Starting phenix.real_space_refine on Tue Feb 11 17:09:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8enr_28277/02_2025/8enr_28277.cif Found real_map, /net/cci-nas-00/data/ceres_data/8enr_28277/02_2025/8enr_28277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8enr_28277/02_2025/8enr_28277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8enr_28277/02_2025/8enr_28277.map" model { file = "/net/cci-nas-00/data/ceres_data/8enr_28277/02_2025/8enr_28277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8enr_28277/02_2025/8enr_28277.cif" } resolution = 3.8 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= 0.002 sd= 0.026 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3776 2.51 5 N 1176 2.21 5 O 1416 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-5592/modules/chem_data/mon_lib" Total number of atoms: 6392 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Link IDs: {'TRANS': 110} Chain: "B" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Link IDs: {'TRANS': 110} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Link IDs: {'TRANS': 110} Chain: "D" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Link IDs: {'TRANS': 110} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Link IDs: {'TRANS': 110} Chain: "F" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Link IDs: {'TRANS': 110} Chain: "G" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Link IDs: {'TRANS': 110} Chain: "H" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Link IDs: {'TRANS': 110} Time building chain proxies: 4.36, per 1000 atoms: 0.68 Number of scatterers: 6392 At special positions: 0 Unit cell: (54.8906, 38.9547, 207.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1416 8.00 N 1176 7.00 C 3776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 952.0 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 65.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 142 removed outlier: 6.303A pdb=" N LEU A 45 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR B 138 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE A 47 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N CYS B 140 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLN A 49 " --> pdb=" O CYS B 140 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE B 142 " --> pdb=" O GLN A 49 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 51 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N SER B 89 " --> pdb=" O MET B 113 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL B 115 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 91 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN B 117 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR B 93 " --> pdb=" O GLN B 117 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLY B 119 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG B 95 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N SER B 43 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN C 136 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU B 45 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR C 138 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE B 47 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N CYS C 140 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN B 49 " --> pdb=" O CYS C 140 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N PHE C 142 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLY B 51 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU C 112 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL C 137 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR C 114 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN C 139 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS C 116 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY C 141 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE C 118 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.529A pdb=" N GLY A 123 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ALA A 148 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA A 125 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLN A 150 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP A 127 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP A 86 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS A 109 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 147 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS B 149 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 60 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY B 123 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ALA B 148 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 125 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLN B 150 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP B 127 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER B 100 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N VAL B 126 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 102 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLN B 128 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 104 " --> pdb=" O GLN B 128 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 107 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 