Starting phenix.real_space_refine on Thu Dec 7 23:10:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/12_2023/8enq_28276.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/12_2023/8enq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/12_2023/8enq_28276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/12_2023/8enq_28276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/12_2023/8enq_28276.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/12_2023/8enq_28276.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "D ASP 127": "OD1" <-> "OD2" Residue "G ASP 80": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/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: 3.79, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.86 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: 1.60 Time building geometry restraints manager: 2.33 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: 98.46 - 105.57: 33 105.57 - 112.67: 2815 112.67 - 119.78: 1763 119.78 - 126.88: 3011 126.88 - 133.99: 36 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 2.520 nonbonded pdb=" NE2 GLN B 49 " pdb=" OE1 GLN B 72 " model vdw 2.284 2.520 nonbonded pdb=" NE2 GLN E 128 " pdb=" OG SER E 133 " model vdw 2.286 2.520 nonbonded pdb=" OG SER C 43 " pdb=" O CYS C 63 " model vdw 2.300 2.440 nonbonded pdb=" OG SER G 43 " pdb=" O CYS G 63 " model vdw 2.312 2.440 ... (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 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.530 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.480 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- 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= 0.249 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (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 TRP 0.016 0.002 TRP G 106 HIS 0.003 0.001 HIS A 73 PHE 0.013 0.002 PHE A 118 TYR 0.011 0.001 TYR A 50 ARG 0.005 0.001 ARG A 64 *********************** 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 fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2020 time to fit residues: 10.1468 Evaluate side-chains 30 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.0170 chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 0.0030 chunk 19 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 overall best weight: 1.5630 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3639 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5663 Z= 0.253 Angle : 0.687 6.882 7658 Z= 0.379 Chirality : 0.045 0.151 812 Planarity : 0.003 0.036 1078 Dihedral : 5.410 16.432 805 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.04 % Allowed : 4.59 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.30), residues: 763 helix: None (None), residues: 0 sheet: 1.09 (0.20), residues: 595 loop : -0.81 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 106 HIS 0.007 0.002 HIS E 149 PHE 0.013 0.002 PHE A 118 TYR 0.012 0.002 TYR G 48 ARG 0.008 0.001 ARG B 64 *********************** 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 43 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 41 average time/residue: 0.1593 time to fit residues: 9.3038 Evaluate side-chains 26 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0538 time to fit residues: 1.0954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 0.2980 chunk 69 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 72 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 105 GLN E 73 HIS ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN F 73 HIS ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN F 139 GLN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4589 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 5663 Z= 0.504 Angle : 1.045 11.203 7658 Z= 0.577 Chirality : 0.054 0.201 812 Planarity : 0.007 0.054 1078 Dihedral : 8.087 27.176 805 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 34.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.59 % Favored : 95.15 % Rotamer: Outliers : 2.04 % Allowed : 6.80 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -0.90 (0.19), residues: 608 loop : -2.66 (0.32), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 106 HIS 0.013 0.003 HIS E 149 PHE 0.023 0.004 PHE E 118 TYR 0.017 0.003 TYR B 48 ARG 0.006 0.001 ARG A 95 *********************** 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 56 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 54 average time/residue: 0.1721 time to fit residues: 12.6718 Evaluate side-chains 41 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.579 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0624 time to fit residues: 1.4395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** 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 60 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN G 105 GLN G 117 GLN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5041 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 5663 Z= 0.566 Angle : 1.134 11.681 7658 Z= 0.637 Chirality : 0.056 0.273 812 Planarity : 0.008 0.053 1078 Dihedral : 9.424 30.333 805 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 42.63 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.63 % Favored : 85.98 % Rotamer: Outliers : 3.74 % Allowed : 10.37 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -2.05 (0.20), residues: 554 loop : -2.78 (0.31), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 106 HIS 0.010 0.004 HIS E 149 PHE 0.023 0.005 PHE E 118 TYR 0.017 0.003 TYR B 48 ARG 0.007 0.001 ARG A 95 *********************** 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 72 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 50 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 68 average time/residue: 0.1732 time to fit residues: 15.7921 Evaluate side-chains 54 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.609 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0617 time to fit residues: 2.1369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4670 moved from start: 0.7591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5663 Z= 0.221 Angle : 0.720 8.844 7658 Z= 0.387 Chirality : 0.045 0.159 812 Planarity : 0.003 0.018 1078 Dihedral : 6.697 23.747 805 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.68 % Allowed : 13.61 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -1.71 (0.21), residues: 526 loop : -2.82 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 106 HIS 0.005 0.001 HIS F 73 PHE 0.016 0.002 PHE D 142 TYR 0.015 0.002 TYR G 50 ARG 0.002 0.000 ARG F 64 *********************** 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 53 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.545 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 52 average time/residue: 0.1823 time to fit residues: 12.7334 Evaluate side-chains 42 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0528 time to fit residues: 0.8436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** B 72 GLN ** 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** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4990 moved from start: 0.8573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5663 Z= 0.364 Angle : 0.890 8.976 7658 Z= 0.497 Chirality : 0.048 0.172 812 Planarity : 0.005 0.018 1078 Dihedral : 7.871 25.455 805 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 35.