Starting phenix.real_space_refine on Mon Jun 23 10:14:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c5y_16444/06_2025/8c5y_16444.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5y_16444/06_2025/8c5y_16444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c5y_16444/06_2025/8c5y_16444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5y_16444/06_2025/8c5y_16444.map" model { file = "/net/cci-nas-00/data/ceres_data/8c5y_16444/06_2025/8c5y_16444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5y_16444/06_2025/8c5y_16444.cif" } resolution = 3.35 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= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15078 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 44 5.16 5 C 9708 2.51 5 N 2578 2.21 5 O 2864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15198 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1420 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain: "B" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "C" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "D" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "G" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "H" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "I" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "J" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "K" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "L" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 897 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 298 SG CYS A 218 100.781 38.199 19.306 1.00 68.58 S ATOM 320 SG CYS A 221 102.966 36.183 21.518 1.00 72.25 S ATOM 442 SG CYS A 236 104.291 37.387 18.089 1.00 70.22 S ATOM 4099 SG CYS D 218 14.845 41.257 86.768 1.00 66.19 S ATOM 4121 SG CYS D 221 12.614 41.978 83.900 1.00 70.31 S ATOM 4243 SG CYS D 236 12.969 44.566 86.746 1.00 66.39 S ATOM 7900 SG CYS G 218 53.699 92.519 19.295 1.00 69.53 S ATOM 7922 SG CYS G 221 51.510 94.158 21.868 1.00 70.11 S ATOM 8044 SG CYS G 236 49.929 92.234 18.956 1.00 73.49 S ATOM 11701 SG CYS J 218 140.233 89.729 86.412 1.00 67.67 S ATOM 11723 SG CYS J 221 142.425 88.387 83.618 1.00 74.25 S ATOM 11845 SG CYS J 236 141.756 86.268 86.751 1.00 71.09 S Time building chain proxies: 9.48, per 1000 atoms: 0.62 Number of scatterers: 15198 At special positions: 0 Unit cell: (155.66, 131.58, 107.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 44 16.00 O 2864 8.00 N 2578 7.00 C 9708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.86 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 239 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 218 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 221 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 236 " pdb=" ZN D 500 " pdb="ZN ZN D 500 " - pdb=" ND1 HIS D 239 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 221 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 218 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 236 " pdb=" ZN G 500 " pdb="ZN ZN G 500 " - pdb=" NE2 HIS G 239 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 218 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 221 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 236 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 239 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 218 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 221 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 236 " Number of angles added : 12 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 22 sheets defined 34.8% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.646A pdb=" N ILE A 193 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 3.736A pdb=" N GLU A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.513A pdb=" N ILE A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.533A pdb=" N PHE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 removed outlier: 3.709A pdb=" N ILE A 311 " --> pdb=" O TYR A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 80 through 87 removed outlier: 3.669A pdb=" N LYS B 83 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 150 removed outlier: 3.648A pdb=" N HIS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 166 through 181 removed outlier: 4.241A pdb=" N LEU B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 removed outlier: 3.727A pdb=" N ILE C 19 " --> pdb=" O ILE C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 114 Proline residue: C 109 - end of helix removed outlier: 4.251A pdb=" N GLY C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 277 through 291 removed outlier: 3.587A pdb=" N ILE D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 306 Processing helix chain 'D' and resid 307 through 311 removed outlier: 4.217A pdb=" N ILE D 310 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE D 311 " --> pdb=" O TYR D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 307 through 311' Processing helix chain 'D' and resid 340 through 356 removed outlier: 4.016A pdb=" N GLU D 344 " --> pdb=" O ASP D 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 17 removed outlier: 3.609A pdb=" N ILE E 15 " --> pdb=" O TYR E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 86 removed outlier: 4.214A pdb=" N ALA E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 86' Processing helix chain 'E' and resid 118 through 150 removed outlier: 4.335A pdb=" N GLU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR E 150 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 167 through 181 removed outlier: 3.932A pdb=" N GLU E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET E 181 " --> pdb=" O TYR E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 114 Proline residue: F 109 - end of helix removed outlier: 3.686A pdb=" N GLY F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 193 Processing helix chain 'G' and resid 267 through 275 Processing helix chain 'G' and resid 277 through 291 removed outlier: 3.522A pdb=" N SER G 291 " --> pdb=" O GLU G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 307 removed outlier: 3.562A pdb=" N PHE G 307 " --> pdb=" O ALA G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 311 removed outlier: 3.663A pdb=" N ILE G 311 " --> pdb=" O TYR G 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 308 through 311' Processing helix chain 'G' and resid 340 through 356 Processing helix chain 'H' and resid 11 through 18 Processing helix chain 'H' and resid 80 through 87 removed outlier: 3.543A pdb=" N LYS H 83 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 