86 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS B 109 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER B 55 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL B 81 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN B 83 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 59 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER B 85 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 147 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 107 " --> pdb=" O GLY C 84 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP C 86 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS C 109 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER C 55 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL C 81 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLN C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C 59 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N SER C 85 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 44 through 51 removed outlier: 6.676A pdb=" N GLU D 44 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE D 70 " --> pdb=" O GLU D 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASN D 46 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLN D 72 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR D 48 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLY D 74 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR D 50 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER D 89 " --> pdb=" O MET D 113 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL D 115 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP D 91 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLN D 117 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR D 93 " --> pdb=" O GLN D 117 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY D 119 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG D 95 " --> pdb=" O GLY D 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 55 through 60 removed outlier: 6.690A pdb=" N SER D 55 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL D 81 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU D 57 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLN D 83 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU D 59 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER D 85 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASP D 86 " --> pdb=" O ASN D 107 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS D 109 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER D 100 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL D 126 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR D 102 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLN D 128 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP D 104 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY D 123 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA D 148 " --> pdb=" O GLY D 123 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA D 125 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLN D 150 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP D 127 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN D 145 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA E 58 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR D 147 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLN E 60 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS D 149 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER E 55 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N VAL E 81 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU E 57 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLN E 83 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU E 59 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER E 85 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR E 61 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY E 78 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU E 103 " --> pdb=" O GLY E 78 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASP E 80 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLN E 105 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY E 82 " --> pdb=" O GLN E 105 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASN E 107 " --> pdb=" O GLY E 82 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N GLY E 84 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS E 109 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP E 86 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER E 100 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL E 126 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR E 102 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLN E 128 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP E 104 " --> pdb=" O GLN E 128 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY E 123 " --> pdb=" O ALA E 146 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA E 148 " --> pdb=" O GLY E 123 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA E 125 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLN E 150 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP E 127 " --> pdb=" O GLN E 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 