Starting phenix.real_space_refine on Tue Mar 11 16:39:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8enr_28277/03_2025/8enr_28277.cif Found real_map, /net/cci-nas-00/data/ceres_data/8enr_28277/03_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_28277/03_2025/8enr_28277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8enr_28277/03_2025/8enr_28277.map" model { file = "/net/cci-nas-00/data/ceres_data/8enr_28277/03_2025/8enr_28277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8enr_28277/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.47, per 1000 atoms: 0.70 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: 1.38 Conformation dependent library (CDL) restraints added in 890.7 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: 0.91 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: 1.79 Time building geometry restraints manager: 1.63 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: 0.840 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.810 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- 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 : 0.700 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: 0.1799 time to fit residues: 26.7289 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 : 0.633 ------------------------------------------------------------------------------- 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: 1.9990 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: 3.3988 ------------------------------------------------------------------------------- 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 E 107 ASN F 73 HIS F 94 GLN F 105 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6448 r_free = 0.6448 target = 0.515389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.7176 r_free = 0.7176 target = 0.393084 restraints weight = 11480.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.7112 r_free = 0.7112 target = 0.391156 restraints weight = 14099.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.7117 r_free = 0.7117 target = 0.394488 restraints weight = 14450.127| |-----------------------------------------------------------------------------| r_work (final): 0.6394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4885 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 6472 Z= 0.404 Angle : 0.937 10.575 8752 Z= 0.518 Chirality : 0.053 0.248 928 Planarity : 0.005 0.032 1232 Dihedral : 6.880 52.486 924 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.23 % Allowed : 8.18 % Favored : 89.58 % 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: -0.34 (0.26), residues: 872 helix: None (None), residues: 0 sheet: 0.80 (0.19), residues: 624 loop : -3.06 (0.22), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 106 HIS 0.012 0.003 HIS A 73 PHE 0.018 0.002 PHE C 118 TYR 0.021 0.003 TYR A 48 ARG 0.008 0.001 ARG D 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 125 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: D 113 MET cc_start: 0.3769 (tpt) cc_final: 0.3213 (tpt) REVERT: F 94 GLN cc_start: 0.7857 (mt0) cc_final: 0.7580 (mt0) REVERT: F 117 GLN cc_start: 0.7243 (mt0) cc_final: 0.6904 (mp10) REVERT: G 44 GLU cc_start: 0.7358 (pt0) cc_final: 0.6462 (pm20) REVERT: G 139 GLN cc_start: 0.7233 (mt0) cc_final: 0.7001 (mt0) REVERT: H 72 GLN cc_start: 0.6820 (mp10) cc_final: 0.6058 (mp10) outliers start: 15 outliers final: 9 residues processed: 116 average time/residue: 0.1690 time to fit residues: 26.8381 Evaluate side-chains 113 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 138 THR 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: 9.9990 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 73 HIS E 83 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN G 105 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6356 r_free = 0.6356 target = 0.500283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.6992 r_free = 0.6992 target = 0.374573 restraints weight = 11694.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.6948 r_free = 0.6948 target = 0.372477 restraints weight = 15873.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.6948 r_free = 0.6948 target = 0.374868 restraints weight = 14742.028| |-----------------------------------------------------------------------------| r_work (final): 0.6305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5287 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 6472 Z= 0.446 Angle : 0.990 16.008 8752 Z= 0.537 Chirality : 0.050 0.258 928 Planarity : 0.005 0.031 1232 Dihedral : 7.492 50.483 924 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.83 % Allowed : 11.01 % Favored : 86.16 % 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: -1.81 (0.25), residues: 872 helix: None (None), residues: 0 sheet: 0.19 (0.23), residues: 480 loop : -3.15 (0.20), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 106 HIS 0.007 0.002 HIS E 73 PHE 0.016 0.003 PHE B 118 TYR 0.028 0.003 TYR C 48 ARG 