Starting phenix.real_space_refine on Thu Aug 6 21:26:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21vq_68038/08_2026/21vq_68038.cif Found real_map, /net/cci-nas-00/data/ceres_data/21vq_68038/08_2026/21vq_68038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21vq_68038/08_2026/21vq_68038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21vq_68038/08_2026/21vq_68038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21vq_68038/08_2026/21vq_68038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21vq_68038/08_2026/21vq_68038.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.057 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 44 5.16 5 C 10698 2.51 5 N 2781 2.21 5 O 3450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16973 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1222 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain breaks: 7 Chain: "E" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1119 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "L" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1026 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "M" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2515 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 10, 'TRANS': 315} Chain: "N" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1525 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 2 Chain: "V" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 189 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "h" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3783 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 16, 'TRANS': 474} Chain breaks: 1 Chain: "o" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3799 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Chain: "t" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1795 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 13, 'TRANS': 230} Time building chain proxies: 3.38, per 1000 atoms: 0.20 Number of scatterers: 16973 At special positions: 0 Unit cell: (148.5, 121, 223.3, 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 44 16.00 O 3450 8.00 N 2781 7.00 C 10698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 884.3 milliseconds 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4054 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 32 sheets defined 26.6% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'D' and resid 13 through 21 removed outlier: 4.154A pdb=" N LYS D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.740A pdb=" N SER D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 56 removed outlier: 3.635A pdb=" N VAL D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 74 removed outlier: 4.088A pdb=" N ASP D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 93 through 97 removed outlier: 3.848A pdb=" N VAL D 97 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 106 No H-bonds generated for 'chain 'D' and resid 105 through 106' Processing helix chain 'D' and resid 108 through 108 No H-bonds generated for 'chain 'D' and resid 108 through 108' Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 141 through 152 removed outlier: 4.149A pdb=" N VAL D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 11 removed outlier: 3.657A pdb=" N ILE E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 23 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'L' and resid 27 through 42 removed outlier: 3.800A pdb=" N ILE L 31 " --> pdb=" O THR L 27 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR L 42 " --> pdb=" O ILE L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 80 removed outlier: 4.060A pdb=" N VAL L 71 " --> pdb=" O LYS L 67 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 74 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE L 75 " --> pdb=" O VAL L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.602A pdb=" N GLU L 126 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR L 127 " --> pdb=" O PRO L 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 122 through 127' Processing helix chain 'M' and resid 90 through 101 removed outlier: 3.749A pdb=" N ILE M 101 " --> pdb=" O ILE M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 153 Processing helix chain 'M' and resid 165 through 178 removed outlier: 3.575A pdb=" N VAL M 169 " --> pdb=" O LYS M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 213 removed outlier: 3.702A pdb=" N ILE M 213 " --> pdb=" O ILE M 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 4.203A pdb=" N ASN N 37 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 33 through 38' Processing helix chain 'N' and resid 49 through 57 removed outlier: 4.339A pdb=" N TYR N 53 " --> pdb=" O ALA N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 90 Processing helix chain 'N' and resid 116 through 120 Processing helix chain 'N' and resid 124 through 139 removed outlier: 3.707A pdb=" N GLN N 128 " --> pdb=" O THR N 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN N 139 " --> pdb=" O LYS N 135 " (cutoff:3.500A) Processing helix chain 'V' and resid 632 through 651 removed outlier: 3.875A pdb=" N SER V 640 " --> pdb=" O ASN V 636 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN V 641 " --> pdb=" O THR V 637 " (cutoff:3.500A) Processing helix chain 'h' and resid 15 through 32 removed outlier: 3.579A pdb=" N ILE h 19 " --> pdb=" O THR h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 66 removed outlier: 3.797A pdb=" N GLN h 45 " --> pdb=" O THR h 41 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET h 61 " --> pdb=" O LEU h 57 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN h 62 " --> pdb=" O TRP h 58 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY h 63 " --> pdb=" O GLU h 59 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 69 No H-bonds generated for 'chain 'h' and resid 67 through 69' Processing helix chain 'h' and resid 74 through 84 removed outlier: 3.784A pdb=" N LEU h 78 " --> pdb=" O GLU h 74 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP h 79 " --> pdb=" O GLY h 75 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS h 84 " --> pdb=" O GLU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 146 through 153 removed outlier: 4.124A pdb=" N GLY h 153 " --> pdb=" O ALA h 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 180 through 193 removed outlier: 3.640A pdb=" N ALA h 191 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN h 192 " --> pdb=" O PHE h 188 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL h 193 " --> pdb=" O ILE h 189 " (cutoff:3.500A) Processing helix chain 'h' and resid 197 through 201 Processing helix chain 'h' and resid 286 through 295 removed outlier: 3.837A pdb=" N PHE h 294 " --> pdb=" O PHE h 290 " (cutoff:3.500A) Processing helix chain 'h' and resid 305 through 316 removed outlier: 3.624A pdb=" N VAL h 310 " --> pdb=" O ARG h 306 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS h 311 " --> pdb=" O ALA h 307 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR h 316 " --> pdb=" O ALA h 312 " (cutoff:3.500A) Processing helix chain 'h' and resid 349 through 361 removed outlier: 3.574A pdb=" N VAL h 353 " --> pdb=" O THR h 349 " (cutoff:3.500A) Processing helix chain 'h' and resid 410 through 426 Processing helix chain 'h' and resid 435 through 446 removed outlier: 3.680A pdb=" N ILE h 439 " --> pdb=" O THR h 435 " (cutoff:3.500A) Processing helix chain 'h' and resid 465 through 469 removed outlier: 3.613A pdb=" N TYR h 469 " --> pdb=" O ASP h 466 " (cutoff:3.500A) Processing helix chain 'o' and resid 15 through 32 removed outlier: 3.667A pdb=" N TYR o 23 " --> pdb=" O ILE o 19 " (cutoff:3.500A) Processing helix chain 'o' and resid 41 through 69 removed outlier: 3.908A pdb=" N ARG o 48 " --> pdb=" O GLY o 44 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE o 49 " --> pdb=" O GLN o 45 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE o 50 " --> pdb=" O LEU o 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU o 57 " --> pdb=" O THR o 53 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR o 69 " --> pdb=" O TYR o 65 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.700A pdb=" N ASP o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG o 85 " --> pdb=" O ILE o 81 " (cutoff:3.500A) Processing helix chain 'o' and resid 146 through 153 removed outlier: 3.882A pdb=" N GLY o 153 " --> pdb=" O ALA o 149 " (cutoff:3.500A) Processing helix chain 'o' and resid 180 through 193 removed outlier: 3.588A pdb=" N ALA o 191 " --> pdb=" O ASN o 187 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN o 192 " --> pdb=" O PHE o 188 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL o 193 " --> pdb=" O ILE o 189 " (cutoff:3.500A) Processing helix chain 'o' and resid 195 through 200 removed outlier: 4.088A pdb=" N ALA o 199 " --> pdb=" O THR o 196 " (cutoff:3.500A) Processing helix chain 'o' and resid 286 through 297 removed outlier: 3.804A pdb=" N PHE o 294 " --> pdb=" O PHE o 290 " (cutoff:3.500A) Processing helix chain 'o' and resid 305 through 316 Processing helix chain 'o' and resid 349 through 361 removed outlier: 3.507A pdb=" N VAL