44 through 52 removed outlier: 6.466A pdb=" N SER E 89 " --> pdb=" O MET E 113 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL E 115 " --> pdb=" O SER E 89 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP E 91 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLN E 117 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR E 93 " --> pdb=" O GLN E 117 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY E 119 " --> pdb=" O THR E 93 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG E 95 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N SER E 134 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ILE F 47 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASN E 136 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N GLN F 49 " --> pdb=" O ASN E 136 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N THR E 138 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N GLY F 51 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N CYS E 140 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU G 45 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE G 47 " --> pdb=" O ASN F 136 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR F 138 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN G 49 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS F 140 " --> pdb=" O GLN G 49 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY G 51 " --> pdb=" O CYS F 140 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE F 142 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU H 45 " --> pdb=" O SER G 134 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE H 47 " --> pdb=" O ASN G 136 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN H 49 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY H 51 " --> pdb=" O CYS G 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 55 through 60 removed outlier: 6.738A pdb=" N SER F 55 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL F 81 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU F 57 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN F 83 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU F 59 " --> pdb=" O GLN F 83 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER F 85 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN F 107 " --> pdb=" O GLY F 84 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP F 86 " --> pdb=" O ASN F 107 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS F 109 " --> pdb=" O ASP F 86 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER F 100 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL F 126 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR F 102 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLN F 128 " --> pdb=" O THR F 102 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP F 104 " --> pdb=" O GLN F 128 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN F 145 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA G 58 " --> pdb=" O ASN F 145 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N THR F 147 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN G 60 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS F 149 " --> pdb=" O GLN G 60 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER G 85 " --> pdb=" O THR G 61 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASP G 86 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS G 109 " --> pdb=" O ASP G 86 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER G 100 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL G 126 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR G 102 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLN G 128 " --> pdb=" O THR G 102 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP G 104 " --> pdb=" O GLN G 128 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY G 123 " --> pdb=" O ALA G 146 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA G 148 " --> pdb=" O GLY G 123 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA G 125 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLN G 150 " --> pdb=" O ALA G 125 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP G 127 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN G 145 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA H 58 " --> pdb=" O ASN G 145 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR G 147 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLN H 60 " --> pdb=" O THR G 147 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N HIS G 149 " --> pdb=" O GLN H 60 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER H 55 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N VAL H 81 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU H 57 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLN H 83 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU H 59 " --> pdb=" O GLN H 83 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER H 85 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP H 86 " --> pdb=" O ASN H 107 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS H 109 " --> pdb=" O ASP H 86 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER H 100 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL H 126 " --> pdb=" O SER H 100 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR H 102 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLN H 128 " --> pdb=" O THR H 102 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP H 104 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY H 123 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA H 148 " --> pdb=" O GLY H 123 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA H 125 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLN H 150 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP H 127 " --> pdb=" O GLN H 150 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.65 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: 2374 1.34 - 1.46: 1280 1.46 - 1.58: 2786 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6472 Sorted by residual: bond pdb=" CA GLY F 82 " pdb=" C GLY F 82 " ideal model delta sigma weight residual 1.514 1.538 -0.023 1.41e-02 5.03e+03 2.75e+00 bond pdb=" CG1 ILE C 47 " pdb=" CD1 ILE C 47 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.82e+00 bond pdb=" CA ASN G 107 " pdb=" CB ASN G 107 " ideal model delta sigma weight residual 1.532 1.551 -0.019 1.43e-02 4.89e+03 1.72e+00 bond pdb=" CB ASN G 107 " pdb=" CG ASN G 107 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CB CYS G 63 " pdb=" SG CYS G 63 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.53e+00 ... (remaining 6467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 8345 1.59 - 3.18: 326 3.18 - 4.77: 56 4.77 - 6.36: 16 6.36 - 7.95: 9 Bond angle restraints: 8752 Sorted by residual: angle pdb=" N GLY A 119 " pdb=" CA GLY A 119 " pdb=" C GLY A 119 " ideal model delta sigma weight residual 111.21 115.55 -4.34 1.04e+00 9.25e-01 1.75e+01 angle pdb=" N GLY C 75 " pdb=" CA GLY C 75 " pdb=" C GLY C 75 " ideal model delta sigma weight residual 110.80 116.78 -5.98 1.71e+00 3.42e-01 1.22e+01 angle pdb=" CA MET G 113 " pdb=" CB MET G 113 " pdb=" CG MET G 113 " ideal model delta sigma weight residual 114.10 120.84 -6.74 2.00e+00 2.50e-01 1.13e+01 angle pdb=" N GLY B 119 " pdb=" CA GLY B 119 " pdb=" C GLY B 119 " ideal model delta sigma weight residual 111.21 114.55 -3.34 1.04e+00 9.25e-01 1.03e+01 angle pdb=" CA LYS D 109 " pdb=" CB LYS D 109 " pdb=" CG LYS D 109 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.08e+00 ... (remaining 8747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 3352 17.61 - 35.23: 280 35.23 - 52.84: 51 52.84 - 70.46: 23 70.46 - 88.07: 6 Dihedral angle restraints: 3712 sinusoidal: 1320 harmonic: 2392 Sorted by residual: dihedral pdb=" CA ASP E 62 " pdb=" C ASP E 62 " pdb=" N CYS E 63 " pdb=" CA CYS E 63 " ideal model delta harmonic sigma weight residual -180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR D 102 " pdb=" C THR D 102 " pdb=" N LEU D 103 " pdb=" CA LEU D 103 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASP G 62 " pdb=" C ASP G 62 " pdb=" N CYS G 63 " pdb=" CA CYS G 63 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 3709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 651 0.041 - 0.082: 186 0.082 - 0.123: 77 0.123 - 0.164: 13 0.164 - 0.205: 1 Chirality restraints: 928 Sorted by residual: chirality pdb=" CG LEU C 45 " pdb=" CB LEU C 45 " pdb=" CD1 LEU C 45 " pdb=" CD2 LEU C 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASN G 107 " pdb=" N ASN G 107 " pdb=" C ASN G 107 " pdb=" CB ASN G 107 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA ILE E 70 " pdb=" N ILE E 70 " pdb=" C ILE E 70 " pdb=" CB ILE E 70 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 925 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 97 " -0.009 2.00e-02 2.50e+03 1.26e-02 2.77e+00 pdb=" CG PHE H 97 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE H 97 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE H 97 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE H 97 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE H 97 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 97 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 145 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C ASN F 145 " 0.027 2.00e-02 2.50e+03 pdb=" O ASN F 145 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA F 146 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 83 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C GLN G 83 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN G 83 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY G 84 " 0.008 2.00e-02 2.50e+03 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 377 2.74 - 3.28: 6121 3.28 - 3.82: 11598 3.82 - 4.36: 13828 4.36 - 4.90: 24256 Nonbonded interactions: 56180 Sorted by model distance: nonbonded pdb=" OE2 GLU H 112 " pdb=" OG1 THR H 114 " model vdw 2.204 3.040 nonbonded pdb=" O ASP H 62 " pdb=" NH1 ARG H 64 " model vdw 2.206 3.120 nonbonded pdb=" NE2 GLN B 128 " pdb=" OE1 GLN B 150 " model vdw 2.222 3.120 nonbonded pdb=" OG SER C 85 " pdb=" OE1 GLN C 105 " model vdw 2.233 3.040 nonbonded pdb=" NE2 GLN C 49 " pdb=" OE1 GLN C 72 " model vdw 2.235 3.120 ... (remaining 56175 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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 group one per residue 