Starting phenix.real_space_refine on Fri Aug 22 15:56:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8enq_28276/08_2025/8enq_28276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8enq_28276/08_2025/8enq_28276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8enq_28276/08_2025/8enq_28276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8enq_28276/08_2025/8enq_28276.map" model { file = "/net/cci-nas-00/data/ceres_data/8enq_28276/08_2025/8enq_28276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8enq_28276/08_2025/8enq_28276.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 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 21 5.16 5 C 3304 2.51 5 N 1029 2.21 5 O 1239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5593 Number of models: 1 Model: "" Number of chains: 7 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} Time building chain proxies: 1.43, per 1000 atoms: 0.26 Number of scatterers: 5593 At special positions: 0 Unit cell: (51.3474, 51.3474, 184.142, 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 21 16.00 O 1239 8.00 N 1029 7.00 C 3304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 180.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1302 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 66.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 142 removed outlier: 6.405A pdb=" N ASP A 67 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LEU A 92 " --> pdb=" O ASP A 67 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 69 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLN A 94 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR A 71 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLY A 96 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS A 73 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU A 44 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE A 70 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 46 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLN A 72 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR A 48 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLY A 74 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR A 50 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 134 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN B 136 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 138 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 49 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS B 140 " --> pdb=" O GLN A 49 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 51 " --> pdb=" O CYS B 140 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE B 142 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP B 67 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU B 92 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 69 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN B 94 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR B 71 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLY B 96 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS B 73 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU B 44 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE B 70 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN B 46 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLN B 72 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 48 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLY B 74 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N TYR B 50 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 60 removed outlier: 6.630A pdb=" N SER A 55 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL A 81 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLN A 83 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU A 59 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N SER A 85 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 107 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP A 86 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS A 109 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY A 123 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA A 148 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 125 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN A 150 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP A 127 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 150 removed outlier: 6.526A pdb=" N GLY B 123 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA B 148 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA B 125 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLN B 150 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP B 127 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER B 100 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL B 126 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR B 102 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLN B 128 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP B 104 " --> pdb=" O GLN B 128 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN B 107 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP B 86 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS B 109 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER B 55 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL B 81 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLN B 83 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 59 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER B 85 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 56 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 49 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE C 47 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 60 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 45 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP C 67 