o 353 " --> pdb=" O THR o 349 " (cutoff:3.500A) Processing helix chain 'o' and resid 410 through 426 Processing helix chain 'o' and resid 435 through 446 removed outlier: 3.538A pdb=" N ILE o 439 " --> pdb=" O THR o 435 " (cutoff:3.500A) Processing helix chain 'o' and resid 465 through 469 Processing helix chain 't' and resid 5 through 19 removed outlier: 3.777A pdb=" N ALA t 9 " --> pdb=" O ASN t 5 " (cutoff:3.500A) Processing helix chain 't' and resid 94 through 100 Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 135 removed outlier: 3.756A pdb=" N ARG D 160 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D 133 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY D 162 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 31 through 34 removed outlier: 4.673A pdb=" N LEU E 129 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 128 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.590A pdb=" N PHE E 81 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET E 68 " --> pdb=" O PHE E 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN E 42 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN N 197 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN N 199 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR E 45 " --> pdb=" O ASN N 199 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY N 201 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N THR E 47 " --> pdb=" O GLY N 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 87 through 94 removed outlier: 3.538A pdb=" N ASN L 87 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR L 107 " --> pdb=" O ASN L 89 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR L 91 " --> pdb=" O ASN L 105 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN L 105 " --> pdb=" O TYR L 91 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER L 93 " --> pdb=" O SER L 103 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER L 103 " --> pdb=" O SER L 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 60 through 62 removed outlier: 7.225A pdb=" N VAL M 107 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS M 123 " --> pdb=" O VAL M 107 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU M 109 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N HIS M 143 " --> pdb=" O GLN M 127 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL M 129 " --> pdb=" O VAL M 141 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL M 141 " --> pdb=" O VAL M 129 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASP M 131 " --> pdb=" O ARG M 139 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG M 139 " --> pdb=" O ASP M 131 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE M 133 " --> pdb=" O ASP M 137 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP M 137 " --> pdb=" O PHE M 133 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN M 81 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE M 69 " --> pdb=" O GLY M 313 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY M 302 " --> pdb=" O LEU M 295 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR M 292 " --> pdb=" O ARG M 236 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA M 238 " --> pdb=" O THR M 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 60 through 62 removed outlier: 7.225A pdb=" N VAL M 107 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS M 123 " --> pdb=" O VAL M 107 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU M 109 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N HIS M 143 " --> pdb=" O GLN M 127 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL M 129 " --> pdb=" O VAL M 141 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL M 141 " --> pdb=" O VAL M 129 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASP M 131 " --> pdb=" O ARG M 139 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG M 139 " --> pdb=" O ASP M 131 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE M 133 " --> pdb=" O ASP M 137 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP M 137 " --> pdb=" O PHE M 133 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN M 81 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE M 69 " --> pdb=" O GLY M 313 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU M 325 " --> pdb=" O VAL M 307 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL M 309 " --> pdb=" O GLU M 323 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU M 323 " --> pdb=" O VAL M 309 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N HIS M 311 " --> pdb=" O THR M 321 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR M 321 " --> pdb=" O HIS M 311 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL M 277 " --> pdb=" O SER M 326 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY M 276 " --> pdb=" O PHE M 253 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS M 278 " --> pdb=" O GLU M 251 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU M 251 " --> pdb=" O LYS M 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 155 through 160 removed outlier: 3.528A pdb=" N THR M 196 " --> pdb=" O TYR M 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 180 through 183 removed outlier: 6.194A pdb=" N GLU M 181 " --> pdb=" O VAL M 224 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N VAL M 226 " --> pdb=" O GLU M 181 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN M 183 " --> pdb=" O VAL M 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 58 through 61 removed outlier: 4.009A pdb=" N ILE N 144 " --> pdb=" O PHE N 39 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE N 143 " --> pdb=" O ASN N 154 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU N 145 " --> pdb=" O TYR N 152 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU N 175 " --> pdb=" O LYS N 158 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE N 160 " --> pdb=" O ASP N 173 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP N 173 " --> pdb=" O ILE N 160 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR N 162 " --> pdb=" O GLN N 171 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLN N 171 " --> pdb=" O TYR N 162 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE N 98 " --> pdb=" O PHE N 176 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR N 97 " --> pdb=" O LYS N 71 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN N 67 " --> pdb=" O SER N 101 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N MET N 103 " --> pdb=" O VAL N 65 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL N 65 " --> pdb=" O MET N 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 74 through 75 Processing sheet with id=AB2, first strand: chain 'h' and resid 202 through 203 removed outlier: 3.663A pdb=" N ILE h 144 " --> pdb=" O VAL h 208 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR h 142 " --> pdb=" O MET h 210 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP h 239 " --> pdb=" O GLY h 140 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR h 142 " --> pdb=" O THR h 237 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR h 237 " --> pdb=" O TYR h 142 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY h 261 " --> pdb=" O ASN h 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 202 through 203 removed outlier: 3.663A pdb=" N ILE h 144 " --> pdb=" O VAL h 208 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR h 142 " --> pdb=" O MET h 210 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP h 239 " --> pdb=" O GLY h 140 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR h 142 " --> pdb=" O THR h 237 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR h 237 " --> pdb=" O TYR h 142 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS h 238 " --> pdb=" O SER h 103 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY h 97 " --> pdb=" O VAL h 244 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP h 271 " --> pdb=" O LYS h 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 112 through 113 removed outlier: 3.696A pdb=" N LEU h 113 " --> pdb=" O THR h 133 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR h 133 " --> pdb=" O LEU h 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'h' and resid 169 through 174 Processing sheet with id=AB6, first strand: chain 'h' and resid 321 through 327 removed outlier: 3.950A pdb=" N LYS h 321 " --> pdb=" O TYR h 346 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR h 340 " --> pdb=" O ASN h 327 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE h 341 " --> pdb=" O TYR h 368 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 321 through 327 removed outlier: 3.950A pdb=" N LYS h 321 " --> pdb=" O TYR h 346 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR h 340 " --> pdb=" O ASN h 327 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE h 341 " --> pdb=" O ARG h 386 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER h 388 " --> pdb=" O PHE h 341 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR h 343 " --> pdb=" O SER h 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'h' and resid 452 through 461 removed outlier: 6.456A pdb=" N ASP