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: 1.050 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.490 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3732 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 : 0.004 0.058 6472 Z= 0.277 Angle : 0.801 7.953 8752 Z= 0.452 Chirality : 0.047 0.205 928 Planarity : 0.004 0.050 1232 Dihedral : 14.876 88.069 2224 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.89 % Allowed : 8.93 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.04 (0.25), residues: 872 helix: None (None), residues: 0 sheet: 1.43 (0.17), residues: 696 loop : -2.58 (0.28), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 106 HIS 0.006 0.002 HIS C 149 PHE 0.029 0.002 PHE H 97 TYR 0.016 0.002 TYR F 151 ARG 0.007 0.001 ARG F 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: B 113 MET cc_start: 0.2711 (tpt) cc_final: 0.2451 (tpt) REVERT: D 68 LEU cc_start: 0.4570 (tt) cc_final: 0.4095 (mt) REVERT: E 112 GLU cc_start: 0.5151 (tm-30) cc_final: 0.4513 (mp0) REVERT: G 44 GLU cc_start: 0.7946 (pt0) cc_final: 0.7486 (pm20) REVERT: H 68 LEU cc_start: 0.6516 (tp) cc_final: 0.6312 (mt) outliers start: 6 outliers final: 4 residues processed: 110 average time/residue: 0.1758 time to fit residues: 26.1026 Evaluate side-chains 94 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 102 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS E 107 ASN F 73 HIS F 94 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS G 105 GLN G 128 GLN ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6435 r_free = 0.6435 target = 0.512651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.7103 r_free = 0.7103 target = 0.393971 restraints weight = 11456.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.7050 r_free = 0.7050 target = 0.395005 restraints weight = 15765.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.7050 r_free = 0.7050 target = 0.398271 restraints weight = 14458.691| |-----------------------------------------------------------------------------| r_work (final): 0.6384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4858 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 6472 Z= 0.452 Angle : 1.000 11.295 8752 Z= 0.555 Chirality : 0.055 0.301 928 Planarity : 0.005 0.034 1232 Dihedral : 7.195 53.380 924 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.53 % Allowed : 8.18 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.50 (0.26), residues: 872 helix: None (None), residues: 0 sheet: 0.67 (0.20), residues: 624 loop : -3.06 (0.22), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 106 HIS 0.013 0.003 HIS A 73 PHE 0.024 0.003 PHE C 118 TYR 0.027 0.003 TYR H 48 ARG 0.008 0.001 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 113 MET cc_start: 0.3751 (tpt) cc_final: 0.3497 (tpt) REVERT: F 94 GLN cc_start: 0.7559 (mt0) cc_final: 0.7222 (mt0) REVERT: F 117 GLN cc_start: 0.7290 (mt0) cc_final: 0.6769 (mp10) REVERT: G 44 GLU cc_start: 0.7381 (pt0) cc_final: 0.6480 (pm20) REVERT: G 139 GLN cc_start: 0.7171 (mt0) cc_final: 0.6951 (mt0) outliers start: 17 outliers final: 8 residues processed: 119 average time/residue: 0.1547 time to fit residues: 25.2874 Evaluate side-chains 110 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN C 132 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6347 r_free = 0.6347 target = 0.496406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.6749 r_free = 0.6749 target = 0.374413 restraints weight = 11568.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.6836 r_free = 0.6836 target = 0.381156 restraints weight = 17086.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.6850 r_free = 0.6850 target = 0.379991 restraints weight = 15371.670| |-----------------------------------------------------------------------------| r_work (final): 0.6291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5300 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 6472 Z= 0.476 Angle : 1.027 15.774 8752 Z= 0.558 Chirality : 0.051 0.267 928 Planarity : 0.005 0.033 1232 Dihedral : 7.685 51.095 924 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.42 % Allowed : 11.01 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.49 (0.27), residues: 872 helix: None (None), residues: 0 sheet: -0.08 (0.21), residues: 608 loop : -3.13 (0.25), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 106 HIS 0.007 0.002 HIS C 149 PHE 0.014 0.003 PHE C 118 TYR 0.018 0.003 TYR A 50 ARG 0.006 0.001 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.4964 (mmp-170) cc_final: 0.4703 (mmp-170) REVERT: B 103 LEU cc_start: 0.8287 (mp) cc_final: 0.7923 (tt) REVERT: F 50 TYR cc_start: 0.5848 (t80) cc_final: 0.5399 (m-10) REVERT: F 94 GLN cc_start: 0.7477 (mt0) cc_final: 0.7245 (mt0) REVERT: F 117 GLN cc_start: 0.7202 (mt0) cc_final: 0.6949 (mp10) REVERT: H 68 LEU cc_start: 0.7824 (tp) cc_final: 0.7380 (mt) outliers start: 23 outliers final: 17 residues processed: 126 average time/residue: 0.1554 time to fit residues: 26.9762 Evaluate side-chains 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6352 r_free = 0.6352 target = 0.497221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.6890 r_free = 0.6890 target = 0.370535 restraints weight = 11688.