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU C 92 " --> pdb=" O ASP C 67 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR C 69 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLN C 94 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR C 71 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY C 96 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HIS C 73 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER C 134 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE D 47 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASN C 136 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLN D 49 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR C 138 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY D 51 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N CYS C 140 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP D 67 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU D 92 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR D 69 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN D 94 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR D 71 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY D 96 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N HIS D 73 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY E 123 " --> pdb=" O ALA E 146 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA E 148 " --> pdb=" O GLY E 123 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA E 125 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLN E 150 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP E 127 " --> pdb=" O GLN E 150 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER E 100 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL E 126 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR E 102 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLN E 128 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP E 104 " --> pdb=" O GLN E 128 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN E 107 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP E 86 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS E 109 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER E 55 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL E 81 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU E 57 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLN E 83 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU E 59 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N SER E 85 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 60 removed outlier: 6.572A pdb=" N SER C 55 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL C 81 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLN C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU C 59 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N SER C 85 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN C 107 " --> pdb=" O GLY C 84 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP C 86 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS C 109 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER C 100 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL C 126 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR C 102 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN C 128 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP C 104 " --> pdb=" O GLN C 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 55 through 60 removed outlier: 6.638A pdb=" N SER D 55 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL D 81 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU D 57 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLN D 83 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU D 59 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N SER D 85 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN D 107 " --> pdb=" O GLY D 84 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP D 86 " --> pdb=" O ASN D 107 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS D 109 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER D 100 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL D 126 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR D 102 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLN D 128 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP D 104 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN D 145 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP E 67 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU E 92 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR E 69 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLN E 94 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR E 71 " --> pdb=" O GLN E 94 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY E 96 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS E 73 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 44 through 52 removed outlier: 6.426A pdb=" N ASP F 67 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU F 92 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR F 69 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLN F 94 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR F 71 " --> pdb=" O GLN F 94 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLY F 96 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N HIS F 73 " --> pdb=" O GLY F 96 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY G 51 " --> pdb=" O CYS F 140 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE F 142 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU G 44 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE G 70 " --> pdb=" O GLU G 44 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN G 46 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLN G 72 " --> pdb=" O ASN G 46 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR G 48 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLY G 74 " --> pdb=" O TYR G 48 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR G 50 " --> pdb=" O GLY G 74 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP G 67 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU G 92 " --> pdb=" O ASP G 67 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR G 69 " --> pdb=" O LEU G 92 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLN G 94 " --> pdb=" O THR G 69 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR G 71 " --> pdb=" O GLN G 94 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLY G 96 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N HIS G 73 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER G 89 " --> pdb=" O MET G 113 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL G 115 " --> pdb=" O SER G 89 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP G 91 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLN G 117 " --> pdb=" O ASP G 91 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR G 93 " --> pdb=" O GLN G 117 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLY G 119 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ARG G 95 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU G 112 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL G 137 " --> pdb=" O GLU G 112 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR G 114 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLN G 139 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS G 116 " --> pdb=" O GLN G 139 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLY G 141 " --> pdb=" O LYS G 116 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE G 118 " --> pdb=" O GLY G 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 55 through 60 removed outlier: 6.664A pdb=" N SER F 55 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL F 81 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU F 57 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLN F 83 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU F 59 " --> pdb=" O GLN F 83 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N SER F 85 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY F 78 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU F 103 " --> pdb=" O GLY F 78 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP F 80 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLN F 105 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY F 82 " --> pdb=" O GLN F 105 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ASN F 107 " --> pdb=" O GLY F 82 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLY F 84 " --> pdb=" O ASN F 107 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS F 109 " --> pdb=" O GLY F 84 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP F 86 " --> pdb=" O LYS F 109 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER F 100 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL F 126 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR F 102 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLN F 128 " --> pdb=" O THR F 102 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP F 104 " --> pdb=" O GLN F 128 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY F 123 " --> pdb=" O ALA F 146 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA F 148 " --> pdb=" O GLY F 123 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA F 125 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLN F 150 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP F 127 " --> pdb=" O GLN F 150 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASN F 145 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ALA G 58 " --> pdb=" O ASN F 145 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR F 147 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN G 60 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N HIS F 149 " --> pdb=" O GLN G 60 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER G 55 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL G 81 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU G 57 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLN G 83 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU G 59 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER G 85 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR G 61 " --> pdb=" O SER G 85 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY G 78 " --> pdb=" O ALA G 101 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU G 103 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP G 80 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN G 105 " --> pdb=" O ASP G 80 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY G 82 " --> pdb=" O GLN G 105 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ASN G 107 " --> pdb=" O GLY G 82 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N GLY G 84 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS G 109 " --> pdb=" O GLY G 84 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP G 86 " --> pdb=" O LYS G 109 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER G 100 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL G 126 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR G 102 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN G 128 " --> pdb=" O THR G 102 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP G 104 " --> pdb=" O GLN G 128 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY G 123 " --> pdb=" O ALA G 146 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ALA G 148 " --> pdb=" O GLY G 123 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA G 125 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLN G 150 " --> pdb=" O ALA G 125 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP G 127 " --> pdb=" O GLN G 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 199 hydrogen bonds defined for protein. 