Starting phenix.real_space_refine on Tue May 20 18:05:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptg_17870/05_2025/8ptg_17870.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptg_17870/05_2025/8ptg_17870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ptg_17870/05_2025/8ptg_17870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptg_17870/05_2025/8ptg_17870.map" model { file = "/net/cci-nas-00/data/ceres_data/8ptg_17870/05_2025/8ptg_17870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptg_17870/05_2025/8ptg_17870.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.043 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: 8 Type Number sf(0) Gaussians P 27 5.49 5 Mg 6 5.21 5 S 102 5.16 5 Be 6 3.05 5 C 12645 2.51 5 N 3600 2.21 5 O 3888 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20292 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "B" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "C" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "D" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "E" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "F" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "R" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.33, per 1000 atoms: 0.61 Number of scatterers: 20292 At special positions: 0 Unit cell: (112.347, 149.139, 137.313, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 102 16.00 P 27 15.00 Mg 6 11.99 F 18 9.00 O 3888 8.00 N 3600 7.00 C 12645 6.00 Be 6 4.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.70 Conformation dependent library (CDL) restraints added in 2.5 seconds 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 23 sheets defined 50.2% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.609A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.977A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.576A pdb=" N HIS A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.511A pdb=" N HIS A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.748A pdb=" N ARG A 299 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.818A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.101A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 404 Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.751A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 3.661A pdb=" N ILE B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.608A pdb=" N ARG B 128 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.871A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.616A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 325 through 339 removed outlier: 3.725A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.502A pdb=" N ALA B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.086A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 403 Processing helix chain 'B' and resid 408 through 419 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.575A pdb=" N ILE C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.577A pdb=" N ILE C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.834A pdb=" N ARG C 128 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 3.952A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 256 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.811A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 4.336A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 419 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.701A pdb=" N MET D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.587A pdb=" N ILE D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 126 through 130 removed outlier: 3.579A pdb=" N ASN D 129 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS D 130 " --> pdb=" O ALA D 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 126 through 130' Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 153 through 166 removed outlier: 3.543A pdb=" N LEU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.565A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 removed outlier: 3.689A pdb=" N LEU D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.848A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 404 Processing helix chain 'D' and resid 408 through 419 Processing helix chain 'E' and resid 2 through 9 removed outlier: 3.535A pdb=" N LEU E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 removed outlier: 3.543A pdb=" N MET E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.519A pdb=" N ILE E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.915A pdb=" N ASN E 129 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.791A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.661A pdb=" N HIS E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 removed outlier: 3.656A pdb=" N LEU E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.642A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 404 Processing helix chain 'E' and resid 408 through 419 Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 10 through 21 Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 123 through 129 removed outlier: 3.902A pdb=" N ASN F 129 " --> pdb=" O ASN F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 153 through 166 removed outlier: 3.513A pdb=" N LEU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 212 through 223 Processing helix chain 'F' and resid 235 through 256 Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 294 through 303 removed outlier: 3.569A pdb=" N LYS F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.728A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 Processing helix chain 'F' and resid 367 through 371 Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 391 through 403 Processing helix chain 'F' and resid 408 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.652A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS A 115 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS A 100 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL A 116 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER A 98 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU A 118 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR A 96 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE A 49 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.791A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 209 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.791A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 145 removed outlier: 4.525A pdb=" N ILE A 168 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 57 removed outlier: 3.823A pdb=" N ILE B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR B 80 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LYS B 115 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.951A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ASP B 265 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 207 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.951A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.348A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 57 removed outlier: 3.819A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TYR C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N LYS C 115 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.674A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 209 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.674A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG C 173 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU C 343 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 345 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 177 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N GLU C 342 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ASN C 361 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HIS C 344 " --> pdb=" O ASP C 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.533A pdb=" N ILE C 168 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.771A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.894A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR D 80 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS D 115 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.659A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.659A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG D 173 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU D 343 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU D 175 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 345 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 177 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLU D 342 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ASN D 361 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS D 344 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.817A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR E 80 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS E 115 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.757A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LEU E 320 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL E 203 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU E 263 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N MET E 205 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.757A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 49 through 57 removed outlier: 3.886A pdb=" N ILE F 79 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR F 80 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LYS F 115 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU F 113 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG F 102 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER F 98 " --> pdb=" O ASN F 117 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL F 119 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR F 96 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.864A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE F 262 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR F 318 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU F 264 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU F 320 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASP F 265 " --> pdb=" O MET F 205 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU F 207 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.864A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 178 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG F 173 " --> pdb=" O MET F 341 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU F 343 " --> pdb=" O ARG F 173 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU F 175 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU F 345 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL F 177 " --> pdb=" O LEU F 345 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N GLU F 342 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ASN F 361 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N HIS F 344 " --> pdb=" O ASP F 359 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.513A pdb=" N ILE F 168 " --> pdb=" O LEU F 145 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2817 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: 6.82 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6746 1.34 - 1.46: 3796 1.46 - 1.58: 9833 1.58 - 1.70: 47 1.70 - 1.83: 198 Bond restraints: 20620 Sorted by residual: bond pdb=" F2 BEF E1002 " pdb="BE BEF E1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" F2 BEF C1002 " pdb="BE BEF C1002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" F2 BEF