0.005 0.001 ARG D 95 *********************** 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 137 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8309 (mp) cc_final: 0.7960 (tt) REVERT: B 113 MET cc_start: 0.4505 (tpt) cc_final: 0.3999 (tpt) REVERT: C 47 ILE cc_start: 0.6881 (mt) cc_final: 0.6573 (mp) REVERT: F 50 TYR cc_start: 0.5764 (t80) cc_final: 0.5275 (m-10) REVERT: F 128 GLN cc_start: 0.5297 (tp-100) cc_final: 0.4735 (tm-30) REVERT: H 68 LEU cc_start: 0.7835 (tp) cc_final: 0.7391 (mt) REVERT: H 94 GLN cc_start: 0.6810 (mt0) cc_final: 0.6354 (mp10) outliers start: 19 outliers final: 15 residues processed: 126 average time/residue: 0.1503 time to fit residues: 26.2151 Evaluate side-chains 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A 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 147 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 138 THR 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 147 THR Chi-restraints excluded: chain H residue 49 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: 9.9990 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 83 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 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 83 GLN ** 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 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 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6369 r_free = 0.6369 target = 0.499735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.7233 r_free = 0.7233 target = 0.364004 restraints weight = 11675.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.7190 r_free = 0.7190 target = 0.362527 restraints weight = 11490.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.7181 r_free = 0.7181 target = 0.363403 restraints weight = 11610.610| |-----------------------------------------------------------------------------| r_work (final): 0.6306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6472 Z= 0.251 Angle : 0.747 10.012 8752 Z= 0.401 Chirality : 0.045 0.181 928 Planarity : 0.003 0.030 1232 Dihedral : 6.343 51.303 924 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.83 % Allowed : 12.35 % Favored : 84.82 % 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: -1.56 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -0.17 (0.20), residues: 624 loop : -3.21 (0.23), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 106 HIS 0.005 0.001 HIS C 149 PHE 0.013 0.001 PHE B 118 TYR 0.014 0.001 TYR C 48 ARG 0.003 0.000 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 132 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8076 (mp) cc_final: 0.7725 (tt) REVERT: B 113 MET cc_start: 0.4547 (tpt) cc_final: 0.4114 (tpt) REVERT: C 47 ILE cc_start: 0.6835 (mt) cc_final: 0.6569 (mp) REVERT: D 113 MET cc_start: 0.4732 (tpt) cc_final: 0.4205 (tpt) REVERT: F 44 GLU cc_start: 0.4531 (tp30) cc_final: 0.3663 (tt0) REVERT: G 44 GLU cc_start: 0.7220 (pt0) cc_final: 0.6173 (pm20) REVERT: H 68 LEU cc_start: 0.7693 (tp) cc_final: 0.7197 (mt) outliers start: 19 outliers final: 16 residues processed: 120 average time/residue: 0.1562 time to fit residues: 25.9301 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 : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 61 THR 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 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 49 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: 20.0000 chunk 39 optimal weight: 4.9990 chunk 87 optimal weight: 0.0170 chunk 62 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** 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 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 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 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** 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 = 0.6365 r_free = 0.6365 target = 0.498510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.7130 r_free = 0.7130 target = 0.363487 restraints weight = 11611.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.7064 r_free = 0.7064 target = 0.362217 restraints weight = 14675.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.7073 r_free = 0.7073 target = 0.365023 restraints weight = 14452.296| |-----------------------------------------------------------------------------| r_work (final): 0.6304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.7503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6472 Z= 0.269 Angle : 0.747 8.831 8752 Z= 0.403 Chirality : 0.045 0.199 928 Planarity : 0.003 0.040 1232 Dihedral : 6.174 48.726 924 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.87 % Allowed : 13.24 % Favored : 82.89 % 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: -1.66 (0.27), residues: 872 helix: None (None), residues: 0 sheet: -0.22 (0.21), residues: 608 loop : -3.17 (0.24), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 106 HIS 0.005 0.001 HIS C 149 PHE 0.018 0.001 PHE A 118 TYR 