579 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: 0.80 Time building geometry restraints manager: 0.53 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: 2058 1.34 - 1.45: 734 1.45 - 1.57: 2843 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 5663 Sorted by residual: bond pdb=" CA GLY F 82 " pdb=" C GLY F 82 " ideal model delta sigma weight residual 1.516 1.529 -0.013 8.10e-03 1.52e+04 2.67e+00 bond pdb=" CA ASN F 110 " pdb=" CB ASN F 110 " ideal model delta sigma weight residual 1.530 1.554 -0.023 1.48e-02 4.57e+03 2.49e+00 bond pdb=" CB PRO E 41 " pdb=" CG PRO E 41 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.96e+00 bond pdb=" CB GLU F 44 " pdb=" CG GLU F 44 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.82e+00 bond pdb=" CB ASN C 145 " pdb=" CG ASN C 145 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.63e+00 ... (remaining 5658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 7302 1.57 - 3.15: 289 3.15 - 4.72: 47 4.72 - 6.30: 11 6.30 - 7.87: 9 Bond angle restraints: 7658 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 111.21 115.53 -4.32 1.04e+00 9.25e-01 1.72e+01 angle pdb=" N GLY C 75 " pdb=" CA GLY C 75 " pdb=" C GLY C 75 " ideal model delta sigma weight residual 110.80 117.67 -6.87 1.71e+00 3.42e-01 1.61e+01 angle pdb=" N GLY D 119 " pdb=" CA GLY D 119 " pdb=" C GLY D 119 " ideal model delta sigma weight residual 111.21 115.17 -3.96 1.04e+00 9.25e-01 1.45e+01 angle pdb=" N GLY A 75 " pdb=" CA GLY A 75 " pdb=" C GLY A 75 " ideal model delta sigma weight residual 110.80 117.28 -6.48 1.71e+00 3.42e-01 1.43e+01 angle pdb=" N GLY C 52 " pdb=" CA GLY C 52 " pdb=" C GLY C 52 " ideal model delta sigma weight residual 110.80 117.10 -6.30 1.71e+00 3.42e-01 1.36e+01 ... (remaining 7653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.07: 2908 14.07 - 28.14: 218 28.14 - 42.21: 77 42.21 - 56.27: 28 56.27 - 70.34: 17 Dihedral angle restraints: 3248 sinusoidal: 1155 harmonic: 2093 Sorted by residual: dihedral pdb=" CA ASP D 62 " pdb=" C ASP D 62 " pdb=" N CYS D 63 " pdb=" CA CYS D 63 " ideal model delta harmonic sigma weight residual 180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP C 62 " pdb=" C ASP C 62 " pdb=" N CYS C 63 " pdb=" CA CYS C 63 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP F 62 " pdb=" C ASP F 62 " pdb=" N CYS F 63 " pdb=" CA CYS F 63 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 503 0.035 - 0.071: 219 0.071 - 0.106: 61 0.106 - 0.142: 19 0.142 - 0.177: 10 Chirality restraints: 812 Sorted by residual: chirality pdb=" CA TYR F 48 " pdb=" N TYR F 48 " pdb=" C TYR F 48 " pdb=" CB TYR F 48 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA TYR C 48 " pdb=" N TYR C 48 " pdb=" C TYR C 48 " pdb=" CB TYR C 48 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.95e-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 2.60 -0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 809 not shown) Planarity restraints: 1078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 42 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.15e+00 pdb=" C ASN F 42 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN F 42 " 0.019 2.00e-02 2.50e+03 pdb=" N SER F 43 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 105 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" CD GLN G 105 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLN G 105 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN G 105 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 49 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" CD GLN F 49 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLN F 49 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN F 49 " 0.010 2.00e-02 2.50e+03 ... (remaining 1075 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 861 2.79 - 3.31: 5002 3.31 - 3.84: 10502 3.84 - 4.37: 12241 4.37 - 4.90: 21351 Nonbonded interactions: 49957 Sorted by model distance: nonbonded pdb=" OD1 ASN D 122 " pdb=" ND2 ASN D 144 " model vdw 2.257 3.120 nonbonded pdb=" NE2 GLN B 49 " pdb=" OE1 GLN B 72 " model vdw 2.284 3.120 nonbonded pdb=" NE2 GLN E 128 " pdb=" OG SER E 133 " model vdw 2.286 3.120 nonbonded pdb=" OG SER C 43 " pdb=" O CYS C 63 " model vdw 2.300 3.040 nonbonded pdb=" OG SER G 43 " pdb=" O CYS G 63 " model vdw 2.312 3.040 ... (remaining 49952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.490 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2978 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 0.070 5663 Z= 0.185 Angle : 0.768 7.871 7658 Z= 0.429 Chirality : 0.046 0.177 812 Planarity : 0.004 0.050 1078 Dihedral : 13.928 70.342 1946 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.27), residues: 763 helix: None (None), residues: 0 sheet: 1.69 (0.19), residues: 609 loop : -2.39 (0.31), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 64 TYR 0.011 0.001 TYR A 50 PHE 0.013 0.002 PHE A 118 TRP 0.016 0.002 TRP G 106 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 5663) covalent geometry : angle 0.76797 ( 7658) hydrogen bonds : bond 0.12176 ( 199) hydrogen bonds : angle 7.06102 ( 579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 ILE cc_start: 0.5250 (mp) cc_final: 0.4805 (mm) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0717 time to fit residues: 3.6468 Evaluate side-chains 30 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 73 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 ASN ** G 105 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 = 0.6607 r_free = 0.6607 target = 0.487202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.7125 r_free = 0.7125 target = 0.432667 restraints weight = 5557.