F1002 " pdb="BE BEF F1002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" F2 BEF B 503 " pdb="BE BEF B 503 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 20615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 27773 5.15 - 10.30: 75 10.30 - 15.45: 11 15.45 - 20.60: 0 20.60 - 25.75: 3 Bond angle restraints: 27862 Sorted by residual: angle pdb=" OP2 C R 92 " pdb=" P C R 92 " pdb=" O5' C R 92 " ideal model delta sigma weight residual 108.00 82.25 25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" OP1 C R 92 " pdb=" P C R 92 " pdb=" O5' C R 92 " ideal model delta sigma weight residual 108.00 83.28 24.72 3.00e+00 1.11e-01 6.79e+01 angle pdb=" OP1 C R 92 " pdb=" P C R 92 " pdb=" OP2 C R 92 " ideal model delta sigma weight residual 119.60 141.04 -21.44 3.00e+00 1.11e-01 5.11e+01 angle pdb=" CA PRO D 76 " pdb=" N PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 112.00 103.80 8.20 1.40e+00 5.10e-01 3.43e+01 angle pdb=" F2 BEF D1002 " pdb="BE BEF D1002 " pdb=" F3 BEF D1002 " ideal model delta sigma weight residual 119.96 106.69 13.27 3.00e+00 1.11e-01 1.96e+01 ... (remaining 27857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 12316 35.90 - 71.80: 435 71.80 - 107.71: 27 107.71 - 143.61: 2 143.61 - 179.51: 6 Dihedral angle restraints: 12786 sinusoidal: 5556 harmonic: 7230 Sorted by residual: dihedral pdb=" O4' U R 14 " pdb=" C1' U R 14 " pdb=" N1 U R 14 " pdb=" C2 U R 14 " ideal model delta sinusoidal sigma weight residual 200.00 49.45 150.55 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" O4' C R 13 " pdb=" C1' C R 13 " pdb=" N1 C R 13 " pdb=" C2 C R 13 " ideal model delta sinusoidal sigma weight residual -128.00 51.51 -179.51 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C R 99 " pdb=" C1' C R 99 " pdb=" N1 C R 99 " pdb=" C2 C R 99 " ideal model delta sinusoidal sigma weight residual -128.00 51.28 -179.28 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2811 0.070 - 0.140: 364 0.140 - 0.210: 1 0.210 - 0.280: 0 0.280 - 0.350: 1 Chirality restraints: 3177 Sorted by residual: chirality pdb=" P C R 92 " pdb=" OP1 C R 92 " pdb=" OP2 C R 92 " pdb=" O5' C R 92 " both_signs ideal model delta sigma weight residual True 2.41 -2.06 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA GLU C 414 " pdb=" N GLU C 414 " pdb=" C GLU C 414 " pdb=" CB GLU C 414 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CG LEU E 403 " pdb=" CB LEU E 403 " pdb=" CD1 LEU E 403 " pdb=" CD2 LEU E 403 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 3174 not shown) Planarity restraints: 3549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 381 " -0.035 2.00e-02 2.50e+03 3.57e-02 3.19e+01 pdb=" CG TRP F 381 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 TRP F 381 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP F 381 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 381 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 381 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 381 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 381 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 381 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 353 " -0.335 9.50e-02 1.11e+02 1.50e-01 1.44e+01 pdb=" NE ARG E 353 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG E 353 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 353 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 353 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 414 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" CD GLU C 414 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU C 414 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU C 414 " -0.021 2.00e-02 2.50e+03 ... (remaining 3546 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 12 2.12 - 2.82: 6089 2.82 - 3.51: 28582 3.51 - 4.21: 48220 4.21 - 4.90: 87892 Nonbonded interactions: 170795 Sorted by model distance: nonbonded pdb=" N LYS E 181 " pdb=" F1 BEF E1002 " model vdw 1.427 3.070 nonbonded pdb=" NH2 ARG C 366 " pdb=" F1 BEF B 503 " model vdw 1.767 3.070 nonbonded pdb=" O2B ADP E1000 " pdb="MG MG E1001 " model vdw 1.969 2.170 nonbonded pdb=" O1B ADP A1000 " pdb="MG MG A1001 " model vdw 2.013 2.170 nonbonded pdb=" OG1 THR C 185 " pdb="MG MG C1001 " model vdw 2.014 2.170 ... (remaining 170790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.000 Normalize map: mean=0, sd=1: 4.650 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: 0.010 Extract box with map and model: 0.840 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.980 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:10.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 : 0.012 0.645 20626 Z= 1.106 Angle : 0.755 25.750 27862 Z= 0.344 Chirality : 0.042 0.350 3177 Planarity : 0.005 0.150 3549 Dihedral : 17.756 179.510 8106 Min Nonbonded Distance : 1.427 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.02 % Allowed : 23.82 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2502 helix: 1.41 (0.16), residues: 1092 sheet: 0.03 (0.26), residues: 441 loop : 0.23 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.005 TRP F 381 HIS 0.004 0.001 HIS F 256 PHE 0.017 0.001 PHE A 62 TYR 0.021 0.001 TYR D 80 ARG 0.015 0.000 ARG C 418 Details of bonding type rmsd hydrogen bonds : bond 0.15749 ( 990) hydrogen bonds : angle 5.97657 ( 2817) covalent geometry : bond 0.00411 (20620) covalent geometry : angle 0.75470 (27862) Misc. bond : bond 0.63994 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 239 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6747 (pmm) REVERT: A 29 MET cc_start: 0.5696 (tmm) cc_final: 0.4109 (pmm) REVERT: C 244 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8184 (mp0) outliers start: 65 outliers final: 53 residues processed: 294 average time/residue: 1.5034 time to fit residues: 