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.6874 r_free = 0.6874 target = 0.370657 restraints weight = 15617.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.6884 r_free = 0.6884 target = 0.372721 restraints weight = 14616.546| |-----------------------------------------------------------------------------| r_work (final): 0.6289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5336 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6472 Z= 0.325 Angle : 0.820 9.339 8752 Z= 0.446 Chirality : 0.047 0.237 928 Planarity : 0.004 0.035 1232 Dihedral : 6.806 53.596 924 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.98 % Allowed : 13.54 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.90 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -0.42 (0.20), residues: 624 loop : -3.32 (0.23), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 106 HIS 0.005 0.001 HIS C 149 PHE 0.015 0.002 PHE A 118 TYR 0.017 0.002 TYR D 48 ARG 0.004 0.001 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8198 (mp) cc_final: 0.7859 (tt) REVERT: D 113 MET cc_start: 0.4855 (tpt) cc_final: 0.4487 (tpt) REVERT: E 72 GLN cc_start: 0.6857 (mt0) cc_final: 0.6335 (mp10) REVERT: F 94 GLN cc_start: 0.7598 (mt0) cc_final: 0.7299 (mt0) REVERT: F 113 MET cc_start: 0.5858 (tpp) cc_final: 0.5433 (tpp) REVERT: F 117 GLN cc_start: 0.7381 (mt0) cc_final: 0.7167 (mp10) REVERT: G 44 GLU cc_start: 0.7606 (pt0) cc_final: 0.6602 (pm20) REVERT: G 106 TRP cc_start: 0.4280 (t60) cc_final: 0.3973 (m-90) REVERT: H 68 LEU cc_start: 0.8005 (tp) cc_final: 0.7460 (mt) REVERT: H 72 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6982 (tp-100) outliers start: 20 outliers final: 15 residues processed: 118 average time/residue: 0.1616 time to fit residues: 26.3717 Evaluate side-chains 117 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 87 optimal weight: 0.0970 chunk 62 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 105 GLN C 110 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6382 r_free = 0.6382 target = 0.503432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.7088 r_free = 0.7088 target = 0.362991 restraints weight = 11706.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 102)---------------| | r_work = 0.7167 r_free = 0.7167 target = 0.367655 restraints weight = 12390.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.7177 r_free = 0.7177 target = 0.367978 restraints weight = 10174.961| |-----------------------------------------------------------------------------| r_work (final): 0.6318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5309 moved from start: 0.7263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6472 Z= 0.180 Angle : 0.655 7.424 8752 Z= 0.352 Chirality : 0.044 0.148 928 Planarity : 0.002 0.024 1232 Dihedral : 5.760 51.341 924 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.53 % Allowed : 14.88 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.65 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -0.26 (0.21), residues: 624 loop : -3.17 (0.23), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 106 HIS 0.004 0.001 HIS C 149 PHE 0.015 0.001 PHE A 118 TYR 0.019 0.001 TYR D 48 ARG 0.003 0.000 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8491 (tptp) cc_final: 0.7992 (tptt) REVERT: B 103 LEU cc_start: 0.8094 (mp) cc_final: 0.7742 (tt) REVERT: C 47 ILE cc_start: 0.6784 (mt) cc_final: 0.6489 (mp) REVERT: C 105 GLN cc_start: 0.5271 (tp40) cc_final: 0.3948 (mt0) REVERT: C 128 GLN cc_start: 0.4738 (mt0) cc_final: 0.4168 (mt0) REVERT: D 72 GLN cc_start: 0.7520 (mp10) cc_final: 0.7319 (mp10) REVERT: D 113 MET cc_start: 0.4944 (tpt) cc_final: 0.3785 (tpp) REVERT: E 72 GLN cc_start: 0.6864 (mt0) cc_final: 0.6525 (mp10) REVERT: F 113 MET cc_start: 0.5713 (tpp) cc_final: 0.5260 (tpp) REVERT: F 117 GLN cc_start: 0.7228 (mt0) cc_final: 0.6944 (mp10) REVERT: G 44 GLU cc_start: 0.7396 (pt0) cc_final: 0.6332 (pm20) REVERT: G 113 MET cc_start: 0.8588 (tmm) cc_final: 0.7815 (tmm) REVERT: H 68 LEU cc_start: 0.7605 (tp) cc_final: 0.7052 (mt) outliers start: 17 outliers final: 13 residues processed: 121 average time/residue: 0.1551 time to fit residues: 25.8628 Evaluate side-chains 122 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 73 HIS ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6281 r_free = 0.6281 target = 0.483923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 217)---------------| | r_work = 0.7040 r_free = 0.7040 target = 0.330217 restraints weight = 11345.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.7039 r_free = 0.7039 target = 0.329995 restraints weight = 12540.