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.7152 r_free = 0.7152 target = 0.436852 restraints weight = 3392.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.7164 r_free = 0.7164 target = 0.439517 restraints weight = 2224.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.7188 r_free = 0.7188 target = 0.441298 restraints weight = 1546.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.7190 r_free = 0.7190 target = 0.442266 restraints weight = 1118.291| |-----------------------------------------------------------------------------| r_work (final): 0.6594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3715 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5663 Z= 0.233 Angle : 0.730 7.660 7658 Z= 0.404 Chirality : 0.046 0.161 812 Planarity : 0.004 0.031 1078 Dihedral : 5.626 16.470 805 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.21 % Allowed : 4.59 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.30), residues: 763 helix: None (None), residues: 0 sheet: 1.09 (0.20), residues: 595 loop : -0.86 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 64 TYR 0.014 0.002 TYR C 151 PHE 0.014 0.002 PHE D 142 TRP 0.010 0.001 TRP G 106 HIS 0.006 0.002 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 5663) covalent geometry : angle 0.72980 ( 7658) hydrogen bonds : bond 0.04201 ( 199) hydrogen bonds : angle 6.27704 ( 579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.198 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 44 average time/residue: 0.0740 time to fit residues: 4.3992 Evaluate side-chains 31 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain F residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 ASN G 60 GLN ** G 105 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 = 0.6518 r_free = 0.6518 target = 0.470758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.7108 r_free = 0.7108 target = 0.403527 restraints weight = 5782.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.7141 r_free = 0.7141 target = 0.407573 restraints weight = 3606.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.7148 r_free = 0.7148 target = 0.409887 restraints weight = 2427.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.7186 r_free = 0.7186 target = 0.411714 restraints weight = 1783.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.7188 r_free = 0.7188 target = 0.412668 restraints weight = 1335.605| |-----------------------------------------------------------------------------| r_work (final): 0.6496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4177 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5663 Z= 0.239 Angle : 0.764 9.490 7658 Z= 0.419 Chirality : 0.047 0.174 812 Planarity : 0.004 0.030 1078 Dihedral : 6.130 19.915 805 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.55 % Allowed : 5.78 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.31), residues: 763 helix: None (None), residues: 0 sheet: 0.23 (0.21), residues: 588 loop : -0.79 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.009 0.002 TYR B 48 PHE 0.015 0.002 PHE D 142 TRP 0.012 0.002 TRP C 106 HIS 0.005 0.002 HIS E 149 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 5663) covalent geometry : angle 0.76358 ( 7658) hydrogen bonds : bond 0.04274 ( 199) hydrogen bonds : angle 6.57147 ( 579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.166 Fit side-chains REVERT: F 118 PHE cc_start: 0.5246 (OUTLIER) cc_final: 0.4041 (m-80) outliers start: 15 outliers final: 8 residues processed: 44 average time/residue: 0.0749 time to fit residues: 4.5279 Evaluate side-chains 36 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain G residue 66 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN C 139 GLN ** C 144 ASN ** 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 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN F 139 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN G 150 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6303 r_free = 0.6303 target = 0.433861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.6863 r_free = 0.6863 target = 0.336487 restraints weight = 6130.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.6871 r_free = 0.6871 target = 0.338842 restraints weight = 5000.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.6916 r_free = 0.6916 target = 0.341126 restraints weight = 4335.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.6943 r_free = 0.6943 target = 0.342824 restraints weight = 3794.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.6945 r_free = 0.6945 target = 0.343321 restraints weight = 3411.265| |-----------------------------------------------------------------------------| r_work (final): 0.5610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5006 moved from start: 0.7353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.105 5663 Z= 0.511 Angle : 1.296 12.151 7658 Z= 0.734 Chirality : 0.062 0.324 812 Planarity : 0.009 0.051 1078 Dihedral : 9.568 31.843 805 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 37.93 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.66 % Favored : 87.81 % Rotamer: Outliers : 4.59 % Allowed : 9.35 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.45 (0.28), residues: 763 helix: None (None), residues: 0 sheet: -1.99 (0.20), residues: 581 loop : -2.42 (0.37), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 95 TYR 0.023 0.004 TYR B 48 PHE 0.031 0.006 PHE E 118 TRP 0.026 0.005 TRP C 106 HIS 0.012 0.004 HIS E 149 Details of bonding type rmsd covalent geometry : bond 0.01047 ( 5663) covalent geometry : angle 1.29576 ( 7658) hydrogen bonds : bond 0.07791 ( 199) hydrogen bonds : angle 8.57565 ( 579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: B 113 MET cc_start: 0.2631 (ttm) cc_final: 0.2192 (ttm) REVERT: B 127 ASP cc_start: 0.5410 (m-30) cc_final: 0.4852 (m-30) REVERT: C 94 GLN cc_start: 0.7257 (mt0) cc_final: 0.6976 (tm-30) REVERT: C 113 MET cc_start: 0.6640 (tpt) cc_final: 0.6317 (mmm) REVERT: F 100 SER cc_start: 0.7231 (OUTLIER) cc_final: 0.6439 (t) REVERT: F 118 PHE cc_start: 0.5855 (OUTLIER) cc_final: 0.5067 (m-80) REVERT: G 50 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.4144 (m-80) outliers start: 27 outliers final: 15 residues processed: 72 average time/residue: 0.0701 time to fit residues: 6.7656 Evaluate side-chains 59 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 117 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 94 GLN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN G 42 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6413 r_free = 0.6413 target = 0.458472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.7049 r_free = 0.7049 target = 0.373293 restraints weight = 6119.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.7093 r_free = 0.7093 target = 0.377952 restraints weight = 4241.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.7120 r_free = 0.7120 target = 0.380900 restraints weight = 3127.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.7125 r_free = 0.7125 target = 0.382754 restraints weight = 2438.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.7151 r_free = 0.7151 target = 0.384385 restraints weight = 2014.421| |-----------------------------------------------------------------------------| r_work (final): 0.5767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4128 moved from start: 0.7171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5663 Z= 0.160 Angle : 0.706 8.042 7658 Z= 0.382 Chirality : 0.045 0.166 812 Planarity : 0.003 0.020 1078 Dihedral : 6.642 24.464 805 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.21 % Allowed : 13.27 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.29), residues: 763 helix: None (None), residues: 0 sheet: -1.54 (0.21), residues: 566 loop : -1.80 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.014 0.002 TYR F 50 PHE 0.017 0.002 PHE A 97 TRP 0.015 0.002 TRP C 106 HIS 0.010 0.002 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5663) covalent geometry : angle 0.70628 ( 7658) hydrogen bonds : bond 0.03335 ( 199) hydrogen bonds : angle 7.15362 ( 579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.1696 (ttm) cc_final: 0.0565 (ttm) REVERT: B 127 ASP cc_start: 0.5304 (m-30) cc_final: 0.4772 (m-30) REVERT: G 113 MET cc_start: 0.5890 (OUTLIER) cc_final: 0.5428 (tmm) outliers start: 13 outliers final: 10 residues processed: 55 average time/residue: 0.0719 time to fit residues: 5.2305 Evaluate side-chains 54 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 113 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 58 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 ASN G 49 GLN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN G 117 GLN ** G 128 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 = 0.6324 r_free = 0.6324 target = 0.443546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.6940 r_free = 0.6940 target = 0.347049 restraints weight = 6147.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.6978 r_free = 0.6978 target = 0.350241 restraints weight = 4868.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.7014 r_free = 0.7014 target = 0.352723 restraints weight = 4003.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.7018 r_free = 0.7018 target = 0.354082 restraints weight = 3420.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.7041 r_free = 0.7041 target = 0.355824 restraints weight = 3049.016| |-----------------------------------------------------------------------------| r_work (final): 0.6267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5081 moved from start: 0.8174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 5663 Z= 0.288 Angle : 0.917 9.187 7658 Z= 0.512 Chirality : 0.048 0.175 812 Planarity : 0.005 0.026 1078 Dihedral : 7.941 26.312 805 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 28.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.89 % Favored : 85.85 % Rotamer: Outliers : 4.08 % Allowed : 13.10 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.72 (0.28), residues: 763 helix: None (None), residues: 0 sheet: -2.21 (0.21), residues: 563 loop : -2.43 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 64 TYR 0.012 0.002 TYR C 50 PHE 0.019 0.004 PHE E 118 TRP 0.023 0.003 TRP C 106 HIS 0.007 0.002 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 5663) covalent geometry : angle 0.91700 ( 7658) hydrogen bonds : bond 0.05130 ( 199) hydrogen bonds : angle 7.77737 ( 579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 113 MET cc_start: 0.2344 (ttm) cc_final: 0.1476 (ttm) REVERT: B 127 ASP cc_start: 0.5547 (m-30) cc_final: 0.5196 (m-30) REVERT: B 128 GLN cc_start: 0.6722 (tt0) cc_final: 0.6470 (tm-30) REVERT: C 66 SER cc_start: 0.6136 (OUTLIER) cc_final: 0.5912 (t) REVERT: D 95 ARG cc_start: 0.5664 (OUTLIER) cc_final: 0.5062 (tpt170) REVERT: E 128 GLN cc_start: 0.5513 (OUTLIER) cc_final: 0.4562 (tp40) REVERT: F 100 SER cc_start: 0.7516 (OUTLIER) cc_final: 0.6889 (t) REVERT: G 113 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.5869 (ttm) REVERT: G 127 ASP cc_start: 0.6123 (m-30) cc_final: 0.5642 (t0) outliers start: 24 outliers final: 11 residues processed: 66 average time/residue: 0.0764 time to fit residues: 6.5926 Evaluate side-chains 60 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 117 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6365 r_free = 0.6365 target = 0.451119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.6996 r_free = 0.6996 target = 0.359408 restraints weight = 6180.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.7050 r_free = 0.7050 target = 0.363601 restraints weight = 4574.