491.3458 Evaluate side-chains 286 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 0.0970 chunk 144 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 GLN C 193 GLN E 42 HIS E 59 GLN E 193 GLN E 241 GLN F 241 GLN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.102130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073277 restraints weight = 41664.265| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.54 r_work: 0.3000 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20626 Z= 0.128 Angle : 0.614 7.998 27862 Z= 0.299 Chirality : 0.042 0.136 3177 Planarity : 0.004 0.054 3549 Dihedral : 13.162 179.961 3128 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.44 % Allowed : 20.94 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2502 helix: 1.57 (0.16), residues: 1095 sheet: 0.19 (0.27), residues: 381 loop : 0.04 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 381 HIS 0.005 0.001 HIS F 256 PHE 0.010 0.001 PHE D 232 TYR 0.016 0.001 TYR D 110 ARG 0.009 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 990) hydrogen bonds : angle 4.68973 ( 2817) covalent geometry : bond 0.00289 (20620) covalent geometry : angle 0.61387 (27862) Misc. bond : bond 0.00137 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 259 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6764 (pmm) REVERT: A 56 GLU cc_start: 0.8784 (tt0) cc_final: 0.8542 (pt0) REVERT: A 128 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7510 (mtt90) REVERT: A 244 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8557 (mm-30) REVERT: A 392 GLU cc_start: 0.8006 (pt0) cc_final: 0.7713 (pt0) REVERT: B 244 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8599 (mm-30) REVERT: B 285 LEU cc_start: 0.9231 (mp) cc_final: 0.9027 (mp) REVERT: B 334 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8373 (tm-30) REVERT: C 244 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: C 414 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: D 41 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8351 (pp30) REVERT: D 374 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8263 (tm-30) REVERT: E 244 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8674 (mm-30) REVERT: E 353 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7962 (ttp-110) REVERT: F 244 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8524 (mm-30) REVERT: F 342 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7883 (pm20) outliers start: 74 outliers final: 32 residues processed: 313 average time/residue: 1.5417 time to fit residues: 535.8456 Evaluate side-chains 278 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 42 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 209 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 89 optimal weight: 0.0270 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN C 193 GLN E 59 GLN E 193 GLN E 241 GLN F 41 GLN F 241 GLN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.099786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.070880 restraints weight = 41396.106| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.52 r_work: 0.2948 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20626 Z= 0.220 Angle : 0.641 8.491 27862 Z= 0.310 Chirality : 0.044 0.142 3177 Planarity : 0.004 0.053 3549 Dihedral : 12.985 179.576 3085 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.27 % Allowed : 20.80 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2502 helix: 1.52 (0.16), residues: 1104 sheet: -0.03 (0.27), residues: 387 loop : -0.04 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 381 HIS 0.006 0.001 HIS E 239 PHE 0.017 0.001 PHE C 232 TYR 0.017 0.001 TYR B 110 ARG 0.007 0.000 ARG B 299 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 990) hydrogen bonds : angle 4.56507 ( 2817) covalent geometry : bond 0.00515 (20620) covalent geometry : angle 0.64104 (27862) Misc. bond : bond 0.00141 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 247 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8810 (tt0) cc_final: 0.8467 (pt0) REVERT: A 244 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8623 (mm-30) REVERT: B 5 GLU cc_start: 0.9465 (mp0) cc_final: 0.9215 (mp0) REVERT: B 244 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8585 (mm-30) REVERT: B 285 LEU cc_start: 0.9221 (mp) cc_final: 0.8993 (mp) REVERT: C 244 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: C 374 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8359 (tp-100) REVERT: C 414 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: D 41 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8386 (pp30) REVERT: D 374 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8247 (tm-30) REVERT: E 244 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8644 (mm-30) REVERT: E 342 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: E 353 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8078 (ttp-110) REVERT: F 29 MET cc_start: 0.5519 (pmm) cc_final: 0.4844 (mpp) REVERT: F 41 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: F 244 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8492 (mm-30) REVERT: F 333 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8144 (mm-30) REVERT: F 342 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7868 (pm20) outliers start: 92 outliers final: 44 residues processed: 312 average time/residue: 1.5546 time to fit residues: 537.8676 Evaluate side-chains 286 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 3 optimal weight: 20.0000 chunk 175 optimal weight: 7.9990 chunk 168 optimal weight: 0.2980 chunk 226 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 chunk 129 optimal weight: 0.0270 chunk 228 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 241 GLN D 193 GLN E 59 GLN E 193 GLN E 241 GLN E 275 ASN F 41 GLN F 241 