h 391 " --> pdb=" O VAL h 481 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER h 483 " --> pdb=" O ASP h 391 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ALA h 393 " --> pdb=" O SER h 483 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'h' and resid 452 through 461 Processing sheet with id=AC1, first strand: chain 'o' and resid 5 through 6 Processing sheet with id=AC2, first strand: chain 'o' and resid 202 through 203 removed outlier: 3.667A pdb=" N TRP o 202 " --> pdb=" O TYR o 209 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE o 144 " --> pdb=" O VAL o 208 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR o 142 " --> pdb=" O MET o 210 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE o 139 " --> pdb=" O GLU o 241 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU o 241 " --> pdb=" O ILE o 139 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA o 141 " --> pdb=" O TRP o 239 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR o 118 " --> pdb=" O ILE o 262 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ILE o 262 " --> pdb=" O TYR o 118 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN o 120 " --> pdb=" O THR o 260 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'o' and resid 202 through 203 removed outlier: 3.667A pdb=" N TRP o 202 " --> pdb=" O TYR o 209 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE o 144 " --> pdb=" O VAL o 208 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR o 142 " --> pdb=" O MET o 210 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE o 139 " --> pdb=" O GLU o 241 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU o 241 " --> pdb=" O ILE o 139 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA o 141 " --> pdb=" O TRP o 239 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP o 271 " --> pdb=" O LYS o 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'o' and resid 112 through 113 Processing sheet with id=AC5, first strand: chain 'o' and resid 169 through 174 Processing sheet with id=AC6, first strand: chain 'o' and resid 321 through 327 removed outlier: 4.005A pdb=" N LYS o 321 " --> pdb=" O TYR o 346 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS o 323 " --> pdb=" O ILE o 344 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR o 340 " --> pdb=" O ASN o 327 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE o 341 " --> pdb=" O TYR o 368 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'o' and resid 321 through 327 removed outlier: 4.005A pdb=" N LYS o 321 " --> pdb=" O TYR o 346 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS o 323 " --> pdb=" O ILE o 344 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR o 340 " --> pdb=" O ASN o 327 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE o 341 " --> pdb=" O ARG o 386 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N SER o 388 " --> pdb=" O PHE o 341 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR o 343 " --> pdb=" O SER o 388 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'o' and resid 452 through 461 removed outlier: 3.541A pdb=" N SER o 454 " --> pdb=" O GLN o 402 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU o 397 " --> pdb=" O ASP o 485 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N ASP o 487 " --> pdb=" O LEU o 397 " (cutoff:3.500A) removed outlier: 12.227A pdb=" N LEU o 399 " --> pdb=" O ASP o 487 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N ILE o 489 " --> pdb=" O LEU o 399 " (cutoff:3.500A) removed outlier: 11.634A pdb=" N TYR o 401 " --> pdb=" O ILE o 489 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N TYR o 491 " --> pdb=" O TYR o 401 " (cutoff:3.500A) removed outlier: 12.077A pdb=" N THR o 403 " --> pdb=" O TYR o 491 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N TYR o 493 " --> pdb=" O THR o 403 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 't' and resid 60 through 64 removed outlier: 5.939A pdb=" N HIS t 61 " --> pdb=" O LEU t 41 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU t 41 " --> pdb=" O HIS t 61 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR t 38 " --> pdb=" O VAL t 32 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL t 32 " --> pdb=" O THR t 38 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR t 40 " --> pdb=" O ILE t 30 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU t 25 " --> pdb=" O VAL t 87 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL t 88 " --> pdb=" O CYS t 120 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS t 120 " --> pdb=" O VAL t 88 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 't' and resid 47 through 49 removed outlier: 3.611A pdb=" N ARG t 49 " --> pdb=" O ASP t 53 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP t 53 " --> pdb=" O ARG t 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 't' and resid 69 through 70 removed outlier: 3.575A pdb=" N GLY t 73 " --> pdb=" O GLY t 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 't' and resid 140 through 144 removed outlier: 3.545A pdb=" N ASN t 144 " --> pdb=" O THR t 148 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR t 148 " --> pdb=" O ASN t 144 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR t 161 " --> pdb=" O TYR t 149 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS t 167 " --> pdb=" O THR t 178 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS t 184 " --> pdb=" O LYS t 195 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 't' and resid 199 through 201 removed outlier: 3.638A pdb=" N VAL t 199 " --> pdb=" O ILE t 206 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 't' and resid 226 through 227 638 hydrogen bonds defined for protein. 1782 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: 2.62 Time building geometry restraints manager: 1.77 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: 5535 1.34 - 1.46: 3796 1.46 - 1.58: 7881 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 17289 Sorted by residual: bond pdb=" N TYR o 276 " pdb=" CA TYR o 276 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 1.95e+01 bond pdb=" N ILE D 121 " pdb=" CA ILE D 121 " ideal model delta sigma weight residual 1.454 1.500 -0.046 1.28e-02 6.10e+03 1.30e+01 bond pdb=" N ILE M 332 " pdb=" CA ILE M 332 " ideal model delta sigma weight residual 1.457 1.496 -0.040 1.15e-02 7.56e+03 1.18e+01 bond pdb=" N VAL M 186 " pdb=" CA VAL M 186 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.15e-02 7.56e+03 1.14e+01 bond pdb=" N VAL N 81 " pdb=" CA VAL N 81 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.23e-02 6.61e+03 1.10e+01 ... (remaining 17284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 22855 2.25 - 4.51: 584 4.51 - 6.76: 53 6.76 - 9.02: 9 9.02 - 11.27: 4 Bond angle restraints: 23505 Sorted by residual: angle pdb=" CA ILE N 190 " pdb=" C ILE N 190 " pdb=" O ILE N 190 " ideal model delta sigma weight residual 122.63 118.31 4.32 8.70e-01 1.32e+00 2.47e+01 angle pdb=" CA GLY o 281 " pdb=" C GLY o 281 " pdb=" O GLY o 281 " ideal model delta sigma weight residual 122.13 117.72 4.41 8.90e-01 1.26e+00 2.45e+01 angle pdb=" CA ILE D 121 " pdb=" C ILE D 121 " pdb=" O ILE D 121 " ideal model delta sigma weight residual 121.72 117.07 4.65 9.60e-01 1.09e+00 2.35e+01 angle pdb=" CB LYS D 91 " pdb=" CG LYS D 91 " pdb=" CD LYS D 91 " ideal model delta sigma weight residual 111.30 121.55 -10.25 2.30e+00 1.89e-01 1.98e+01 angle pdb=" C SER D 99 " pdb=" CA SER D 99 " pdb=" CB SER D 99 " ideal model delta sigma weight residual 116.54 111.56 4.98 1.15e+00 7.56e-01 1.88e+01 ... (remaining 23500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9136 17.92 - 35.83: 868 35.83 - 53.75: 204 53.75 - 71.66: 28 71.66 - 89.58: 5 Dihedral angle restraints: 10241 sinusoidal: 3889 harmonic: 6352 Sorted by residual: dihedral pdb=" CA SER M 328 " pdb=" C SER M 328 " pdb=" N VAL M 329 " pdb=" CA VAL M 329 " ideal model delta harmonic sigma weight residual -180.00 -150.23 -29.77 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA GLN t 112 " pdb=" C GLN t 112 " pdb=" N PRO t 113 " pdb=" CA PRO t 113 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASP D 105 " pdb=" C ASP D 105 " pdb=" N ILE D 106 " pdb=" CA ILE D 106 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 10238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2031 0.050 - 0.100: 492 0.100 - 0.150: 150 0.150 - 0.200: 30 0.200 - 0.250: 8 Chirality restraints: 2711 Sorted by residual: chirality pdb=" CB VAL o 310 " pdb=" CA VAL o 310 " pdb=" CG1 VAL o 310 " pdb=" CG2 VAL o 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CG LEU h 313 " pdb=" CB LEU h 313 " pdb=" CD1 LEU h 313 " pdb=" CD2 LEU h 313 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE D 121 " pdb=" N ILE D 121 " pdb=" C ILE D 121 " pdb=" CB ILE D 121 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2708 not shown) Planarity restraints: 3034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN t 112 " 0.091 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO t 113 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO t 113 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO t 113 