: C 80 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.8275 (mtm-85) REVERT: D 57 LYS cc_start: 0.8678 (mmtm) cc_final: 0.8450 (mmtt) REVERT: E 52 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.7279 (mtm110) REVERT: E 76 GLN cc_start: 0.8507 (tt0) cc_final: 0.8218 (tt0) REVERT: G 60 TYR cc_start: 0.8979 (t80) cc_final: 0.8633 (t80) REVERT: H 33 ARG cc_start: 0.6728 (ttm170) cc_final: 0.6486 (ttp80) REVERT: H 106 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8206 (mt) outliers start: 18 outliers final: 10 residues processed: 126 average time/residue: 0.8878 time to fit residues: 117.7121 Evaluate side-chains 128 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU 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 105 GLU 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 78 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.0370 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116046 restraints weight = 12980.210| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.80 r_work: 0.3124 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11786 Z= 0.133 Angle : 0.472 8.972 17012 Z= 0.276 Chirality : 0.031 0.155 1941 Planarity : 0.003 0.033 1262 Dihedral : 28.827 176.009 3618 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.29 % Allowed : 19.90 % 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 aren not related in a simple way. whole: 1.50 (0.32), residues: 722 helix: 1.85 (0.24), residues: 521 sheet: None (None), residues: 0 loop : -1.32 (0.35), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.007 0.001 TYR H 121 PHE 0.007 0.001 PHE F 61 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00295 (11786) covalent geometry : angle 0.47244 (17012) hydrogen bonds : bond 0.02801 ( 269) hydrogen bonds : angle 2.64451 ( 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 139 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.301 Fit side-chains REVERT: A 59 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: A 65 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8657 (mt) REVERT: A 79 LYS cc_start: 0.7562 (tttm) cc_final: 0.7323 (tttm) REVERT: C 20 SER cc_start: 0.9001 (p) cc_final: 0.8757 (m) REVERT: C 80 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.8246 (mtm-85) REVERT: E 52 ARG cc_start: 0.7559 (mtt-85) cc_final: 0.7291 (mtm110) REVERT: E 76 GLN cc_start: 0.8484 (tt0) cc_final: 0.8182 (tt0) REVERT: E 120 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.7839 (mmm) REVERT: G 60 TYR cc_start: 0.8980 (t80) cc_final: 0.8635 (t80) REVERT: H 106 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8276 (mt) outliers start: 20 outliers final: 9 residues processed: 129 average time/residue: 0.8487 time to fit residues: 115.5108 Evaluate side-chains 130 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 112 SER 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 40 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 112 SER 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: 1.9990 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109036 restraints weight = 13021.162| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 0.83 r_work: 0.3002 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.7771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11786 Z= 0.234 Angle : 0.593 9.444 17012 Z= 0.338 Chirality : 0.037 0.153 1941 Planarity : 0.004 0.034 1262 Dihedral : 29.450 167.419 3618 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.78 % Allowed : 19.41 % 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 aren not related in a simple way. whole: 1.01 (0.31), residues: 722 helix: 1.47 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.50 (0.35), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 35 TYR 0.012 0.002 TYR A 54 PHE 0.011 0.002 PHE E 78 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00543 (11786) covalent geometry : angle 0.59310 (17012) hydrogen bonds : bond 0.04146 ( 269) hydrogen bonds : angle 2.99327 ( 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 147 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.348 Fit side-chains REVERT: A 115 LYS cc_start: 0.8364 (mttp) cc_final: 0.8141 (mttt) REVERT: C 21 GLN cc_start: 0.8115 (tt0) cc_final: 0.7699 (tt0) REVERT: C 80 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8368 (mtm-85) REVERT: E 52 ARG cc_start: 0.7765 (mtt-85) cc_final: 0.7398 (mtm110) REVERT: E 76 GLN cc_start: 0.8540 (tt0) cc_final: 0.8208 (tt0) REVERT: E 77 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8063 (p0) REVERT: G 37 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8412 (mtpt) REVERT: G 60 TYR cc_start: 0.9081 (t80) cc_final: 0.8742 (t80) REVERT: H 33 ARG cc_start: 0.6441 (ttm170) cc_final: 0.6225 (ttp80) REVERT: H 93 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7861 (mp0) outliers start: 23 outliers final: 14 residues processed: 135 average time/residue: 0.8531 time to fit residues: 121.4821 Evaluate side-chains 131 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 86 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 77 ASP 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 H residue 48 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111813 restraints weight = 12873.953| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 0.80 r_work: 0.3053 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.7759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11786 Z= 0.158 Angle : 0.516 9.883 17012 Z= 0.300 Chirality : 0.033 0.141 1941 Planarity : 0.003 0.033 1262 Dihedral : 29.096 167.295 3618 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.47 % Allowed : 21.