GLN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.101751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072798 restraints weight = 41792.375| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.59 r_work: 0.2960 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20626 Z= 0.112 Angle : 0.600 9.110 27862 Z= 0.287 Chirality : 0.042 0.140 3177 Planarity : 0.004 0.051 3549 Dihedral : 12.619 179.780 3080 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.90 % Allowed : 21.96 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2502 helix: 1.64 (0.16), residues: 1104 sheet: 0.07 (0.27), residues: 393 loop : -0.03 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 PHE 0.009 0.001 PHE A 62 TYR 0.021 0.001 TYR D 110 ARG 0.010 0.000 ARG E 238 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 990) hydrogen bonds : angle 4.42904 ( 2817) covalent geometry : bond 0.00252 (20620) covalent geometry : angle 0.60019 (27862) Misc. bond : bond 0.00055 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 255 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8615 (tt0) cc_final: 0.8292 (pt0) REVERT: A 244 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8353 (mm-30) REVERT: A 348 LYS cc_start: 0.8955 (ptpp) cc_final: 0.8526 (ptmm) REVERT: B 5 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9202 (mp0) REVERT: B 42 HIS cc_start: 0.8168 (t-90) cc_final: 0.7944 (t-90) REVERT: B 244 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8273 (mm-30) REVERT: B 298 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8606 (mmmm) REVERT: B 334 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8259 (tm-30) REVERT: C 244 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: C 374 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8045 (tp-100) REVERT: C 414 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: D 374 GLN cc_start: 0.8296 (tm-30) cc_final: 0.8002 (tm-30) REVERT: E 244 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8380 (mm-30) REVERT: E 342 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: E 353 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7926 (ttp-110) REVERT: F 29 MET cc_start: 0.5644 (pmm) cc_final: 0.4918 (mpp) REVERT: F 244 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8264 (mm-30) REVERT: F 272 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8333 (mmm-85) REVERT: F 342 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7450 (pm20) outliers start: 84 outliers final: 42 residues processed: 318 average time/residue: 1.5132 time to fit residues: 534.7431 Evaluate side-chains 290 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 210 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 241 GLN B 378 GLN E 59 GLN E 193 GLN E 241 GLN F 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.099231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.070027 restraints weight = 42320.507| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.59 r_work: 0.2896 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20626 Z= 0.242 Angle : 0.659 9.981 27862 Z= 0.316 Chirality : 0.044 0.147 3177 Planarity : 0.004 0.050 3549 Dihedral : 12.584 179.545 3074 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.13 % Allowed : 22.33 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2502 helix: 1.55 (0.16), residues: 1107 sheet: -0.09 (0.27), residues: 384 loop : -0.10 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 381 HIS 0.006 0.001 HIS E 239 PHE 0.017 0.001 PHE C 232 TYR 0.016 0.001 TYR B 110 ARG 0.009 0.000 ARG C 418 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 990) hydrogen bonds : angle 4.45976 ( 2817) covalent geometry : bond 0.00567 (20620) covalent geometry : angle 0.65872 (27862) Misc. bond : bond 0.00123 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 240 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.4436 (OUTLIER) cc_final: 0.4106 (pmt-80) REVERT: A 56 GLU cc_start: 0.8806 (tt0) cc_final: 0.8383 (pt0) REVERT: A 128 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7625 (mtm-85) REVERT: A 244 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8589 (mm-30) REVERT: A 348 LYS cc_start: 0.9058 (ptpp) cc_final: 0.8756 (ptmm) REVERT: B 5 GLU cc_start: 0.9466 (OUTLIER) cc_final: 0.9220 (mp0) REVERT: B 42 HIS cc_start: 0.8175 (t-90) cc_final: 0.7902 (t-90) REVERT: B 87 ARG cc_start: 0.8558 (ptp90) cc_final: 0.8329 (ptm-80) REVERT: B 244 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8597 (mm-30) REVERT: B 334 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8457 (tm-30) REVERT: C 244 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8578 (mp0) REVERT: C 374 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8370 (tp-100) REVERT: C 414 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: D 374 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8258 (tm-30) REVERT: E 42 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7851 (t-90) REVERT: E 244 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8610 (mm-30) REVERT: E 342 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: E 353 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8193 (ttp-170) REVERT: F 29 MET cc_start: 0.5801 (pmm) cc_final: 0.5299 (mpp) REVERT: F 244 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8478 (mm-30) outliers start: 89 outliers final: 45 residues processed: 310 average time/residue: 1.5679 time to fit residues: 539.7146 Evaluate side-chains 283 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 87 optimal weight: 0.5980 chunk 135 optimal weight: 0.5980 chunk 206 optimal weight: 5.9990 chunk 92 optimal weight: 0.0370 chunk 107 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 212 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 220 GLN B 241 GLN E 59 GLN E 193 GLN E 241 