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 20 " 0.016 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C ASP D 20 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP D 20 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU D 21 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 134 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C ASN M 134 " 0.052 2.00e-02 2.50e+03 pdb=" O ASN M 134 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN M 135 " -0.017 2.00e-02 2.50e+03 ... (remaining 3031 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 602 2.70 - 3.25: 16325 3.25 - 3.80: 24183 3.80 - 4.35: 29665 4.35 - 4.90: 51043 Nonbonded interactions: 121818 Sorted by model distance: nonbonded pdb=" O ASN M 134 " pdb=" ND2 ASN M 134 " model vdw 2.154 3.120 nonbonded pdb=" O SER V 651 " pdb=" OG SER V 652 " model vdw 2.183 3.040 nonbonded pdb=" OD1 ASP o 287 " pdb=" N ALA o 288 " model vdw 2.198 3.120 nonbonded pdb=" OD2 ASP L 6 " pdb=" OG1 THR h 41 " model vdw 2.202 3.040 nonbonded pdb=" O GLU D 84 " pdb=" OG1 THR D 88 " model vdw 2.210 3.040 ... (remaining 121813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'h' selection = (chain 'o' and (resid 3 through 376 or resid 379 through 495)) } 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.020 Find NCS groups from input model: 0.320 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 : 0.006 0.083 17289 Z= 0.322 Angle : 0.823 11.275 23505 Z= 0.496 Chirality : 0.051 0.250 2711 Planarity : 0.007 0.137 3034 Dihedral : 14.596 89.580 6187 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.82 % Favored : 92.72 % Rotamer: Outliers : 1.01 % Allowed : 16.76 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.17), residues: 2157 helix: 0.93 (0.23), residues: 492 sheet: 0.47 (0.24), residues: 468 loop : -1.85 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 229 TYR 0.045 0.002 TYR E 53 PHE 0.021 0.002 PHE h 181 TRP 0.013 0.002 TRP M 320 HIS 0.007 0.002 HIS M 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.32 (17289) covalent geometry : angle 0.82281 / 0.50 (23505) hydrogen bonds : bond 0.24094 / 15.36 ( 578) hydrogen bonds : angle 7.61997 / 5.17 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 389 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.7622 (m-80) cc_final: 0.7393 (m-80) REVERT: L 41 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7443 (mpt180) REVERT: L 100 ARG cc_start: 0.5709 (ptt90) cc_final: 0.3560 (ptt-90) REVERT: M 51 ASP cc_start: 0.6918 (m-30) cc_final: 0.6675 (m-30) REVERT: M 104 ASN cc_start: 0.8439 (m-40) cc_final: 0.8156 (m-40) REVERT: h 134 MET cc_start: 0.6325 (tpp) cc_final: 0.5450 (ttm) REVERT: h 198 ARG cc_start: 0.8202 (tpp80) cc_final: 0.8000 (tpp80) REVERT: o 339 MET cc_start: 0.7409 (mmt) cc_final: 0.7115 (mmt) REVERT: t 46 LYS cc_start: 0.5962 (mptt) cc_final: 0.4925 (mptt) REVERT: t 147 GLN cc_start: 0.8547 (mm-40) cc_final: 0.7304 (tt0) outliers start: 19 outliers final: 1 residues processed: 398 average time/residue: 0.1400 time to fit residues: 81.8956 Evaluate side-chains 236 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 203 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 116 GLN ** M 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.124566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089269 restraints weight = 42225.386| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.27 r_work: 0.3135 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17289 Z= 0.241 Angle : 0.724 10.060 23505 Z= 0.398 Chirality : 0.048 0.179 2711 Planarity : 0.006 0.109 3034 Dihedral : 5.360 23.634 2366 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.03 % Favored : 93.69 % Rotamer: Outliers : 3.78 % Allowed : 16.76 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2157 helix: 1.49 (0.24), residues: 481 sheet: 0.83 (0.25), residues: 435 loop : -1.82 (0.15), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 96 TYR 0.017 0.002 TYR L 95 PHE 0.023 0.002 PHE D 26 TRP 0.020 0.002 TRP M 320 HIS 0.013 0.002 HIS M 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (17289) covalent geometry : angle 0.72379 / 0.40 (23505) hydrogen bonds : bond 0.07483 / 5.15 ( 578) hydrogen bonds : angle 5.16334 / 3.52 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 236 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 ASP cc_start: 0.8865 (m-30) cc_final: 0.8606 (t70) REVERT: D 88 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8401 (p) REVERT: L 86 ASP cc_start: 0.8299 (t0) cc_final: 0.8096 (t0) REVERT: L 100 ARG cc_start: 0.5147 (ptt90) cc_final: 0.2767 (ptt180) REVERT: M 33 ARG cc_start: 0.8482 (ptt180) cc_final: 0.8200 (ptp-170) REVERT: M 49 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8074 (pp) REVERT: M 51 ASP cc_start: 0.8356 (m-30) cc_final: 0.8107 (m-30) REVERT: M 83 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7809 (mm-30) REVERT: M 185 HIS cc_start: 0.6308 (OUTLIER) cc_final: 0.5507 (p-80) REVERT: M 251 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7271 (pt0) REVERT: M 278 LYS cc_start: 0.8052 (tttt) cc_final: 0.7786 (tttm) REVERT: N 103 MET cc_start: 0.9220 (ttm) cc_final: 0.9009 (tpp) REVERT: h 455 LEU cc_start: 0.7419 (tp) cc_final: 0.7163 (mt) REVERT: o 162 GLN cc_start: 0.8082 (pt0) cc_final: 0.7340 (pp30) REVERT: o 373 ILE cc_start: 0.4952 (mm) cc_final: 0.4551 (mp) REVERT: o 451 ARG cc_start: 0.4985 (tpt170) cc_final: 0.4344 (tpt-90) REVERT: t 42 GLU cc_start: 0.8400 (tt0) cc_final: 0.8042 (mt-10) REVERT: t 46 LYS cc_start: 0.5538 (mptt) cc_final: 0.4102 (pttm) REVERT: t 147 GLN cc_start: 0.8987 (mm-40) cc_final: 0.7171 (tt0) REVERT: t 166 MET cc_start: 0.8323 (mpp) cc_final: 0.8120 (mpp) outliers start: 71 outliers final: 44 residues processed: 290 average time/residue: 0.1248 time to fit residues: 55.5439 Evaluate side-chains 244 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 HIS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 133 PHE Chi-restraints excluded: chain M residue 135 ASN Chi-restraints excluded: chain M residue 185 HIS Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 153 GLU Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 193 LYS Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain V residue 631 LEU Chi-restraints excluded: chain V residue 650 LEU Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 229 PHE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain h residue 240 SER Chi-restraints excluded: chain h residue 282 THR Chi-restraints excluded: chain h residue 452 LEU Chi-restraints excluded: chain h residue 484 PHE Chi-restraints excluded: chain h residue 489 ILE Chi-restraints excluded: chain o residue 67 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 113 LEU Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 179 THR Chi-restraints excluded: chain o residue 196 THR Chi-restraints excluded: chain o residue 265 THR Chi-restraints excluded: chain o residue 299 ASP Chi-restraints excluded: chain o residue 349 THR Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain t residue 129 THR Chi-restraints excluded: chain t residue 131 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 166 optimal weight: 20.0000 chunk 185 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 134 ASN ** M 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 382 GLN o 402 GLN t 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.120444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.085547 restraints weight = 42574.559| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.26 r_work: 0.3076 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17289 Z= 0.220 Angle : 0.657 10.253 23505 Z= 0.363 Chirality : 0.046 0.162 2711 Planarity : 0.005 0.100 3034 Dihedral : 5.169 24.309 2364 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.93 % Favored : 93.74 % Rotamer: Outliers : 4.84 % Allowed : 16.50 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2157 helix: 1.60 (0.24), residues: 485 sheet: 0.42 (0.24), residues: 478 loop : -1.77 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 96 TYR 0.018 0.002 TYR h 368 PHE 0.017 0.002 PHE h 47 TRP 0.018 0.002 TRP D 11 HIS 0.009 0.002 HIS M 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (17289) covalent geometry : angle 0.65726 / 0.36 (23505) hydrogen bonds : bond 0.07681 / 5.20 ( 578) hydrogen bonds : angle 5.04131 / 3.43 ( 1782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 205 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 25 ASP cc_start: 0.9014 (m-30) cc_final: 0.8792 (t70) REVERT: L 100 ARG cc_start: 0.4795 (OUTLIER) cc_final: 0.2737 (ptm160) REVERT: M 49 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8115 (pp) REVERT: M 51 ASP cc_start: 0.8396 (m-30) cc_final: 0.8190 (m-30) REVERT: M 118 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7999 (mt) REVERT: M 251 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7284 (pt0) REVERT: M 278 LYS cc_start: 0.8172 (tttt) cc_final: 0.7807 (tttm) REVERT: h 224 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9042 (p) REVERT: h 335 HIS cc_start: 0.4521 (OUTLIER) cc_final: 0.3784 (m90) REVERT: h 368 