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.7060 r_free = 0.7060 target = 0.366090 restraints weight = 3550.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.7095 r_free = 0.7095 target = 0.368277 restraints weight = 2931.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.7099 r_free = 0.7099 target = 0.369556 restraints weight = 2472.586| |-----------------------------------------------------------------------------| r_work (final): 0.5687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4343 moved from start: 0.8324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5663 Z= 0.178 Angle : 0.732 8.683 7658 Z= 0.399 Chirality : 0.045 0.164 812 Planarity : 0.003 0.021 1078 Dihedral : 6.701 23.238 805 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 3.06 % Allowed : 14.12 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.48 (0.29), residues: 763 helix: None (None), residues: 0 sheet: -2.07 (0.21), residues: 556 loop : -2.25 (0.35), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.015 0.002 TYR F 50 PHE 0.018 0.002 PHE G 118 TRP 0.015 0.002 TRP C 106 HIS 0.005 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5663) covalent geometry : angle 0.73166 ( 7658) hydrogen bonds : bond 0.03514 ( 199) hydrogen bonds : angle 7.24830 ( 579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: B 113 MET cc_start: 0.2057 (ttm) cc_final: 0.1393 (ttm) REVERT: B 127 ASP cc_start: 0.5398 (m-30) cc_final: 0.4972 (m-30) REVERT: C 113 MET cc_start: 0.6145 (mmm) cc_final: 0.5778 (tpt) REVERT: E 128 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.4692 (tm-30) REVERT: F 100 SER cc_start: 0.6697 (OUTLIER) cc_final: 0.6095 (t) REVERT: F 118 PHE cc_start: 0.5322 (OUTLIER) cc_final: 0.4798 (m-80) REVERT: G 113 MET cc_start: 0.5624 (OUTLIER) cc_final: 0.5298 (tmm) REVERT: G 127 ASP cc_start: 0.5544 (m-30) cc_final: 0.4940 (t0) outliers start: 18 outliers final: 11 residues processed: 55 average time/residue: 0.0704 time to fit residues: 5.1423 Evaluate side-chains 56 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 117 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN ** G 128 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 = 0.6463 r_free = 0.6463 target = 0.581794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.6912 r_free = 0.6912 target = 0.450362 restraints weight = 8479.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.6917 r_free = 0.6917 target = 0.449619 restraints weight = 12002.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.6936 r_free = 0.6936 target = 0.449066 restraints weight = 11711.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 92)----------------| | r_work = 0.7162 r_free = 0.7162 target = 0.443213 restraints weight = 11151.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 108)---------------| | r_work = 0.7299 r_free = 0.7299 target = 0.441483 restraints weight = 11677.939| |-----------------------------------------------------------------------------| r_work (final): 0.5514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5152 moved from start: 0.9350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 5663 Z= 0.314 Angle : 0.964 9.891 7658 Z= 0.539 Chirality : 0.050 0.168 812 Planarity : 0.005 0.032 1078 Dihedral : 8.409 27.590 805 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 28.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 3.91 % Allowed : 15.31 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.33 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -2.62 (0.20), residues: 571 loop : -2.73 (0.33), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 95 TYR 0.025 0.003 TYR F 48 PHE 0.030 0.004 PHE G 118 TRP 0.025 0.003 TRP C 106 HIS 0.006 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00649 ( 5663) covalent geometry : angle 0.96376 ( 7658) hydrogen bonds : bond 0.05375 ( 199) hydrogen bonds : angle 8.12441 ( 579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: B 50 TYR cc_start: 0.4039 (OUTLIER) cc_final: 0.1891 (m-10) REVERT: B 113 MET cc_start: 0.2816 (ttm) cc_final: 0.2451 (ttm) REVERT: B 127 ASP cc_start: 0.5492 (m-30) cc_final: 0.5176 (m-30) REVERT: B 128 GLN cc_start: 0.6868 (tt0) cc_final: 0.6478 (tm-30) REVERT: C 113 MET cc_start: 0.6486 (mmm) cc_final: 0.6048 (tpt) REVERT: D 113 MET cc_start: 0.5296 (tmm) cc_final: 0.4327 (tpt) REVERT: E 57 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6480 (tt) REVERT: F 118 PHE cc_start: 0.5740 (OUTLIER) cc_final: 0.4896 (m-80) REVERT: G 113 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5655 (ttm) REVERT: G 127 ASP cc_start: 0.5479 (m-30) cc_final: 0.5129 (t0) outliers start: 23 outliers final: 14 residues processed: 65 average time/residue: 0.0787 time to fit residues: 6.6785 Evaluate side-chains 64 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain G residue 113 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 70 optimal weight: 0.4980 chunk 46 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6353 r_free = 0.6353 target = 0.448471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.7014 r_free = 0.7014 target = 0.356799 restraints weight = 6122.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.7018 r_free = 0.7018 target = 0.359285 restraints weight = 4653.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.7071 r_free = 0.7071 target = 0.362137 restraints weight = 3803.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.7073 r_free = 0.7073 target = 0.363480 restraints weight = 3190.