0.015 0.002 TYR C 48 ARG 0.003 0.000 ARG A 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 135 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 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: 0.8134 (mp) cc_final: 0.7823 (tt) REVERT: B 113 MET cc_start: 0.4789 (tpt) cc_final: 0.4542 (tpt) REVERT: C 44 GLU cc_start: -0.3153 (OUTLIER) cc_final: -0.3421 (mt-10) REVERT: C 47 ILE cc_start: 0.6923 (mt) cc_final: 0.6585 (mp) REVERT: C 105 GLN cc_start: 0.5299 (tp-100) cc_final: 0.4704 (mt0) REVERT: D 113 MET cc_start: 0.4969 (tpt) cc_final: 0.4561 (tpt) REVERT: E 72 GLN cc_start: 0.6622 (mt0) cc_final: 0.6214 (mp10) REVERT: F 95 ARG cc_start: 0.6682 (ttt-90) cc_final: 0.6386 (tpt-90) REVERT: F 113 MET cc_start: 0.5767 (tpp) cc_final: 0.5241 (tpp) REVERT: H 68 LEU cc_start: 0.7777 (tp) cc_final: 0.7320 (mt) outliers start: 26 outliers final: 19 residues processed: 124 average time/residue: 0.1483 time to fit residues: 25.6776 Evaluate side-chains 122 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 44 GLU 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 61 THR 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 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 49 GLN 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: 9.9990 chunk 59 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN C 132 ASN ** 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 72 GLN ** 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6317 r_free = 0.6317 target = 0.491845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.6862 r_free = 0.6862 target = 0.345717 restraints weight = 11524.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.6958 r_free = 0.6958 target = 0.348518 restraints weight = 13706.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.7030 r_free = 0.7030 target = 0.348550 restraints weight = 12498.640| |-----------------------------------------------------------------------------| r_work (final): 0.6234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.8551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6472 Z= 0.388 Angle : 0.865 9.145 8752 Z= 0.476 Chirality : 0.048 0.191 928 Planarity : 0.004 0.029 1232 Dihedral : 7.082 50.550 924 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.42 % Allowed : 14.43 % Favored : 82.14 % 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: -2.31 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -0.43 (0.22), residues: 536 loop : -3.43 (0.21), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 106 HIS 0.008 0.001 HIS C 149 PHE 0.023 0.002 PHE A 118 TYR 0.023 0.002 TYR C 48 ARG 0.004 0.001 ARG A 64 *********************** 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 141 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8292 (mp) cc_final: 0.7942 (tt) REVERT: C 44 GLU cc_start: -0.3336 (OUTLIER) cc_final: -0.3584 (mt-10) REVERT: C 134 SER cc_start: 0.4882 (t) cc_final: 0.3880 (m) REVERT: D 128 GLN cc_start: 0.3798 (OUTLIER) cc_final: 0.3403 (tt0) REVERT: E 72 GLN cc_start: 0.6970 (mt0) cc_final: 0.6764 (mp10) REVERT: F 44 GLU cc_start: 0.4468 (tp30) cc_final: 0.3844 (tt0) REVERT: F 113 MET cc_start: 0.5778 (tpp) cc_final: 0.5451 (tpp) REVERT: G 113 MET cc_start: 0.6691 (mpp) cc_final: 0.6488 (mpp) REVERT: H 68 LEU cc_start: 0.7649 (tp) cc_final: 0.7036 (mt) outliers start: 23 outliers final: 19 residues processed: 129 average time/residue: 0.1516 time to fit residues: 27.3301 Evaluate side-chains 130 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 44 GLU 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 61 THR Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 87 ASP 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 147 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 111 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 7.9990 chunk 31 optimal weight: 0.3980 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 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** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.6312 r_free = 0.6312 target = 0.492192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.6915 r_free = 0.6915 target = 0.344009 restraints weight = 11457.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.6985 r_free = 0.6985 target = 0.344666 restraints weight = 13143.