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6779 (t80) REVERT: o 162 GLN cc_start: 0.8042 (pt0) cc_final: 0.7152 (tm-30) REVERT: o 373 ILE cc_start: 0.5218 (mm) cc_final: 0.4725 (mp) REVERT: o 425 GLN cc_start: 0.8340 (pt0) cc_final: 0.8082 (tt0) REVERT: o 451 ARG cc_start: 0.5518 (tpt170) cc_final: 0.5083 (tpt-90) REVERT: t 42 GLU cc_start: 0.8340 (tt0) cc_final: 0.7898 (mt-10) REVERT: t 46 LYS cc_start: 0.4987 (mptt) cc_final: 0.3927 (pttm) outliers start: 91 outliers final: 56 residues processed: 275 average time/residue: 0.1145 time to fit residues: 48.8905 Evaluate side-chains 248 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 186 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 56 HIS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 185 HIS Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 283 MET Chi-restraints excluded: chain M residue 295 LEU Chi-restraints excluded: chain M residue 312 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 153 GLU Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 193 LYS Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain V residue 631 LEU Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 224 VAL Chi-restraints excluded: chain h residue 229 PHE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain h residue 240 SER Chi-restraints excluded: chain h residue 282 THR Chi-restraints excluded: chain h residue 313 LEU Chi-restraints excluded: chain h residue 335 HIS Chi-restraints excluded: chain h residue 368 TYR Chi-restraints excluded: chain h residue 385 ILE Chi-restraints excluded: chain h residue 452 LEU Chi-restraints excluded: chain o residue 67 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 235 ILE Chi-restraints excluded: chain o residue 260 THR Chi-restraints excluded: chain o residue 265 THR Chi-restraints excluded: chain o residue 314 LEU Chi-restraints excluded: chain o residue 349 THR Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 166 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 135 ASN ** M 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 ASN V 641 ASN ** h 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.121681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.087115 restraints weight = 42017.258| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.19 r_work: 0.3111 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17289 Z= 0.149 Angle : 0.581 9.443 23505 Z= 0.317 Chirality : 0.043 0.141 2711 Planarity : 0.005 0.087 3034 Dihedral : 4.824 25.236 2364 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.56 % Favored : 94.11 % Rotamer: Outliers : 3.83 % Allowed : 17.14 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2157 helix: 1.89 (0.24), residues: 488 sheet: 0.88 (0.24), residues: 439 loop : -1.74 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 25 TYR 0.015 0.001 TYR h 368 PHE 0.013 0.001 PHE t 65 TRP 0.032 0.002 TRP h 109 HIS 0.005 0.001 HIS M 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (17289) covalent geometry : angle 0.58095 / 0.32 (23505) hydrogen bonds : bond 0.05823 / 4.00 ( 578) hydrogen bonds : angle 4.68018 / 3.19 ( 1782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 211 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: D 25 ASP cc_start: 0.8902 (m-30) cc_final: 0.8691 (t0) REVERT: L 100 ARG cc_start: 0.5199 (ptt90) cc_final: 0.2789 (ptt-90) REVERT: M 33 ARG cc_start: 0.8297 (ptt180) cc_final: 0.7972 (ptp-170) REVERT: M 49 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8177 (pp) REVERT: M 51 ASP cc_start: 0.8372 (m-30) cc_final: 0.8138 (m-30) REVERT: M 171 LYS cc_start: 0.8503 (tppt) cc_final: 0.8044 (ttpp) REVERT: M 185 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6714 (p-80) REVERT: M 268 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8321 (mmtt) REVERT: h 335 HIS cc_start: 0.4785 (OUTLIER) cc_final: 0.4221 (m90) REVERT: h 368 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6949 (t80) REVERT: h 383 GLU cc_start: 0.7831 (tt0) cc_final: 0.7359 (mp0) REVERT: o 134 MET cc_start: 0.8536 (mtp) cc_final: 0.8208 (mtp) REVERT: o 162 GLN cc_start: 0.8094 (pt0) cc_final: 0.7168 (tm-30) REVERT: o 210 MET cc_start: 0.8368 (mtm) cc_final: 0.8147 (mtp) REVERT: o 271 ASP cc_start: 0.8075 (t0) cc_final: 0.7869 (t0) REVERT: o 306 ARG cc_start: 0.9112 (ptp90) cc_final: 0.8647 (mmt180) REVERT: o 373 ILE cc_start: 0.5533 (mm) cc_final: 0.5056 (mp) REVERT: o 425 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: o 451 ARG cc_start: 0.5642 (tpt170) cc_final: 0.5310 (tpt170) REVERT: t 42 GLU cc_start: 0.8258 (tt0) cc_final: 0.7839 (mt-10) REVERT: t 46 LYS cc_start: 0.5005 (mptt) cc_final: 0.3942 (pttm) REVERT: t 166 MET cc_start: 0.8693 (mpp) cc_final: 0.8357 (mmm) outliers start: 72 outliers final: 59 residues processed: 264 average time/residue: 0.1250 time to fit residues: 51.1096 Evaluate side-chains 255 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 HIS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 133 PHE Chi-restraints excluded: chain M residue 135 ASN Chi-restraints excluded: chain M residue 185 HIS Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 283 MET Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 153 GLU Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 193 LYS Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain V residue 631 LEU Chi-restraints excluded: chain V residue 650 LEU Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 229 PHE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain h residue 240 SER Chi-restraints excluded: chain h residue 282 THR Chi-restraints excluded: chain h residue 313 LEU Chi-restraints excluded: chain h residue 335 HIS Chi-restraints excluded: chain h residue 358 TYR Chi-restraints excluded: chain h residue 368 TYR Chi-restraints excluded: chain h residue 434 VAL Chi-restraints excluded: chain h residue 439 ILE Chi-restraints excluded: chain h residue 452 LEU Chi-restraints excluded: chain o residue 67 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 113 LEU Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 218 VAL Chi-restraints excluded: chain o residue 235 ILE Chi-restraints excluded: chain o residue 260 THR Chi-restraints excluded: chain o residue 265 THR Chi-restraints excluded: chain o residue 314 LEU Chi-restraints excluded: chain o residue 331 HIS Chi-restraints excluded: chain o residue 349 THR Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 425 GLN Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 129 THR Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 199 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 186 optimal weight: 7.9990 chunk 209 optimal weight: 0.0060 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 overall best weight: 5.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 135 ASN ** M 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.118451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084107 restraints weight = 42227.252| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.18 r_work: 0.3047 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17289 Z= 0.205 Angle : 0.643 10.694 23505 Z= 0.353 Chirality : 0.045 0.164 2711 Planarity : 0.005 0.081 3034 Dihedral : 5.065 26.873 2364 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.26 % Favored : 93.42 % Rotamer: Outliers : 4.74 % Allowed : 17.51 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.17), residues: 2157 helix: 1.70 (0.24), residues: 489 sheet: 0.36 (0.23), residues: 478 loop : -1.79 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 112 TYR 0.014 0.002 TYR h 368 PHE 0.017 0.002 PHE h 47 TRP 0.045 0.003 TRP h 109 HIS 0.009 0.001 HIS M 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (17289) covalent geometry : angle 0.64342 / 0.35 (23505) hydrogen bonds : bond 0.07231 / 4.92 ( 578) hydrogen bonds : angle 4.86123 / 3.32 ( 1782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 199 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 25 ASP cc_start: 0.9056 (m-30) cc_final: 0.8789 (t0) REVERT: L 100 ARG cc_start: 0.4985 (OUTLIER) cc_final: 0.2552 (ptt-90) REVERT: M 49 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8138 (pp) REVERT: M 118 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8010 (mt) REVERT: M 133 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: M 171 LYS cc_start: 0.8407 (tppt) cc_final: 0.8003 (ttpp) REVERT: M 185 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6455 (p-80) REVERT: M 256 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6231 (t70) REVERT: M 259 PRO cc_start: 0.7097 (Cg_endo) cc_final: 0.6285 (Cg_exo) REVERT: M 268 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8354 (mmtt) REVERT: N 18 GLN cc_start: 0.8832 (pm20) cc_final: 0.8447 (pm20) REVERT: h 334 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7340 (pp20) REVERT: h 368 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.7059 (t80) REVERT: o 134 MET cc_start: 0.8567 (mtp) cc_final: 0.7853 (mtp) REVERT: o 162 GLN cc_start: 0.8118 (pt0) cc_final: 0.7192 (tm-30) REVERT: o 271 ASP cc_start: 0.8036 (t0) cc_final: 0.7779 (t0) REVERT: o 306 ARG cc_start: 0.9093 (ptp90) cc_final: 