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.12 % Favored : 83.88 % Rotamer: Outliers : 2.72 % Allowed : 13.78 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -2.19 (0.21), residues: 560 loop : -3.02 (0.31), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 106 HIS 0.007 0.002 HIS F 73 PHE 0.017 0.003 PHE E 118 TYR 0.014 0.002 TYR C 50 ARG 0.004 0.001 ARG A 64 *********************** 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 65 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 49 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 61 average time/residue: 0.2026 time to fit residues: 17.2888 Evaluate side-chains 56 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1402 time to fit residues: 2.6240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 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 60 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN G 73 HIS ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4705 moved from start: 0.8456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5663 Z= 0.192 Angle : 0.693 15.470 7658 Z= 0.368 Chirality : 0.045 0.148 812 Planarity : 0.002 0.010 1078 Dihedral : 6.132 20.927 805 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.68 % Allowed : 14.12 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.28), residues: 763 helix: None (None), residues: 0 sheet: -1.85 (0.22), residues: 526 loop : -2.58 (0.33), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 106 HIS 0.004 0.001 HIS F 73 PHE 0.016 0.002 PHE A 97 TYR 0.016 0.002 TYR F 50 ARG 0.002 0.001 ARG D 95 *********************** 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 47 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.611 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.1788 time to fit residues: 11.2557 Evaluate side-chains 45 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0760 time to fit residues: 1.2207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** 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 122 ASN ** 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 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5216 moved from start: 0.9588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.173 5663 Z= 0.519 Angle : 1.072 13.999 7658 Z= 0.600 Chirality : 0.053 0.205 812 Planarity : 0.007 0.063 1078 Dihedral : 8.543 28.114 805 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 40.18 Ramachandran Plot: Outliers : 0.52 % Allowed : 19.92 % Favored : 79.55 % Rotamer: Outliers : 1.36 % Allowed : 15.48 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.28), residues: 763 helix: None (None), residues: 0 sheet: -2.71 (0.20), residues: 556 loop : -2.79 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 106 HIS 0.008 0.002 HIS G 73 PHE 0.023 0.004 PHE D 97 TYR 0.018 0.003 TYR C 151 ARG 0.006 0.001 ARG D 95 *********************** 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 60 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.637 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.1716 time to fit residues: 13.8679 Evaluate side-chains 50 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.595 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0626 time to fit residues: 1.5475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 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 117 GLN ** 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 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4937 moved from start: 0.9440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5663 Z= 0.242 Angle : 0.789 13.475 7658 Z= 0.424 Chirality : 0.047 0.164 812 Planarity : 0.003 0.014 1078 Dihedral : 7.012 23.360 805 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 0.51 % Allowed : 16.84 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -2.47 (0.20), residues: 569 loop : -2.77 (0.33), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 106 HIS 0.006 0.001 HIS F 73 PHE 0.019 0.002 PHE F 118 TYR 0.020 0.002 TYR F 50 ARG 0.004 0.001 ARG F 95 *********************** 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 46 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.607 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1739 time to fit residues: 10.4603 Evaluate side-chains 42 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0555 time to fit residues: 0.9283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 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 117 GLN ** 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 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5146 moved from start: 0.9985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5663 Z= 0.370 Angle : 0.945 13.122 7658 Z= 0.514 Chirality : 0.050 0.167 812 Planarity : 0.005 0.020 1078 Dihedral : 7.876 27.204 805 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 34.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.40 % Favored : 80.60 % Rotamer: Outliers : 0.34 % Allowed : 17.69 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -2.54 (0.21), residues: 520 loop : -2.99 (0.32), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 106 HIS 0.006 0.002 HIS G 73 PHE 0.019 0.003 PHE F 118 TYR 0.016 0.002 TYR F 48 ARG 0.005 0.001 ARG F 95 ********************** 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 51 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.605 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.1631 time to fit residues: 11.3729 Evaluate side-chains 47 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0537 time to fit residues: 0.9561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 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 117 GLN ** 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 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** G 139 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 = 0.6313 r_free = 0.6313 target = 0.440873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.6982 r_free = 0.6982 target = 0.339711 restraints weight = 6150.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.7001 r_free = 0.7001 target = 0.342026 restraints weight = 5106.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.7003 r_free = 0.7003 target = 0.342904 restraints weight = 4414.577| |-----------------------------------------------------------------------------| r_work (final): 0.5582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4722 moved from start: 1.0182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5663 Z= 0.294 Angle : 0.843 12.491 7658 Z= 0.456 Chirality : 0.048 0.159 812 Planarity : 0.004 0.015 1078 Dihedral : 7.336 25.224 805 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 29.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 0.68 % Allowed : 17.69 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -2.57 (0.21), residues: 540 loop : -2.84 (0.33), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 106 HIS 0.006 0.001 HIS F 73 PHE 0.016 0.003 PHE D 142 TYR 0.018 0.002 TYR F 50 ARG 0.002 0.000 ARG F 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1311.74 seconds wall clock time: 24 minutes 58.43 seconds (1498.43 seconds total)