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.7043 r_free = 0.7043 target = 0.330043 restraints weight = 12405.766| |-----------------------------------------------------------------------------| r_work (final): 0.6188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.8879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 6472 Z= 0.580 Angle : 1.067 14.283 8752 Z= 0.594 Chirality : 0.053 0.201 928 Planarity : 0.005 0.027 1232 Dihedral : 8.122 53.392 924 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 3.72 % Allowed : 14.88 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.89 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -1.11 (0.21), residues: 616 loop : -3.71 (0.20), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 106 HIS 0.010 0.002 HIS C 149 PHE 0.022 0.003 PHE A 118 TYR 0.020 0.003 TYR A 50 ARG 0.006 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASN cc_start: 0.6929 (t0) cc_final: 0.6725 (t0) REVERT: A 70 ILE cc_start: 0.8601 (mt) cc_final: 0.8364 (mp) REVERT: B 103 LEU cc_start: 0.8433 (mp) cc_final: 0.8015 (tt) REVERT: C 66 SER cc_start: 0.6860 (m) cc_final: 0.6362 (t) REVERT: D 128 GLN cc_start: 0.4021 (OUTLIER) cc_final: 0.3681 (tt0) REVERT: F 117 GLN cc_start: 0.7425 (mt0) cc_final: 0.7198 (mp10) REVERT: G 106 TRP cc_start: 0.4852 (m-90) cc_final: 0.4643 (m100) REVERT: G 113 MET cc_start: 0.8625 (tmm) cc_final: 0.8168 (tmm) REVERT: H 68 LEU cc_start: 0.7728 (tp) cc_final: 0.7197 (mt) REVERT: H 72 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7114 (tp-100) REVERT: H 132 ASN cc_start: 0.6000 (m-40) cc_final: 0.5588 (t0) outliers start: 25 outliers final: 20 residues processed: 133 average time/residue: 0.1361 time to fit residues: 25.7430 Evaluate side-chains 127 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6326 r_free = 0.6326 target = 0.492925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.7056 r_free = 0.7056 target = 0.361983 restraints weight = 11471.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.7008 r_free = 0.7008 target = 0.360535 restraints weight = 14689.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.7010 r_free = 0.7010 target = 0.363427 restraints weight = 14272.582| |-----------------------------------------------------------------------------| r_work (final): 0.6268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5379 moved from start: 0.8901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6472 Z= 0.258 Angle : 0.736 8.971 8752 Z= 0.397 Chirality : 0.045 0.151 928 Planarity : 0.003 0.016 1232 Dihedral : 6.586 54.258 924 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.83 % Allowed : 17.86 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.71 (0.25), residues: 872 helix: None (None), residues: 0 sheet: -0.87 (0.22), residues: 552 loop : -3.43 (0.19), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 106 HIS 0.004 0.001 HIS C 149 PHE 0.015 0.002 PHE A 118 TYR 0.028 0.002 TYR D 48 ARG 0.002 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.7942 (mmtt) cc_final: 0.7590 (mmmt) REVERT: A 116 LYS cc_start: 0.8550 (tptp) cc_final: 0.8176 (tptp) REVERT: B 103 LEU cc_start: 0.8328 (mp) cc_final: 0.7997 (tt) REVERT: C 113 MET cc_start: 0.3820 (tmm) cc_final: 0.0931 (mtp) REVERT: F 44 GLU cc_start: 0.4479 (tp30) cc_final: 0.3303 (tt0) REVERT: F 117 GLN cc_start: 0.7457 (mt0) cc_final: 0.7180 (mp10) REVERT: G 106 TRP cc_start: 0.4808 (m-90) cc_final: 0.4498 (m100) REVERT: G 113 MET cc_start: 0.8410 (tmm) cc_final: 0.7102 (tmm) REVERT: H 68 LEU cc_start: 0.7882 (tp) cc_final: 0.7241 (mt) REVERT: H 132 ASN cc_start: 0.5915 (m-40) cc_final: 0.5611 (t0) outliers start: 19 outliers final: 17 residues processed: 123 average time/residue: 0.1516 time to fit residues: 25.9245 Evaluate side-chains 125 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6319 r_free = 0.6319 target = 0.490344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.6927 r_free = 0.6927 target = 0.384359 restraints weight = 11465.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.6860 r_free = 0.6860 target = 0.386594 restraints weight = 20235.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.6876 r_free = 0.6876 target = 0.388844 restraints weight = 18421.482| |-----------------------------------------------------------------------------| r_work (final): 0.6280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4857 moved from start: 0.9370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6472 Z= 0.305 Angle : 0.785 10.027 8752 Z= 0.424 Chirality : 0.046 0.215 928 Planarity : 0.003 0.017 1232 Dihedral : 6.737 57.943 924 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.57 % Allowed : 18.30 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.80 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -1.22 (0.21), residues: 624 loop : -3.18 (0.22), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 106 HIS 0.007 0.001 HIS C 149 PHE 0.018 0.002 PHE D 118 TYR 0.026 0.002 TYR D 48 ARG 0.001 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8408 (mt) cc_final: 0.8207 (mp) REVERT: A 116 LYS cc_start: 0.8575 (tptp) cc_final: 0.8113 (tptt) REVERT: B 103 LEU cc_start: 0.8234 (mp) cc_final: 0.7966 (tt) REVERT: C 105 GLN cc_start: 0.5467 (tp40) cc_final: 0.4895 (mt0) REVERT: F 117 GLN cc_start: 0.8230 (mt0) cc_final: 0.7817 (mp10) REVERT: G 106 TRP cc_start: 0.4888 (m-90) cc_final: 0.4577 (m100) REVERT: G 113 MET cc_start: 0.8095 (tmm) cc_final: 0.7037 (tmm) REVERT: H 68 LEU cc_start: 0.7875 (tp) cc_final: 0.7249 (mt) REVERT: H 132 ASN cc_start: 0.5901 (m-40) cc_final: 0.5502 (t0) outliers start: 24 outliers final: 24 residues processed: 126 average time/residue: 0.1560 time to fit residues: 27.1370 Evaluate side-chains 133 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 150 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6340 r_free = 0.6340 target = 0.495903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.6777 r_free = 0.6777 target = 0.362839 restraints weight = 11765.