0.8637 (mmt180) REVERT: o 397 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8598 (tt) REVERT: o 425 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: o 451 ARG cc_start: 0.5961 (tpt170) cc_final: 0.5411 (tpt170) REVERT: t 46 LYS cc_start: 0.4968 (mptt) cc_final: 0.3727 (pttm) REVERT: t 166 MET cc_start: 0.8755 (mpp) cc_final: 0.8515 (mpp) outliers start: 89 outliers final: 69 residues processed: 268 average time/residue: 0.1262 time to fit residues: 52.4806 Evaluate side-chains 260 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 181 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 HIS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 133 PHE Chi-restraints excluded: chain M residue 135 ASN Chi-restraints excluded: chain M residue 185 HIS Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 256 ASP Chi-restraints excluded: chain M residue 312 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 153 GLU Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 193 LYS Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain V residue 631 LEU Chi-restraints excluded: chain V residue 650 LEU Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 229 PHE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain h residue 240 SER Chi-restraints excluded: chain h residue 313 LEU Chi-restraints excluded: chain h residue 334 GLU Chi-restraints excluded: chain h residue 335 HIS Chi-restraints excluded: chain h residue 368 TYR Chi-restraints excluded: chain h residue 434 VAL Chi-restraints excluded: chain h residue 439 ILE Chi-restraints excluded: chain h residue 452 LEU Chi-restraints excluded: chain o residue 67 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 113 LEU Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 196 THR Chi-restraints excluded: chain o residue 218 VAL Chi-restraints excluded: chain o residue 235 ILE Chi-restraints excluded: chain o residue 252 ASN Chi-restraints excluded: chain o residue 260 THR Chi-restraints excluded: chain o residue 265 THR Chi-restraints excluded: chain o residue 314 LEU Chi-restraints excluded: chain o residue 331 HIS Chi-restraints excluded: chain o residue 349 THR Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 397 LEU Chi-restraints excluded: chain o residue 425 GLN Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 129 THR Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 146 LYS Chi-restraints excluded: chain t residue 199 VAL Chi-restraints excluded: chain t residue 223 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 189 optimal weight: 0.0070 chunk 131 optimal weight: 5.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 135 ASN M 185 HIS N 21 ASN N 83 ASN o 470 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.120013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.085945 restraints weight = 42081.396| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.19 r_work: 0.3085 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17289 Z= 0.144 Angle : 0.576 11.196 23505 Z= 0.313 Chirality : 0.043 0.140 2711 Planarity : 0.004 0.075 3034 Dihedral : 4.779 26.794 2364 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.07 % Favored : 93.60 % Rotamer: Outliers : 4.36 % Allowed : 18.63 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.18), residues: 2157 helix: 1.99 (0.24), residues: 483 sheet: 0.57 (0.24), residues: 457 loop : -1.78 (0.16), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 25 TYR 0.013 0.001 TYR h 368 PHE 0.013 0.001 PHE h 47 TRP 0.039 0.002 TRP h 109 HIS 0.004 0.001 HIS M 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (17289) covalent geometry : angle 0.57592 / 0.31 (23505) hydrogen bonds : bond 0.05735 / 3.93 ( 578) hydrogen bonds : angle 4.61054 / 3.15 ( 1782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 204 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 20 ASP cc_start: 0.9208 (t0) cc_final: 0.8803 (t0) REVERT: D 25 ASP cc_start: 0.9024 (m-30) cc_final: 0.8767 (t0) REVERT: L 100 ARG cc_start: 0.4783 (OUTLIER) cc_final: 0.2425 (ptt-90) REVERT: M 49 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8107 (pp) REVERT: M 133 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: M 171 LYS cc_start: 0.8441 (tppt) cc_final: 0.8044 (ttpp) REVERT: M 256 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6183 (t70) REVERT: M 259 PRO cc_start: 0.7182 (Cg_endo) cc_final: 0.6223 (Cg_exo) REVERT: M 268 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8351 (mmtt) REVERT: h 334 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7261 (pp20) REVERT: h 383 GLU cc_start: 0.7885 (tt0) cc_final: 0.7419 (mp0) REVERT: o 134 MET cc_start: 0.8508 (mtp) cc_final: 0.7872 (mtp) REVERT: o 162 GLN cc_start: 0.8120 (pt0) cc_final: 0.7175 (tm-30) REVERT: o 271 ASP cc_start: 0.8018 (t0) cc_final: 0.7783 (t0) REVERT: o 306 ARG cc_start: 0.9070 (ptp90) cc_final: 0.8630 (mmt180) REVERT: o 397 LEU cc_start: 0.9050 (pp) cc_final: 0.8673 (tt) REVERT: o 451 ARG cc_start: 0.5793 (tpt170) cc_final: 0.5255 (tpt-90) REVERT: o 491 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.7157 (p90) REVERT: t 42 GLU cc_start: 0.8304 (tt0) cc_final: 0.8009 (mt-10) REVERT: t 46 LYS cc_start: 0.4954 (mptt) cc_final: 0.3696 (pttm) REVERT: t 166 MET cc_start: 0.8743 (mpp) cc_final: 0.8517 (mpp) outliers start: 82 outliers final: 66 residues processed: 266 average time/residue: 0.1276 time to fit residues: 52.4582 Evaluate side-chains 259 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 187 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 HIS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 133 PHE Chi-restraints excluded: chain M residue 135 ASN Chi-restraints excluded: chain M residue 185 HIS Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 256 ASP Chi-restraints excluded: chain M residue 283 MET Chi-restraints excluded: chain M residue 312 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 153 GLU Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 193 LYS Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain V residue 650 LEU Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 229 PHE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain h residue 240 SER Chi-restraints excluded: chain h residue 313 LEU Chi-restraints excluded: chain h residue 334 GLU Chi-restraints excluded: chain h residue 335 HIS Chi-restraints excluded: chain h residue 434 VAL Chi-restraints excluded: chain h residue 439 ILE Chi-restraints excluded: chain h residue 452 LEU Chi-restraints excluded: chain h residue 454 SER Chi-restraints excluded: chain o residue 67 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 113 LEU Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 196 THR Chi-restraints excluded: chain o residue 235 ILE Chi-restraints excluded: chain o residue 260 THR Chi-restraints excluded: chain o residue 265 THR Chi-restraints excluded: chain o residue 331 HIS Chi-restraints excluded: chain o residue 349 THR Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 367 THR Chi-restraints excluded: chain o residue 452 LEU Chi-restraints excluded: chain o residue 470 ASN Chi-restraints excluded: chain o residue 491 TYR Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 129 THR Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 199 VAL Chi-restraints excluded: chain t residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 44 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 182 optimal weight: 50.0000 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 0.0270 chunk 186 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 135 ASN M 185 HIS N 21 ASN N 83 ASN o 392 ASN o 470 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.120045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.085995 restraints weight = 42056.575| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.15 r_work: 0.3089 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17289 Z= 0.139 Angle : 0.575 11.144 23505 Z= 0.311 Chirality : 0.043 0.142 2711 Planarity : 0.004 0.072 3034 Dihedral : 4.702 26.545 2364 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.31 % Favored : 93.37 % Rotamer: Outliers : 4.15 % Allowed : 18.84 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.18), residues: 2157 helix: 2.04 (0.24), residues: 485 sheet: 0.57 (0.24), residues: 465 loop : -1.75 (0.16), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 25 TYR 0.010 0.001 TYR E 44 PHE 0.013 0.001 PHE h 47 TRP 0.063 0.002 TRP h 109 HIS 0.003 0.001 HIS M 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (17289) covalent geometry : angle 0.57485 / 0.31 (23505) hydrogen bonds : bond 0.05617 / 3.86 ( 578) hydrogen bonds : angle 4.53964 / 3.10 ( 1782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 198 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 20 ASP cc_start: 0.9213 (t0) cc_final: 0.8805 (t0) REVERT: D 25 ASP cc_start: 0.8975 (m-30) cc_final: 0.8747 (t0) REVERT: L 100 ARG cc_start: 0.5334 (OUTLIER) cc_final: 0.2884 (ptt-90) REVERT: M 49 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8096 (pp) REVERT: M 133 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: M 171 