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 76)----------------| | r_work = 0.7041 r_free = 0.7041 target = 0.344936 restraints weight = 13052.573| |-----------------------------------------------------------------------------| r_work (final): 0.6223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.8926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6472 Z= 0.331 Angle : 0.798 9.098 8752 Z= 0.433 Chirality : 0.047 0.256 928 Planarity : 0.003 0.030 1232 Dihedral : 6.700 49.892 924 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.87 % Allowed : 15.33 % Favored : 80.80 % 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: -2.63 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -1.06 (0.21), residues: 616 loop : -3.21 (0.22), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 106 HIS 0.004 0.001 HIS C 149 PHE 0.019 0.002 PHE A 118 TYR 0.025 0.002 TYR D 48 ARG 0.002 0.000 ARG D 64 *********************** 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 139 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7700 (mmmt) REVERT: A 116 LYS cc_start: 0.8532 (tptp) cc_final: 0.8183 (tptp) REVERT: B 103 LEU cc_start: 0.8332 (mp) cc_final: 0.7976 (tt) REVERT: C 134 SER cc_start: 0.5196 (t) cc_final: 0.4111 (m) REVERT: F 44 GLU cc_start: 0.4439 (tp30) cc_final: 0.3787 (tt0) REVERT: F 113 MET cc_start: 0.5626 (tpp) cc_final: 0.5367 (tpp) REVERT: H 68 LEU cc_start: 0.7630 (tp) cc_final: 0.6971 (mt) outliers start: 26 outliers final: 24 residues processed: 128 average time/residue: 0.1569 time to fit residues: 27.8441 Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 68 LEU 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 57 LEU Chi-restraints excluded: chain D residue 61 THR 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 97 PHE 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 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 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** 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 94 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6316 r_free = 0.6316 target = 0.492414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.6752 r_free = 0.6752 target = 0.349519 restraints weight = 11492.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 90)----------------| | r_work = 0.7041 r_free = 0.7041 target = 0.346287 restraints weight = 14042.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 109)---------------| | r_work = 0.7045 r_free = 0.7045 target = 0.346599 restraints weight = 13677.037| |-----------------------------------------------------------------------------| r_work (final): 0.6220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.9286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6472 Z= 0.277 Angle : 0.751 8.808 8752 Z= 0.406 Chirality : 0.046 0.182 928 Planarity : 0.003 0.027 1232 Dihedral : 6.387 48.936 924 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.02 % Allowed : 16.96 % Favored : 79.02 % 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: -2.66 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -1.14 (0.21), residues: 616 loop : -3.01 (0.24), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 106 HIS 0.005 0.001 HIS C 149 PHE 0.015 0.002 PHE A 118 TYR 0.026 0.002 TYR D 48 ARG 0.002 0.000 ARG D 64 *********************** 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 144 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.5007 (pp) REVERT: A 109 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7778 (mmmt) REVERT: A 116 LYS cc_start: 0.8508 (tptp) cc_final: 0.8168 (tptp) REVERT: B 103 LEU cc_start: 0.8302 (mp) cc_final: 0.7878 (tt) REVERT: E 80 ASP cc_start: 0.7660 (t0) cc_final: 0.7443 (t0) REVERT: F 44 GLU cc_start: 0.4381 (tp30) cc_final: 0.3773 (tt0) REVERT: F 113 MET cc_start: 0.5492 (tpp) cc_final: 0.5272 (tpp) REVERT: G 132 ASN cc_start: 0.8371 (m-40) cc_final: 0.8099 (m-40) REVERT: H 68 LEU cc_start: 0.7680 (tp) cc_final: 0.6985 (mt) outliers start: 27 outliers final: 19 residues processed: 131 average time/residue: 0.1595 time to fit residues: 29.2589 Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 97 PHE 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 68 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN ** C 128 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 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6295 r_free = 0.6295 target = 0.487204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.6847 r_free = 0.6847 target = 0.382029 restraints weight = 11590.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.6825 r_free = 0.6825 target = 0.387588 restraints weight = 20431.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.6857 r_free = 0.6857 target = 0.390567 restraints weight = 15468.444| |-----------------------------------------------------------------------------| r_work (final): 0.6261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4855 moved from start: 1.0118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 6472 Z= 0.393 Angle : 0.901 10.991 8752 Z= 0.489 Chirality : 0.050 0.258 928 Planarity : 0.004 0.018 1232 Dihedral : 7.336 51.352 924 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 4.32 % Allowed : 17.11 % Favored : 78.57 % 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: -2.95 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -1.35 (0.21), residues: 600 loop : -3.05 (0.23), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 106 HIS 0.007 0.001 HIS C 149 PHE 0.021 0.003 PHE D 118 TYR 0.031 0.002 TYR D 48 ARG 0.003 0.001 ARG D 95 *********************** 