Starting phenix.real_space_refine on Sun Mar 10 22:23:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/03_2024/8enq_28276.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/03_2024/8enq_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_28276/03_2024/8enq_28276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/03_2024/8enq_28276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/03_2024/8enq_28276.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enq_28276/03_2024/8enq_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-dev-5265/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: 3.56, per 1000 atoms: 0.64 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: 1.98 Conformation dependent library (CDL) restraints added in 1.0 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: 0.71 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: 1.54 Time building geometry restraints manager: 2.17 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 2.430 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.370 Find NCS groups from input model: 0.370 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- 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 : 0.576 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: 0.1882 time to fit residues: 9.7262 Evaluate side-chains 30 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 9.9990 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3604 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5663 Z= 0.241 Angle : 0.680 7.338 7658 Z= 0.373 Chirality : 0.045 0.162 812 Planarity : 0.003 0.021 1078 Dihedral : 5.361 15.741 805 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.87 % Allowed : 4.76 % 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: 1.07 (0.30), residues: 763 helix: None (None), residues: 0 sheet: 1.14 (0.20), residues: 595 loop : -0.82 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 106 HIS 0.006 0.002 HIS A 149 PHE 0.012 0.002 PHE A 118 TYR 0.012 0.002 TYR G 48 ARG 0.010 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 42 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLN cc_start: 0.5980 (OUTLIER) cc_final: 0.5265 (mt0) REVERT: E 113 MET cc_start: 0.3377 (OUTLIER) cc_final: 0.3160 (ptm) REVERT: E 128 GLN cc_start: 0.3272 (tp40) cc_final: 0.3008 (tp40) outliers start: 11 outliers final: 2 residues processed: 39 average time/residue: 0.1659 time to fit residues: 9.1989 Evaluate side-chains 26 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain E residue 113 MET 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 38 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 73 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 F 136 ASN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** 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 117 GLN G 128 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4398 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 5663 Z= 0.409 Angle : 0.929 10.907 7658 Z= 0.511 Chirality : 0.052 0.214 812 Planarity : 0.006 0.049 1078 Dihedral : 7.284 23.213 805 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 2.72 % Allowed : 6.12 % 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: -0.89 (0.30), residues: 763 helix: None (None), residues: 0 sheet: -0.32 (0.20), residues: 588 loop : -1.04 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 106 HIS 0.008 0.003 HIS E 149 PHE 0.020 0.003 PHE E 118 TYR 0.015 0.002 TYR B 48 ARG 0.005 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 51 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 35 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 118 PHE cc_start: 0.5461 (OUTLIER) cc_final: 0.4118 (m-80) outliers start: 16 outliers final: 11 residues processed: 48 average time/residue: 0.1766 time to fit residues: 11.6268 Evaluate side-chains 41 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 29 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain E residue 113 MET 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 69 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN ** 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 49 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN E 73 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN F 117 GLN F 139 GLN F 144 ASN G 49 GLN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4534 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5663 Z= 0.306 Angle : 0.761 9.241 7658 Z= 0.420 Chirality : 0.045 0.159 812 Planarity : 0.004 0.023 1078 Dihedral : 6.650 23.106 805 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.06 % Allowed : 8.67 % Favored : 88.27 % 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: -2.23 (0.28), residues: 763 helix: None (None), residues: 0 sheet: -1.05 (0.20), residues: 602 loop : -2.47 (0.33), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 106 HIS 0.006 0.002 HIS F 149 PHE 0.016 0.003 PHE C 118 TYR 0.012 0.002 TYR C 50 ARG 0.004 0.001 ARG D 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 62 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6843 (m-40) REVERT: B 127 ASP cc_start: 0.5524 (m-30) cc_final: 0.5268 (m-30) REVERT: D 113 MET cc_start: 0.4785 (tpt) cc_final: 0.4565 (tmm) REVERT: E 128 GLN cc_start: 0.4355 (OUTLIER) cc_final: 0.3540 (tp-100) outliers start: 18 outliers final: 9 residues processed: 56 average time/residue: 0.1525 time to fit residues: 11.8060 Evaluate side-chains 47 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain G residue 66 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 83 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** B 72 GLN ** 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 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** G 105 GLN G 139 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5024 moved from start: 0.7843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 5663 Z= 0.513 Angle : 1.076 10.751 7658 Z= 0.606 Chirality : 0.054 0.169 812 Planarity : 0.007 0.033 1078 Dihedral : 8.843 26.815 805 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 40.47 Ramachandran Plot: Outliers : 0.39 % Allowed : 14.02 % Favored : 85.58 % Rotamer: Outliers : 4.76 % Allowed : 12.07 % 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: -3.86 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -2.35 (0.20), residues: 574 loop : -2.32 (0.36), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 106 HIS 0.009 0.003 HIS E 149 PHE 0.021 0.004 PHE E 118 TYR 0.052 0.004 TYR F 48 ARG 0.006 0.001 ARG D 95 *********************** 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 76 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 48 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.5032 (OUTLIER) cc_final: 0.4397 (tp) REVERT: B 50 TYR cc_start: 0.3961 (OUTLIER) cc_final: 0.1486 (m-80) REVERT: B 128 GLN cc_start: 0.6566 (tt0) cc_final: 0.6068 (tm-30) REVERT: D 113 MET cc_start: 0.5446 (tpt) cc_final: 0.4632 (tpt) REVERT: E 113 MET cc_start: 0.5586 (OUTLIER) cc_final: 0.5349 (ttm) REVERT: F 100 SER cc_start: 0.8002 (OUTLIER) cc_final: 0.7003 (t) REVERT: F 118 PHE cc_start: 0.5672 (OUTLIER) cc_final: 0.4789 (m-80) REVERT: G 50 TYR cc_start: 0.5870 (OUTLIER) cc_final: 0.3922 (m-80) REVERT: G 104 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6849 (t0) outliers start: 28 outliers final: 14 residues processed: 71 average time/residue: 0.1516 time to fit residues: 14.7911 Evaluate side-chains 63 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 42 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 147 THR 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 G residue 50 TYR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 117 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 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** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** 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** F 144 ASN ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4731 moved from start: 0.7772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5663 Z= 0.241 Angle : 0.722 7.982 7658 Z= 0.392 Chirality : 0.045 0.158 812 Planarity : 0.003 0.016 1078 Dihedral : 6.635 23.357 805 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.74 % Allowed : 13.78 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.28), residues: 763 helix: None (None), residues: 0 sheet: -2.00 (0.20), residues: 556 loop : -2.22 (0.35), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 106 HIS 0.009 0.001 HIS B 149 PHE 0.018 0.002 PHE A 97 TYR 0.012 0.002 TYR C 48 ARG 0.002 0.000 ARG B 95 *********************** 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 66 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 44 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 THR cc_start: 0.5074 (OUTLIER) cc_final: 0.4820 (p) REVERT: B 128 GLN cc_start: 0.6442 (tt0) cc_final: 0.6095 (tm-30) REVERT: D 113 MET cc_start: 0.5310 (tpt) cc_final: 0.4589 (tpt) REVERT: E 128 GLN cc_start: 0.4340 (OUTLIER) cc_final: 0.1557 (tm-30) REVERT: G 104 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6370 (t0) outliers start: 22 outliers final: 17 residues processed: 61 average time/residue: 0.1609 time to fit residues: 13.5716 Evaluate side-chains 62 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 42 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 54 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 54 ASN 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 D residue 61 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 104 ASP 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 8 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 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 60 GLN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** 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 144 ASN ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4888 moved from start: 0.8371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5663 Z= 0.305 Angle : 0.783 8.073 7658 Z= 0.432 Chirality : 0.046 0.158 812 Planarity : 0.004 0.018 1078 Dihedral : 6.984 23.589 805 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 29.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.63 % Favored : 86.37 % Rotamer: Outliers : 5.10 % Allowed : 13.78 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.28), residues: 763 helix: None (None), residues: 0 sheet: -2.08 (0.22), residues: 507 loop : -2.40 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 106 HIS 0.006 0.001 HIS F 73 PHE 0.017 0.003 PHE A 97 TYR 0.019 0.002 TYR F 48 ARG 0.004 0.001 ARG A 64 *********************** 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 74 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 44 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: B 113 MET cc_start: 0.5194 (ppp) cc_final: 0.4671 (ppp) REVERT: D 113 MET cc_start: 0.5264 (tpt) cc_final: 0.4583 (tpt) REVERT: E 113 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.4934 (ttm) REVERT: E 128 GLN cc_start: 0.4633 (OUTLIER) cc_final: 0.3475 (tp40) REVERT: F 118 PHE cc_start: 0.5572 (OUTLIER) cc_final: 0.4831 (m-80) REVERT: G 104 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6609 (t0) outliers start: 30 outliers final: 20 residues processed: 69 average time/residue: 0.1505 time to fit residues: 14.3636 Evaluate side-chains 68 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 43 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 60 GLN 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 90 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 54 ASN 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 D residue 61 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 147 THR 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 83 GLN Chi-restraints excluded: chain G residue 104 ASP 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 22 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 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: 0.4951 moved from start: 0.8794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5663 Z= 0.317 Angle : 0.831 11.100 7658 Z= 0.453 Chirality : 0.047 0.156 812 Planarity : 0.004 0.019 1078 Dihedral : 7.204 23.695 805 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 30.