LYS cc_start: 0.8464 (tppt) cc_final: 0.8092 (ttpp) REVERT: M 256 ASP cc_start: 0.6802 (OUTLIER) cc_final: 0.6236 (t70) REVERT: M 259 PRO cc_start: 0.7317 (Cg_endo) cc_final: 0.6413 (Cg_exo) REVERT: M 268 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8372 (mmtt) REVERT: N 18 GLN cc_start: 0.8669 (pm20) cc_final: 0.8159 (pm20) REVERT: h 334 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7162 (pp20) REVERT: h 383 GLU cc_start: 0.7761 (tt0) cc_final: 0.7402 (mp0) REVERT: o 134 MET cc_start: 0.8532 (mtp) cc_final: 0.7880 (mtp) REVERT: o 160 TYR cc_start: 0.8484 (m-10) cc_final: 0.8204 (m-10) REVERT: o 162 GLN cc_start: 0.8121 (pt0) cc_final: 0.7170 (tm-30) REVERT: o 271 ASP cc_start: 0.8038 (t0) cc_final: 0.7781 (t0) REVERT: o 306 ARG cc_start: 0.9052 (ptp90) cc_final: 0.8623 (mmt180) REVERT: o 425 GLN cc_start: 0.8314 (tt0) cc_final: 0.7962 (tp-100) REVERT: o 451 ARG cc_start: 0.5800 (tpt170) cc_final: 0.5265 (tpt-90) REVERT: o 491 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.7222 (p90) REVERT: t 42 GLU cc_start: 0.8283 (tt0) cc_final: 0.8002 (mt-10) REVERT: t 46 LYS cc_start: 0.4978 (mptt) cc_final: 0.3691 (pttm) REVERT: t 166 MET cc_start: 0.8781 (mpp) cc_final: 0.8559 (mpp) outliers start: 78 outliers final: 62 residues processed: 256 average time/residue: 0.1253 time to fit residues: 49.7685 Evaluate side-chains 260 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 192 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 HIS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 133 PHE Chi-restraints excluded: chain M residue 135 ASN Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 256 ASP Chi-restraints excluded: chain M residue 283 MET Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain V residue 650 LEU Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 40 ASP Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 229 PHE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain h residue 240 SER Chi-restraints excluded: chain h residue 313 LEU Chi-restraints excluded: chain h residue 334 GLU Chi-restraints excluded: chain h residue 335 HIS Chi-restraints excluded: chain h residue 434 VAL Chi-restraints excluded: chain h residue 439 ILE Chi-restraints excluded: chain h residue 452 LEU Chi-restraints excluded: chain h residue 454 SER Chi-restraints excluded: chain o residue 67 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 113 LEU Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 196 THR Chi-restraints excluded: chain o residue 235 ILE Chi-restraints excluded: chain o residue 252 ASN Chi-restraints excluded: chain o residue 260 THR Chi-restraints excluded: chain o residue 265 THR Chi-restraints excluded: chain o residue 331 HIS Chi-restraints excluded: chain o residue 349 THR Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 367 THR Chi-restraints excluded: chain o residue 373 ILE Chi-restraints excluded: chain o residue 452 LEU Chi-restraints excluded: chain o residue 491 TYR Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 129 THR Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 146 LYS Chi-restraints excluded: chain t residue 199 VAL Chi-restraints excluded: chain t residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 119 optimal weight: 0.1980 chunk 172 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 114 optimal weight: 0.0270 chunk 192 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 135 ASN N 83 ASN V 654 GLN h 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.122572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088843 restraints weight = 42272.232| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.17 r_work: 0.3127 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17289 Z= 0.113 Angle : 0.544 11.843 23505 Z= 0.293 Chirality : 0.042 0.148 2711 Planarity : 0.004 0.070 3034 Dihedral : 4.433 24.224 2364 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.61 % Favored : 94.07 % Rotamer: Outliers : 3.25 % Allowed : 20.12 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.18), residues: 2157 helix: 2.18 (0.24), residues: 485 sheet: 0.58 (0.24), residues: 485 loop : -1.72 (0.16), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 25 TYR 0.013 0.001 TYR h 111 PHE 0.012 0.001 PHE t 65 TRP 0.030 0.002 TRP h 109 HIS 0.003 0.001 HIS M 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (17289) covalent geometry : angle 0.54390 / 0.29 (23505) hydrogen bonds : bond 0.04609 / 3.18 ( 578) hydrogen bonds : angle 4.35759 / 2.97 ( 1782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: D 20 ASP cc_start: 0.9229 (t0) cc_final: 0.8851 (t0) REVERT: D 25 ASP cc_start: 0.8896 (m-30) cc_final: 0.8682 (t0) REVERT: M 133 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: M 171 LYS cc_start: 0.8482 (tppt) cc_final: 0.8117 (ttpp) REVERT: M 256 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6030 (t70) REVERT: M 258 LYS cc_start: 0.7432 (tppt) cc_final: 0.7118 (tptp) REVERT: M 259 PRO cc_start: 0.7230 (Cg_endo) cc_final: 0.6441 (Cg_exo) REVERT: M 268 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8368 (mmtt) REVERT: h 334 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7158 (pp20) REVERT: h 383 GLU cc_start: 0.7662 (tt0) cc_final: 0.7326 (mp0) REVERT: o 134 MET cc_start: 0.8470 (mtp) cc_final: 0.7853 (mtp) REVERT: o 162 GLN cc_start: 0.8003 (pt0) cc_final: 0.7057 (tm-30) REVERT: o 271 ASP cc_start: 0.8135 (t0) cc_final: 0.7888 (t0) REVERT: o 306 ARG cc_start: 0.9026 (ptp90) cc_final: 0.8616 (mmt180) REVERT: o 365 THR cc_start: 0.7345 (OUTLIER) cc_final: 0.6952 (p) REVERT: o 425 GLN cc_start: 0.8388 (tt0) cc_final: 0.8080 (tp-100) REVERT: o 451 ARG cc_start: 0.5788 (tpt170) cc_final: 0.5450 (tpt170) REVERT: o 491 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.7216 (p90) REVERT: t 42 GLU cc_start: 0.8209 (tt0) cc_final: 0.7933 (mt-10) REVERT: t 46 LYS cc_start: 0.5033 (mptt) cc_final: 0.3710 (pttm) REVERT: t 166 MET cc_start: 0.8773 (mpp) cc_final: 0.8560 (mpp) outliers start: 61 outliers final: 45 residues processed: 253 average time/residue: 0.1214 time to fit residues: 47.5765 Evaluate side-chains 246 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 133 PHE Chi-restraints excluded: chain M residue 135 ASN Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 256 ASP Chi-restraints excluded: chain M residue 283 MET Chi-restraints excluded: chain M residue 312 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 193 LYS Chi-restraints excluded: chain V residue 650 LEU Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 229 PHE Chi-restraints excluded: chain h residue 240 SER Chi-restraints excluded: chain h residue 313 LEU Chi-restraints excluded: chain h residue 334 GLU Chi-restraints excluded: chain h residue 335 HIS Chi-restraints excluded: chain h residue 434 VAL Chi-restraints excluded: chain h residue 439 ILE Chi-restraints excluded: chain h residue 452 LEU Chi-restraints excluded: chain o residue 67 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 113 LEU Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 235 ILE Chi-restraints excluded: chain o residue 265 THR Chi-restraints excluded: chain o residue 331 HIS Chi-restraints excluded: chain o residue 349 THR Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 452 LEU Chi-restraints excluded: chain o residue 491 TYR Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 199 VAL Chi-restraints excluded: chain t residue 227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 210 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 135 ASN N 83 ASN ** o 364 ASN ** 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 = 0.3800 r_free = 0.3800 target = 0.122136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088387 restraints weight = 41800.156| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.10 r_work: 0.3136 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17289 Z= 0.110 Angle : 0.537 12.647 23505 Z= 0.287 Chirality : 0.041 0.161 2711 Planarity : 0.004 0.067 3034 Dihedral : 4.339 24.065 2364 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.61 % Favored : 94.07 % Rotamer: Outliers : 3.19 % Allowed : 20.12 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2157 helix: 2.20 (0.24), residues: 485 sheet: 0.77 (0.24), residues: 469 loop : -1.66 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 25 TYR 0.008 0.001 TYR h 111 PHE 0.012 0.001 PHE t 65 TRP 0.027 0.002 TRP h 109 HIS 0.005 0.001 HIS M 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17289) covalent geometry : angle 0.53737 / 0.29 (23505) hydrogen bonds : bond 0.04494 / 3.10 ( 578) hydrogen bonds : angle 4.28999 / 2.92 ( 1782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 217 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: D 20 ASP cc_start: 0.9223 (t0) cc_final: 0.8891 (t0) REVERT: D 25 ASP cc_start: 0.8856 (m-30) cc_final: 0.8579 (t0) REVERT: D 96 ARG cc_start: 0.7144 (mmp-170) cc_final: 0.6917 (mmm160) REVERT: E 117 ASN cc_start: 0.9064 (t0) cc_final: 0.8648 (t0) REVERT: L 100 ARG cc_start: 0.5135 (OUTLIER) cc_final: 0.2690 (ptt-90) REVERT: M 133 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: M 171 LYS cc_start: 0.8507 (tppt) cc_final: 0.8153 (ttpp) REVERT: M 256 ASP cc_start: 0.6693 (OUTLIER) cc_final: 0.6178 (t70) REVERT: M 258 LYS cc_start: 0.7427 (tppt) cc_final: 0.7135 (tptp) REVERT: M 259 PRO cc_start: 0.7223 (Cg_endo) cc_final: 0.6445 (Cg_exo) REVERT: M 268 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8380 (mmtt) REVERT: N 18 GLN cc_start: 0.8793 (pm20) cc_final: 0.8318 (pm20) REVERT: h 109 TRP cc_start: 0.6243 (t-100) cc_final: 0.4925 (t-100) REVERT: h 334 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7081 (pp20) REVERT: h 362 PRO cc_start: 0.5307 (Cg_exo) cc_final: 0.5078 (Cg_endo) REVERT: h 383 GLU cc_start: 0.7636 (tt0) cc_final: 0.7306 (mp0) REVERT: o 134 MET cc_start: 0.8535 (mtp) cc_final: 0.7930 (mtp) REVERT: o 160 TYR cc_start: 0.8673 (m-80) cc_final: 0.8387 (m-10) REVERT: o 162 GLN cc_start: 0.7998 (pt0) cc_final: 0.7053 (tm-30) REVERT: o 271 ASP cc_start: 0.8118 (t0) cc_final: 0.7895 (t0) REVERT: o 306 ARG cc_start: 0.9022 (ptp90) cc_final: 0.8617 (mmt180) REVERT: o 365 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7145 (p) REVERT: o 397 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8503 (tt) REVERT: o 425 GLN cc_start: 0.8344 (tt0) cc_final: 0.8036 (tp-100) REVERT: o 451 ARG cc_start: 0.5830 (tpt170) cc_final: 0.5371 (tpt-90) REVERT: o 491 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.7236 (p90) REVERT: t 42 GLU cc_start: 0.8185 (tt0) cc_final: 0.7917 (mt-10) REVERT: t 46 LYS cc_start: 0.4640 (mptt) cc_final: 0.3606 (pttm) REVERT: t 166 MET cc_start: 0.8776 (mpp) cc_final: 0.8562 (mpp) outliers start: 60 outliers final: 49 residues processed: 260 average time/residue: 0.1155 time to fit residues: 46.7010 Evaluate side-chains 260 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 133 PHE Chi-restraints excluded: chain M residue 135 ASN Chi-restraints excluded: chain M residue 185 HIS Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 256 ASP Chi-restraints excluded: chain M residue 283 MET Chi-restraints excluded: chain M residue 312 THR Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 229 PHE Chi-restraints excluded: chain h residue 240 SER Chi-restraints excluded: chain h residue 282 THR Chi-restraints excluded: chain h residue 284 VAL Chi-restraints excluded: chain h residue 313 LEU Chi-restraints excluded: chain h residue 334 GLU Chi-restraints excluded: chain h residue 335 HIS Chi-restraints excluded: chain h residue 434 VAL Chi-restraints excluded: chain h residue 439 ILE Chi-restraints excluded: chain h residue 452 LEU Chi-restraints excluded: chain o residue 67 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 113 LEU Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 235 ILE Chi-restraints excluded: chain o residue 265 THR Chi-restraints excluded: chain o residue 349 THR Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 373 ILE Chi-restraints excluded: chain o residue 397 LEU Chi-restraints excluded: chain o residue 452 LEU Chi-restraints excluded: chain o residue 491 TYR Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 199 VAL Chi-restraints excluded: chain t residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 57 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 134 ASN N 83 ASN ** o 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.123373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089966 restraints weight = 41891.357| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.34 r_work: 0.3145 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17289 Z= 0.102 Angle : 0.531 13.738 23505 Z= 0.282 Chirality : 0.041 0.165 2711 Planarity : 0.004 0.066 3034 Dihedral : 4.180 22.669 2364 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.24 % Favored : 94.48 % Rotamer: Outliers : 2.61 % Allowed : 20.70 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2157 helix: 2.27 (0.24), residues: 486 sheet: 0.84 (0.24), residues: 467 loop : -1.62 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 25 TYR 0.010 0.001 TYR E 44 PHE 0.011 0.001 PHE t 65 TRP 0.016 0.001 TRP M 320 HIS 0.004 0.001 HIS M 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (17289) covalent geometry : angle 0.53083 / 0.28 (23505) hydrogen bonds : bond 0.04026 / 2.78 ( 578) hydrogen bonds : angle 4.18345 / 2.85 ( 1782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: D 20 ASP cc_start: 0.9256 (t0) cc_final: 0.8930 (t0) REVERT: D 25 ASP cc_start: 0.8861 (m-30) cc_final: 0.8535 (t0) REVERT: D 83 ASP cc_start: 0.8935 (t0) cc_final: 0.8613 (p0) REVERT: D 96 ARG cc_start: 0.7172 (mmp-170) cc_final: 0.6967 (mmm160) REVERT: E 117 ASN cc_start: 0.9026 (t0) cc_final: 0.8624 (t0) REVERT: M 64 GLU cc_start: 0.8301 (tp30) cc_final: 0.8085 (tp30) REVERT: M 103 ASN cc_start: 0.7816 (t0) cc_final: 0.7354 (m-40) REVERT: M 104 ASN cc_start: 0.8854 (m-40) cc_final: 0.8427 (m-40) REVERT: M 171 LYS cc_start: 0.8494 (tppt) cc_final: 0.8146 (ttpp) REVERT: M 258 LYS cc_start: 0.7443 (tppt) cc_final: 0.7230 (tptp) REVERT: M 268 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8484 (mptt) REVERT: N 18 GLN cc_start: 0.8824 (pm20) cc_final: 0.8338 (pm20) REVERT: h 334 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7181 (pp20) REVERT: h 362 PRO cc_start: 0.5088 (Cg_exo) cc_final: 0.4835 (Cg_endo) REVERT: h 383 GLU cc_start: 0.7801 (tt0) cc_final: 0.7458 (mp0) REVERT: o 134 MET cc_start: 0.8505 (mtp) cc_final: 0.7898 (mtp) REVERT: o 160 TYR cc_start: 0.8646 (m-80) cc_final: 0.8401 (m-10) REVERT: o 162 GLN cc_start: 0.7983 (pt0) cc_final: 0.6956 (tm-30) REVERT: o 184 ASP cc_start: 0.8001 (m-30) cc_final: 0.7577 (t0) REVERT: o 271 ASP cc_start: 0.8089 (t0) cc_final: 0.7872 (t0) REVERT: o 306 ARG cc_start: 0.9013 (ptp90) cc_final: 0.8612 (mmt180) REVERT: o 365 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7222 (p) REVERT: o 397 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8591 (tt) REVERT: o 425 GLN cc_start: 0.8314 (tt0) cc_final: 0.8028 (tp-100) REVERT: o 451 ARG cc_start: 0.5824 (tpt170) cc_final: 0.5308 (tpt-90) REVERT: o 491 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7295 (p90) REVERT: t 42 GLU cc_start: 0.8175 (tt0) cc_final: 0.7926 (mt-10) REVERT: t 46 LYS cc_start: 0.4753 (mptt) cc_final: 0.3661 (pttm) REVERT: t 166 MET cc_start: 0.8768 (mpp) cc_final: 0.8554 (mpp) outliers start: 49 outliers final: 40 residues processed: 253 average time/residue: 0.1157 time to fit residues: 45.6389 Evaluate side-chains 247 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 283 MET Chi-restraints excluded: chain M residue 312 THR Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 229 PHE Chi-restraints excluded: chain h residue 240 SER Chi-restraints excluded: chain h residue 282 THR Chi-restraints excluded: chain h residue 284 VAL Chi-restraints excluded: chain h residue 313 LEU Chi-restraints excluded: chain h residue 334 GLU Chi-restraints excluded: chain h residue 335 HIS Chi-restraints excluded: chain h residue 434 VAL Chi-restraints excluded: chain h residue 439 ILE Chi-restraints excluded: chain h residue 452 LEU Chi-restraints excluded: chain o residue 67 THR Chi-restraints excluded: chain o residue 70 LEU Chi-restraints excluded: chain o residue 113 LEU Chi-restraints excluded: chain o residue 235 ILE Chi-restraints excluded: chain o residue 349 THR Chi-restraints excluded: chain o residue 365 THR Chi-restraints excluded: chain o residue 397 LEU Chi-restraints excluded: chain o residue 452 LEU Chi-restraints excluded: chain o residue 470 ASN Chi-restraints excluded: chain o residue 491 TYR Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 199 VAL Chi-restraints excluded: chain t residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 45 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 50 optimal weight: 0.0970 chunk 203 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 188 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.0060 chunk 174 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 135 ASN N 83 ASN ** o 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.122244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088571 restraints weight = 42207.611| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.12 r_work: 0.3140 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17289 Z= 0.112 Angle : 0.547 13.411 23505 Z= 0.290 Chirality : 0.041 0.158 2711 Planarity : 0.004 0.078 3034 Dihedral : 4.200 21.203 2364 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.56 % Favored : 94.16 % Rotamer: Outliers : 2.66 % Allowed : 20.70 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 2157 helix: 2.21 (0.24), residues: 489 sheet: 0.85 (0.24), residues: 467 loop : -1.57 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 25 TYR 0.013 0.001 TYR o 469 PHE 0.012 0.001 PHE t 65 TRP 0.014 0.001 TRP M 320 HIS 0.004 0.001 HIS M 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (17289) covalent geometry : angle 0.54651 / 0.29 (23505) hydrogen bonds : bond 0.04446 / 3.06 ( 578) hydrogen bonds : angle 4.19019 / 2.85 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4472.03 seconds wall clock time: 77 minutes 12.71 seconds (4632.71 seconds total)