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.7045 r_free = 0.7045 target = 0.360780 restraints weight = 14552.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.7038 r_free = 0.7038 target = 0.358591 restraints weight = 13350.660| |-----------------------------------------------------------------------------| r_work (final): 0.6277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5499 moved from start: 0.9399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6472 Z= 0.224 Angle : 0.716 9.419 8752 Z= 0.378 Chirality : 0.044 0.151 928 Planarity : 0.003 0.020 1232 Dihedral : 6.090 58.068 924 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.68 % Allowed : 19.49 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.62 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -1.15 (0.21), residues: 624 loop : -2.94 (0.23), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 106 HIS 0.004 0.001 HIS C 149 PHE 0.015 0.001 PHE A 118 TYR 0.022 0.002 TYR D 48 ARG 0.002 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8250 (mp) REVERT: A 116 LYS cc_start: 0.8490 (tptp) cc_final: 0.7957 (tptt) REVERT: B 103 LEU cc_start: 0.8323 (mp) cc_final: 0.7947 (tt) REVERT: C 105 GLN cc_start: 0.4973 (tp40) cc_final: 0.4714 (mt0) REVERT: F 117 GLN cc_start: 0.7500 (mt0) cc_final: 0.7247 (mp10) REVERT: G 106 TRP cc_start: 0.4473 (m-90) cc_final: 0.4200 (m100) REVERT: G 113 MET cc_start: 0.8388 (tmm) cc_final: 0.7053 (tmm) REVERT: H 68 LEU cc_start: 0.7886 (tp) cc_final: 0.7183 (mt) REVERT: H 132 ASN cc_start: 0.5733 (m-40) cc_final: 0.5381 (t0) outliers start: 18 outliers final: 17 residues processed: 121 average time/residue: 0.1662 time to fit residues: 27.3957 Evaluate side-chains 126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6324 r_free = 0.6324 target = 0.492098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.6888 r_free = 0.6888 target = 0.384908 restraints weight = 11792.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.6863 r_free = 0.6863 target = 0.387589 restraints weight = 19848.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.6882 r_free = 0.6882 target = 0.391343 restraints weight = 15739.301| |-----------------------------------------------------------------------------| r_work (final): 0.6294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4829 moved from start: 0.9770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6472 Z= 0.279 Angle : 0.762 9.535 8752 Z= 0.407 Chirality : 0.045 0.177 928 Planarity : 0.003 0.020 1232 Dihedral : 6.340 53.167 924 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 3.42 % Allowed : 19.20 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.77 (0.27), residues: 872 helix: None (None), residues: 0 sheet: -1.24 (0.21), residues: 624 loop : -3.03 (0.23), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 106 HIS 0.007 0.001 HIS C 149 PHE 0.017 0.002 PHE A 118 TYR 0.022 0.002 TYR D 48 ARG 0.002 0.000 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8616 (tptp) cc_final: 0.8126 (tptt) REVERT: B 103 LEU cc_start: 0.8234 (mp) cc_final: 0.7898 (tt) REVERT: F 117 GLN cc_start: 0.8303 (mt0) cc_final: 0.7870 (mp10) REVERT: G 63 CYS cc_start: 0.5185 (OUTLIER) cc_final: 0.4286 (p) REVERT: G 106 TRP cc_start: 0.4680 (m-90) cc_final: 0.4429 (m100) REVERT: G 113 MET cc_start: 0.8123 (tmm) cc_final: 0.7069 (tmm) REVERT: G 132 ASN cc_start: 0.8476 (m-40) cc_final: 0.8008 (m110) REVERT: H 68 LEU cc_start: 0.8052 (tp) cc_final: 0.7379 (mt) REVERT: H 132 ASN cc_start: 0.5871 (m-40) cc_final: 0.5487 (t0) outliers start: 23 outliers final: 21 residues processed: 124 average time/residue: 0.1396 time to fit residues: 24.4095 Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6292 r_free = 0.6292 target = 0.486551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.6900 r_free = 0.6900 target = 0.380243 restraints weight = 11796.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.6835 r_free = 0.6835 target = 0.381603 restraints weight = 21091.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.6845 r_free = 0.6845 target = 0.384549 restraints weight = 17836.590| |-----------------------------------------------------------------------------| r_work (final): 0.6251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4908 moved from start: 1.0489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6472 Z= 0.370 Angle : 0.857 10.214 8752 Z= 0.464 Chirality : 0.047 0.244 928 Planarity : 0.004 0.020 1232 Dihedral : 7.052 50.872 924 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 3.42 % Allowed : 19.94 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.05 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -1.15 (0.22), residues: 544 loop : -3.48 (0.20), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 106 HIS 0.007 0.001 HIS C 149 PHE 0.021 0.002 PHE D 118 TYR 0.027 0.002 TYR D 48 ARG 0.003 0.001 ARG F 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1988.73 seconds wall clock time: 36 minutes 44.51 seconds (2204.51 seconds total)