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.101286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072441 restraints weight = 41790.156| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.58 r_work: 0.2950 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20626 Z= 0.116 Angle : 0.616 10.080 27862 Z= 0.292 Chirality : 0.042 0.139 3177 Planarity : 0.004 0.050 3549 Dihedral : 12.395 179.630 3074 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.76 % Allowed : 22.84 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.17), residues: 2502 helix: 1.69 (0.16), residues: 1104 sheet: -0.05 (0.26), residues: 393 loop : -0.05 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 381 HIS 0.005 0.001 HIS A 239 PHE 0.008 0.001 PHE C 398 TYR 0.023 0.001 TYR D 110 ARG 0.010 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 990) hydrogen bonds : angle 4.36637 ( 2817) covalent geometry : bond 0.00265 (20620) covalent geometry : angle 0.61606 (27862) Misc. bond : bond 0.00047 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 250 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.4107 (OUTLIER) cc_final: 0.3596 (pmt-80) REVERT: A 29 MET cc_start: 0.5379 (tmm) cc_final: 0.3752 (mmp) REVERT: A 56 GLU cc_start: 0.8576 (tt0) cc_final: 0.8215 (pt0) REVERT: A 128 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7609 (mtm-85) REVERT: A 244 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8326 (mm-30) REVERT: A 274 TYR cc_start: 0.8572 (m-10) cc_final: 0.8327 (m-10) REVERT: A 348 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8483 (ptmm) REVERT: B 5 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9227 (mp0) REVERT: B 42 HIS cc_start: 0.8163 (t-90) cc_final: 0.7914 (t-90) REVERT: B 244 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8242 (mm-30) REVERT: B 334 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 244 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: C 374 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8096 (tp-100) REVERT: C 414 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: D 374 GLN cc_start: 0.8299 (tm-30) cc_final: 0.8002 (tm-30) REVERT: E 42 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7830 (t-90) REVERT: E 244 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8384 (mm-30) REVERT: E 327 MET cc_start: 0.8453 (ttt) cc_final: 0.8121 (ttt) REVERT: E 342 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: E 353 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7964 (ttp-110) REVERT: F 29 MET cc_start: 0.5735 (pmm) cc_final: 0.5143 (mpp) REVERT: F 87 ARG cc_start: 0.8865 (tpp-160) cc_final: 0.8412 (mmp80) REVERT: F 211 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: F 244 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8272 (mm-30) REVERT: F 334 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8489 (tp30) REVERT: F 342 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: F 378 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8806 (mm-40) outliers start: 81 outliers final: 41 residues processed: 313 average time/residue: 1.5099 time to fit residues: 524.1164 Evaluate side-chains 286 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 98 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 84 optimal weight: 0.0770 chunk 156 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 97 optimal weight: 0.0030 chunk 243 optimal weight: 0.0970 chunk 241 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 0.3146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 193 GLN E 241 GLN F 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.102224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.073520 restraints weight = 41815.424| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.59 r_work: 0.2997 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20626 Z= 0.107 Angle : 0.628 10.586 27862 Z= 0.296 Chirality : 0.042 0.137 3177 Planarity : 0.004 0.054 3549 Dihedral : 12.155 179.454 3071 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.11 % Allowed : 23.54 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2502 helix: 1.75 (0.16), residues: 1101 sheet: -0.02 (0.26), residues: 393 loop : -0.00 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.005 0.001 HIS F 256 PHE 0.018 0.001 PHE A 62 TYR 0.023 0.001 TYR B 332 ARG 0.012 0.000 ARG C 418 Details of bonding type rmsd hydrogen bonds : bond 0.02902 ( 990) hydrogen bonds : angle 4.31436 ( 2817) covalent geometry : bond 0.00242 (20620) covalent geometry : angle 0.62753 (27862) Misc. bond : bond 0.00041 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 255 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.4252 (OUTLIER) cc_final: 0.3726 (pmt-80) REVERT: A 29 MET cc_start: 0.5379 (tmm) cc_final: 0.3716 (mmp) REVERT: A 56 GLU cc_start: 0.8675 (tt0) cc_final: 0.8332 (pt0) REVERT: A 128 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7492 (mtm-85) REVERT: A 244 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8457 (mm-30) REVERT: A 274 TYR cc_start: 0.8601 (m-10) cc_final: 0.8365 (m-10) REVERT: A 348 LYS cc_start: 0.8937 (ptpp) cc_final: 0.8495 (ptmm) REVERT: B 5 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9216 (mp0) REVERT: B 42 HIS cc_start: 0.8123 (t-90) cc_final: 0.7916 (t-90) REVERT: B 244 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8543 (mm-30) REVERT: C 244 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: C 341 MET cc_start: 0.9197 (tmm) cc_final: 0.8993 (tmt) REVERT: C 374 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8212 (tp-100) REVERT: C 392 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: C 414 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: D 374 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8165 (tm-30) REVERT: E 42 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7736 (t-90) REVERT: E 226 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: E 244 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8580 (mm-30) REVERT: E 342 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: E 353 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8123 (ttp-110) REVERT: F 29 MET cc_start: 0.5700 (pmm) cc_final: 0.5102 (mpp) REVERT: F 244 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8464 (mm-30) REVERT: F 269 ARG cc_start: 0.8562 (mtt90) cc_final: 0.8361 (mtt90) REVERT: F 342 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7803 (pm20) REVERT: F 378 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8883 (mm-40) outliers start: 67 outliers final: 34 residues processed: 306 average time/residue: 1.5689 time to fit residues: 533.0096 Evaluate side-chains 290 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 18 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 232 optimal weight: 0.0060 chunk 205 optimal weight: 20.0000 chunk 120 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 202 optimal weight: 0.0570 chunk 155 optimal weight: 3.9990 overall best weight: 0.5114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 193 GLN E 241 GLN ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.102265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073489 restraints weight = 42074.511| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.60 r_work: 0.2995 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20626 Z= 0.114 Angle : 0.636 11.139 27862 Z= 0.300 Chirality : 0.042 0.143 3177 Planarity : 0.004 0.055 3549 Dihedral : 12.059 179.470 3067 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.20 % Allowed : 23.96 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.17), residues: 2502 helix: 1.77 (0.16), residues: 1104 sheet: -0.21 (0.25), residues: 423 loop : 0.16 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 PHE 0.016 0.001 PHE A 62 TYR 0.028 0.001 TYR B 332 ARG 0.012 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.02923 ( 990) hydrogen bonds : angle 4.27410 ( 2817) covalent geometry : bond 0.00261 (20620) covalent geometry : angle 0.63551 (27862) Misc. bond : bond 0.00039 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 247 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8527 (tt0) cc_final: 0.8192 (pt0) REVERT: A 128 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7560 (mtm-85) REVERT: A 244 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8271 (mm-30) REVERT: A 274 TYR cc_start: 0.8518 (m-10) cc_final: 0.8232 (m-10) REVERT: A 348 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8448 (ptmm) REVERT: B 5 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.9210 (mp0) REVERT: B 42 HIS cc_start: 0.8171 (t-90) cc_final: 0.7930 (t-90) REVERT: B 244 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8243 (mm-30) REVERT: B 374 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8203 (tp40) REVERT: C 244 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: C 374 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8017 (tp-100) REVERT: C 392 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7783 (pt0) REVERT: C 414 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: D 374 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7979 (tm-30) REVERT: E 20 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8523 (p0) REVERT: E 226 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: E 244 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8347 (mm-30) REVERT: E 342 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: E 353 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8048 (ttp-110) REVERT: F 29 MET cc_start: 0.5675 (pmm) cc_final: 0.5078 (mpp) REVERT: F 241 GLN cc_start: 0.8607 (mt0) cc_final: 0.8385 (mt0) REVERT: F 244 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8270 (mm-30) REVERT: F 269 ARG cc_start: 0.8356 (mtt90) cc_final: 0.8134 (mtt90) REVERT: F 342 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7477 (pm20) outliers start: 69 outliers final: 34 residues processed: 300 average time/residue: 1.5963 time to fit residues: 533.6608 Evaluate side-chains 287 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 135 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 233 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 220 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN E 193 GLN E 241 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072704 restraints weight = 41817.594| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.58 r_work: 0.2960 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20626 Z= 0.136 Angle : 0.666 12.236 27862 Z= 0.315 Chirality : 0.042 0.143 3177 Planarity : 0.004 0.059 3549 Dihedral : 12.019 179.791 3065 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.46 % Allowed : 24.88 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.17), residues: 2502 helix: 1.76 (0.16), residues: 1104 sheet: -0.09 (0.27), residues: 375 loop : -0.01 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 PHE 0.016 0.001 PHE A 62 TYR 0.024 0.001 TYR B 332 ARG 0.014 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.03079 ( 990) hydrogen bonds : angle 4.29884 ( 2817) covalent geometry : bond 0.00321 (20620) covalent geometry : angle 0.66595 (27862) Misc. bond : bond 0.00047 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 248 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.5293 (tmm) cc_final: 0.4044 (mmp) REVERT: A 244 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8329 (mm-30) REVERT: A 274 TYR cc_start: 0.8545 (m-10) cc_final: 0.8287 (m-10) REVERT: A 348 LYS cc_start: 0.8894 (ptpp) cc_final: 0.8469 (ptmm) REVERT: B 5 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.9235 (mp0) REVERT: B 42 