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 140 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8525 (tptp) cc_final: 0.8275 (tptp) REVERT: B 103 LEU cc_start: 0.8178 (mp) cc_final: 0.7868 (tt) REVERT: B 105 GLN cc_start: 0.6290 (tp40) cc_final: 0.5476 (tp-100) REVERT: B 128 GLN cc_start: 0.5656 (mm110) cc_final: 0.5151 (mm110) REVERT: C 42 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7967 (m-40) REVERT: F 44 GLU cc_start: 0.4306 (tp30) cc_final: 0.3806 (tt0) REVERT: G 132 ASN cc_start: 0.8394 (m-40) cc_final: 0.8109 (m-40) REVERT: H 68 LEU cc_start: 0.8055 (tp) cc_final: 0.7359 (mt) REVERT: H 127 ASP cc_start: 0.6262 (m-30) cc_final: 0.5378 (t0) outliers start: 29 outliers final: 24 residues processed: 128 average time/residue: 0.1429 time to fit residues: 25.6264 Evaluate side-chains 132 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 61 THR 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 97 PHE 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 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 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 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 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 150 GLN G 117 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** 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 = 0.6331 r_free = 0.6331 target = 0.494624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.6947 r_free = 0.6947 target = 0.390714 restraints weight = 11853.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.6912 r_free = 0.6912 target = 0.392637 restraints weight = 19561.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.6925 r_free = 0.6925 target = 0.397365 restraints weight = 15078.773| |-----------------------------------------------------------------------------| r_work (final): 0.6296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4711 moved from start: 1.0070 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= 0.235 Angle : 0.745 9.209 8752 Z= 0.393 Chirality : 0.046 0.167 928 Planarity : 0.003 0.023 1232 Dihedral : 6.180 50.501 924 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.12 % Allowed : 19.20 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.79 (0.26), residues: 872 helix: None (None), residues: 0 sheet: -1.28 (0.21), residues: 616 loop : -2.93 (0.24), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 106 HIS 0.004 0.001 HIS C 149 PHE 0.019 0.002 PHE E 142 TYR 0.021 0.002 TYR D 48 ARG 0.003 0.000 ARG E 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 129 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.7484 (mp) cc_final: 0.7267 (tt) REVERT: B 128 GLN cc_start: 0.5267 (mm110) cc_final: 0.4757 (mt0) REVERT: D 72 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7019 (mp10) REVERT: F 44 GLU cc_start: 0.4032 (tp30) cc_final: 0.3708 (tt0) REVERT: G 106 TRP cc_start: 0.4129 (t60) cc_final: 0.3836 (m-90) REVERT: G 132 ASN cc_start: 0.8407 (m-40) cc_final: 0.8094 (m-40) REVERT: H 68 LEU cc_start: 0.7952 (tp) cc_final: 0.7251 (mt) REVERT: H 127 ASP cc_start: 0.6157 (m-30) cc_final: 0.5397 (t0) REVERT: H 132 ASN cc_start: 0.6029 (m-40) cc_final: 0.5697 (m-40) outliers start: 21 outliers final: 18 residues processed: 119 average time/residue: 0.1421 time to fit residues: 23.8051 Evaluate side-chains 125 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 97 PHE 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 133 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 32 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** 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 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6307 r_free = 0.6307 target = 0.489119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.6672 r_free = 0.6672 target = 0.393790 restraints weight = 11848.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.6799 r_free = 0.6799 target = 0.393210 restraints weight = 17966.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.6826 r_free = 0.6826 target = 0.393726 restraints weight = 14338.073| |-----------------------------------------------------------------------------| r_work (final): 0.6268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4844 moved from start: 1.0354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6472 Z= 0.316 Angle : 0.811 10.388 8752 Z= 0.433 Chirality : 0.046 0.217 928 Planarity : 0.003 0.038 1232 Dihedral : 6.577 51.231 924 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.27 % Allowed : 19.05 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.74 (0.27), residues: 872 helix: None (None), residues: 0 sheet: -1.22 (0.21), residues: 592 loop : -2.87 (0.26), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 106 HIS 0.006 0.001 HIS C 149 PHE 0.054 0.002 PHE A 118 TYR 0.022 0.002 TYR D 48 ARG 0.002 0.000 ARG D 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2201.13 seconds wall clock time: 39 minutes 18.23 seconds (2358.23 seconds total)