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.7103 r_free = 0.7103 target = 0.365067 restraints weight = 2797.842| |-----------------------------------------------------------------------------| r_work (final): 0.6316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4925 moved from start: 0.9186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5663 Z= 0.165 Angle : 0.738 9.275 7658 Z= 0.400 Chirality : 0.045 0.156 812 Planarity : 0.003 0.013 1078 Dihedral : 6.656 24.171 805 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.89 % Allowed : 17.35 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.20 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -2.36 (0.21), residues: 562 loop : -3.32 (0.26), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.017 0.002 TYR F 50 PHE 0.015 0.002 PHE C 118 TRP 0.020 0.002 TRP C 106 HIS 0.005 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5663) covalent geometry : angle 0.73846 ( 7658) hydrogen bonds : bond 0.03289 ( 199) hydrogen bonds : angle 7.30790 ( 579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: B 127 ASP cc_start: 0.5666 (m-30) cc_final: 0.5422 (m-30) REVERT: C 113 MET cc_start: 0.6252 (mmm) cc_final: 0.5979 (tpt) REVERT: D 113 MET cc_start: 0.4931 (tmm) cc_final: 0.4219 (tpt) REVERT: E 57 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6466 (tt) REVERT: E 128 GLN cc_start: 0.5031 (OUTLIER) cc_final: 0.3261 (tm-30) REVERT: G 113 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5758 (tmm) REVERT: G 127 ASP cc_start: 0.6004 (m-30) cc_final: 0.5674 (t0) outliers start: 17 outliers final: 10 residues processed: 57 average time/residue: 0.0720 time to fit residues: 5.4908 Evaluate side-chains 58 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain G residue 113 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6481 r_free = 0.6481 target = 0.585778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 145)---------------| | r_work = 0.7251 r_free = 0.7251 target = 0.452011 restraints weight = 8660.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.7326 r_free = 0.7326 target = 0.453255 restraints weight = 10333.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.7357 r_free = 0.7357 target = 0.454202 restraints weight = 8803.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.7380 r_free = 0.7380 target = 0.453819 restraints weight = 7784.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.7389 r_free = 0.7389 target = 0.454297 restraints weight = 7129.595| |-----------------------------------------------------------------------------| r_work (final): 0.6276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5115 moved from start: 0.9468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5663 Z= 0.216 Angle : 0.815 13.719 7658 Z= 0.444 Chirality : 0.046 0.161 812 Planarity : 0.004 0.016 1078 Dihedral : 7.055 25.132 805 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.50 % Favored : 86.50 % Rotamer: Outliers : 2.89 % Allowed : 17.01 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.04 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -2.38 (0.21), residues: 537 loop : -2.83 (0.31), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 64 TYR 0.015 0.002 TYR F 48 PHE 0.015 0.003 PHE C 118 TRP 0.022 0.003 TRP C 106 HIS 0.003 0.001 HIS E 149 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 5663) covalent geometry : angle 0.81489 ( 7658) hydrogen bonds : bond 0.04044 ( 199) hydrogen bonds : angle 7.45979 ( 579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.6254 (mmm) cc_final: 0.5950 (tpt) REVERT: D 113 MET cc_start: 0.4891 (tmm) cc_final: 0.4250 (tpt) REVERT: E 57 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6320 (tt) REVERT: E 128 GLN cc_start: 0.5618 (OUTLIER) cc_final: 0.4754 (tp-100) REVERT: F 100 SER cc_start: 0.7473 (OUTLIER) cc_final: 0.6941 (t) REVERT: F 118 PHE cc_start: 0.5565 (OUTLIER) cc_final: 0.4886 (m-80) REVERT: G 113 MET cc_start: 0.5783 (OUTLIER) cc_final: 0.5209 (ttm) REVERT: G 127 ASP cc_start: 0.5823 (m-30) cc_final: 0.5588 (t0) outliers start: 17 outliers final: 9 residues processed: 58 average time/residue: 0.0666 time to fit residues: 5.1188 Evaluate side-chains 56 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain G residue 113 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 47 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 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 = 0.6308 r_free = 0.6308 target = 0.439019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.6987 r_free = 0.6987 target = 0.340383 restraints weight = 6140.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.7007 r_free = 0.7007 target = 0.342934 restraints weight = 4910.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.7011 r_free = 0.7011 target = 0.344310 restraints weight = 4134.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.7043 r_free = 0.7043 target = 0.346004 restraints weight = 3642.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.7045 r_free = 0.7045 target = 0.346521 restraints weight = 3259.823| |-----------------------------------------------------------------------------| r_work (final): 0.5606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4629 moved from start: 1.0092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5663 Z= 0.240 Angle : 0.877 12.435 7658 Z= 0.480 Chirality : 0.048 0.164 812 Planarity : 0.004 0.028 1078 Dihedral : 7.651 27.753 805 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.86 % Favored : 84.14 % Rotamer: Outliers : 2.89 % Allowed : 17.18 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.42 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -2.64 (0.20), residues: 559 loop : -2.99 (0.30), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 95 TYR 0.016 0.002 TYR F 48 PHE 0.017 0.003 PHE C 118 TRP 0.024 0.003 TRP C 106 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 5663) covalent geometry : angle 0.87680 ( 7658) hydrogen bonds : bond 0.04605 ( 199) hydrogen bonds : angle 7.89072 ( 579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 915.83 seconds wall clock time: 16 minutes 34.01 seconds (994.01 seconds total)