HIS cc_start: 0.8162 (t-90) cc_final: 0.7894 (t-90) REVERT: B 244 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8250 (mm-30) REVERT: C 244 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: C 374 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8064 (tp-100) REVERT: C 392 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: C 414 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: D 374 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7950 (tm-30) REVERT: E 42 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7887 (t-90) REVERT: E 226 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: E 244 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8358 (mm-30) REVERT: E 342 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: E 353 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8073 (ttp-110) REVERT: F 244 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8260 (mm-30) REVERT: F 269 ARG cc_start: 0.8412 (mtt90) cc_final: 0.8172 (mtt90) REVERT: F 342 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7489 (pm20) outliers start: 53 outliers final: 34 residues processed: 288 average time/residue: 1.6331 time to fit residues: 520.1252 Evaluate side-chains 283 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 224 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 232 optimal weight: 0.0980 chunk 149 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 239 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 220 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN E 241 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.101946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.073139 restraints weight = 41864.891| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.59 r_work: 0.2968 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20626 Z= 0.126 Angle : 0.670 12.587 27862 Z= 0.318 Chirality : 0.042 0.189 3177 Planarity : 0.004 0.062 3549 Dihedral : 11.962 179.734 3065 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.55 % Allowed : 24.88 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2502 helix: 1.73 (0.16), residues: 1107 sheet: -0.07 (0.27), residues: 375 loop : 0.01 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 PHE 0.017 0.001 PHE A 62 TYR 0.025 0.001 TYR D 110 ARG 0.014 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 990) hydrogen bonds : angle 4.29188 ( 2817) covalent geometry : bond 0.00296 (20620) covalent geometry : angle 0.67002 (27862) Misc. bond : bond 0.00038 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.5404 (tmm) cc_final: 0.4045 (mmp) REVERT: A 244 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8341 (mm-30) REVERT: A 274 TYR cc_start: 0.8551 (m-10) cc_final: 0.8286 (m-10) REVERT: A 348 LYS cc_start: 0.8887 (ptpp) cc_final: 0.8462 (ptmm) REVERT: B 21 MET cc_start: 0.8376 (tmm) cc_final: 0.7555 (ppp) REVERT: B 42 HIS cc_start: 0.8177 (t-90) cc_final: 0.7931 (t-90) REVERT: B 266 SER cc_start: 0.8515 (m) cc_final: 0.7913 (p) REVERT: B 334 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8459 (tm-30) REVERT: C 244 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: C 374 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8054 (tp-100) REVERT: C 392 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7800 (pt0) REVERT: C 414 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: D 374 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7955 (tm-30) REVERT: E 20 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8490 (p0) REVERT: E 42 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7859 (t-90) REVERT: E 226 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: E 244 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8354 (mm-30) REVERT: E 342 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: E 353 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8067 (ttp-110) REVERT: F 244 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8261 (mm-30) REVERT: F 269 ARG cc_start: 0.8390 (mtt90) cc_final: 0.8157 (mtt90) REVERT: F 342 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7487 (pm20) outliers start: 55 outliers final: 35 residues processed: 288 average time/residue: 1.5813 time to fit residues: 504.2808 Evaluate side-chains 284 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 341 MET Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 144 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 153 optimal weight: 0.3980 chunk 184 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 33 optimal weight: 0.0270 chunk 164 optimal weight: 10.0000 chunk 111 optimal weight: 0.0000 chunk 71 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 220 GLN E 193 GLN E 241 GLN ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.102701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.074163 restraints weight = 41887.636| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.57 r_work: 0.2993 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20626 Z= 0.115 Angle : 0.671 12.221 27862 Z= 0.319 Chirality : 0.042 0.207 3177 Planarity : 0.004 0.061 3549 Dihedral : 11.841 179.536 3065 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.51 % Allowed : 25.21 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.17), residues: 2502 helix: 1.75 (0.16), residues: 1101 sheet: -0.38 (0.26), residues: 405 loop : 0.27 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 PHE 0.017 0.001 PHE A 62 TYR 0.024 0.001 TYR B 332 ARG 0.015 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 990) hydrogen bonds : angle 4.29676 ( 2817) covalent geometry : bond 0.00267 (20620) covalent geometry : angle 0.67135 (27862) Misc. bond : bond 0.00031 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15979.95 seconds wall clock time: 275 minutes 46.70 seconds (16546.70 seconds total)