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.32), residues: 722 helix: 1.77 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.39 (0.36), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 35 TYR 0.013 0.001 TYR C 60 PHE 0.006 0.001 PHE F 61 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00359 (11786) covalent geometry : angle 0.51601 (17012) hydrogen bonds : bond 0.02950 ( 269) hydrogen bonds : angle 2.80810 ( 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 132 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.288 Fit side-chains REVERT: A 59 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: A 79 LYS cc_start: 0.7613 (tttm) cc_final: 0.7319 (tttm) REVERT: E 52 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7365 (mtm110) REVERT: E 76 GLN cc_start: 0.8506 (tt0) cc_final: 0.8203 (tt0) REVERT: G 60 TYR cc_start: 0.9099 (t80) cc_final: 0.8789 (t80) outliers start: 15 outliers final: 9 residues processed: 127 average time/residue: 0.9057 time to fit residues: 120.8579 Evaluate side-chains 123 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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 D residue 112 SER 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 H residue 78 SER Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 0.0770 chunk 68 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112070 restraints weight = 13050.651| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 0.81 r_work: 0.3010 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.7824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11786 Z= 0.148 Angle : 0.505 10.261 17012 Z= 0.294 Chirality : 0.032 0.154 1941 Planarity : 0.003 0.031 1262 Dihedral : 29.102 165.325 3618 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.97 % Allowed : 22.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.32), residues: 722 helix: 1.95 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.26 (0.36), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 35 TYR 0.010 0.001 TYR C 60 PHE 0.007 0.001 PHE F 61 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00334 (11786) covalent geometry : angle 0.50454 (17012) hydrogen bonds : bond 0.02935 ( 269) hydrogen bonds : angle 2.72133 ( 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 131 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.281 Fit side-chains REVERT: A 65 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8826 (mt) REVERT: A 79 LYS cc_start: 0.7633 (tttm) cc_final: 0.7325 (tttm) REVERT: E 52 ARG cc_start: 0.7652 (mtt-85) cc_final: 0.7341 (mtm110) REVERT: E 76 GLN cc_start: 0.8536 (tt0) cc_final: 0.8236 (tt0) REVERT: G 60 TYR cc_start: 0.9093 (t80) cc_final: 0.8772 (t80) REVERT: H 93 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7833 (mp0) outliers start: 12 outliers final: 8 residues processed: 126 average time/residue: 0.7774 time to fit residues: 103.4071 Evaluate side-chains 125 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 D residue 112 SER 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 H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 0.0060 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112689 restraints weight = 13010.304| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 0.81 r_work: 0.3053 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.7842 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= 0.139 Angle : 0.502 10.254 17012 Z= 0.293 Chirality : 0.032 0.147 1941 Planarity : 0.003 0.033 1262 Dihedral : 29.055 164.654 3618 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.14 % Allowed : 22.70 % Favored : 75.16 % 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 aren not related in a simple way. whole: 1.81 (0.32), residues: 722 helix: 2.07 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.19 (0.36), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 35 TYR 0.009 0.001 TYR C 60 PHE 0.006 0.001 PHE F 61 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00309 (11786) covalent geometry : angle 0.50202 (17012) hydrogen bonds : bond 0.02799 ( 269) hydrogen bonds : angle 2.73059 ( 778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4145.20 seconds wall clock time: 71 minutes 7.88 seconds (4267.88 seconds total)