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 4.08 % Allowed : 16.33 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.28), residues: 763 helix: None (None), residues: 0 sheet: -2.24 (0.21), residues: 525 loop : -2.48 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 106 HIS 0.006 0.002 HIS F 73 PHE 0.018 0.003 PHE A 97 TYR 0.019 0.002 TYR F 48 ARG 0.005 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 72 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 48 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.5661 (ppp) cc_final: 0.4893 (ppp) REVERT: B 128 GLN cc_start: 0.6796 (tt0) cc_final: 0.6282 (tm-30) REVERT: D 113 MET cc_start: 0.5523 (tpt) cc_final: 0.4878 (tpt) REVERT: E 113 MET cc_start: 0.5392 (OUTLIER) cc_final: 0.5000 (ttm) REVERT: E 128 GLN cc_start: 0.4813 (OUTLIER) cc_final: 0.3672 (tp40) REVERT: G 104 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6641 (t0) outliers start: 24 outliers final: 17 residues processed: 70 average time/residue: 0.1490 time to fit residues: 14.4607 Evaluate side-chains 66 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 81 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 54 ASN 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 D residue 61 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 117 GLN 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: 0.9980 chunk 30 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 105 GLN ** A 117 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** G 49 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4801 moved from start: 0.8830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5663 Z= 0.211 Angle : 0.695 9.969 7658 Z= 0.375 Chirality : 0.044 0.147 812 Planarity : 0.003 0.014 1078 Dihedral : 6.234 23.196 805 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 25.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 3.74 % Allowed : 17.69 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.28), residues: 763 helix: None (None), residues: 0 sheet: -2.17 (0.21), residues: 516 loop : -2.35 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 106 HIS 0.004 0.001 HIS B 149 PHE 0.012 0.002 PHE F 118 TYR 0.012 0.002 TYR C 48 ARG 0.002 0.000 ARG A 64 *********************** 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 62 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 40 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 THR cc_start: 0.4970 (OUTLIER) cc_final: 0.4722 (p) REVERT: B 113 MET cc_start: 0.5290 (ppp) cc_final: 0.4753 (ppp) REVERT: D 113 MET cc_start: 0.5515 (tpt) cc_final: 0.4897 (tpt) outliers start: 22 outliers final: 16 residues processed: 58 average time/residue: 0.1414 time to fit residues: 11.7565 Evaluate side-chains 55 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 38 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 54 ASN 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 D residue 61 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain G residue 117 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 83 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 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 122 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** 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** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5046 moved from start: 0.9379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5663 Z= 0.356 Angle : 0.869 9.235 7658 Z= 0.482 Chirality : 0.048 0.163 812 Planarity : 0.005 0.018 1078 Dihedral : 7.365 24.202 805 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 32.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.43 % Favored : 82.44 % Rotamer: Outliers : 3.40 % Allowed : 18.03 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.28), residues: 763 helix: None (None), residues: 0 sheet: -2.55 (0.21), residues: 542 loop : -2.24 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 106 HIS 0.008 0.002 HIS F 149 PHE 0.016 0.003 PHE D 97 TYR 0.023 0.002 TYR F 48 ARG 0.004 0.001 ARG D 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 66 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.5640 (ppp) cc_final: 0.4989 (ppp) REVERT: D 113 MET cc_start: 0.5288 (tpt) cc_final: 0.4775 (tpt) REVERT: E 128 GLN cc_start: 0.4821 (OUTLIER) cc_final: 0.3891 (tp-100) REVERT: F 118 PHE cc_start: 0.5686 (OUTLIER) cc_final: 0.4810 (m-80) outliers start: 20 outliers final: 14 residues processed: 64 average time/residue: 0.1685 time to fit residues: 14.6426 Evaluate side-chains 60 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 81 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 54 ASN 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 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 128 GLN Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 139 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 83 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 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 149 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 ASN D 144 ASN ** F 83 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 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 = 0.6246 r_free = 0.6246 target = 0.433195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.6923 r_free = 0.6923 target = 0.326647 restraints weight = 6230.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.6971 r_free = 0.6971 target = 0.328785 restraints weight = 5429.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.6972 r_free = 0.6972 target = 0.329090 restraints weight = 4812.077| |-----------------------------------------------------------------------------| r_work (final): 0.5512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5252 moved from start: 1.0517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 5663 Z= 0.468 Angle : 1.051 10.443 7658 Z= 0.586 Chirality : 0.052 0.176 812 Planarity : 0.006 0.036 1078 Dihedral : 8.903 28.856 805 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 40.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.66 % Favored : 80.34 % Rotamer: Outliers : 3.74 % Allowed : 18.03 % Favored : 78.23 % 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: -4.84 (0.27), residues: 763 helix: None (None), residues: 0 sheet: -3.15 (0.19), residues: 546 loop : -2.49 (0.35), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 106 HIS 0.009 0.002 HIS F 73 PHE 0.026 0.004 PHE D 97 TYR 0.036 0.003 TYR F 48 ARG 0.008 0.001 ARG D 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1263.92 seconds wall clock time: 24 minutes 1.04 seconds (1441.04 seconds total)