150 removed outlier: 3.883A pdb=" N HIS H 136 " --> pdb=" O GLU H 132 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU H 145 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE H 146 " --> pdb=" O ILE H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 166 through 181 removed outlier: 4.339A pdb=" N LEU H 170 " --> pdb=" O GLU H 166 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU H 171 " --> pdb=" O GLU H 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 19 removed outlier: 3.531A pdb=" N ILE I 19 " --> pdb=" O ILE I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 114 Proline residue: I 109 - end of helix removed outlier: 3.955A pdb=" N GLY I 113 " --> pdb=" O PRO I 109 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 193 Processing helix chain 'J' and resid 267 through 275 Processing helix chain 'J' and resid 277 through 291 removed outlier: 3.592A pdb=" N ILE J 281 " --> pdb=" O SER J 277 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER J 291 " --> pdb=" O GLU J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 306 Processing helix chain 'J' and resid 340 through 356 Processing helix chain 'K' and resid 11 through 17 removed outlier: 3.802A pdb=" N ILE K 15 " --> pdb=" O TYR K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 86 removed outlier: 4.233A pdb=" N ALA K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS K 86 " --> pdb=" O THR K 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 81 through 86' Processing helix chain 'K' and resid 118 through 150 removed outlier: 3.523A pdb=" N TRP K 122 " --> pdb=" O HIS K 118 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU K 145 " --> pdb=" O LYS K 141 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE K 146 " --> pdb=" O ILE K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 167 through 181 removed outlier: 4.019A pdb=" N GLU K 171 " --> pdb=" O GLU K 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 19 Processing helix chain 'L' and resid 94 through 114 Proline residue: L 109 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 187 removed outlier: 6.307A pdb=" N THR A 186 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ARG A 203 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLU A 314 " --> pdb=" O ASP A 338 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP A 338 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 316 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TRP A 336 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ARG A 318 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N TYR A 260 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N LEU A 331 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 262 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA A 333 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A 264 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N SER A 335 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N PHE A 266 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N GLU A 337 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 245 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR A 215 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET A 247 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 213 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A 249 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG A 211 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASP A 251 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL A 209 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 253 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 228 removed outlier: 3.584A pdb=" N VAL A 233 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 8 through 9 Processing sheet with id=AA4, first strand: chain 'B' and resid 8 through 9 removed outlier: 7.526A pdb=" N LEU B 93 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS B 116 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN B 95 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 114 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 97 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS B 107 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TRP B 74 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE B 78 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 11.398A pdb=" N GLY B 113 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.525A pdb=" N VAL C 12 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ILE C 29 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG C 71 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ALA C 83 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 73 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE C 81 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASN C 75 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE C 79 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N ILE C 79 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE C 52 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 81 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 34 " --> pdb=" O TRP C 43 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP C 45 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL C 32 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 186 through 187 removed outlier: 6.292A pdb=" N THR D 186 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ARG D 203 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL D 316 " --> pdb=" O TRP D 336 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TRP D 336 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ARG D 318 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N TYR D 260 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LEU D 331 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG D 262 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA D 333 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR D 264 " --> pdb=" O ALA D 333 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER D 335 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N PHE D 266 " --> pdb=" O SER D 335 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N GLU D 337 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY D 253 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL D 209 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASP D 255 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA D 207 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 226 through 228 removed outlier: 3.565A pdb=" N VAL D 233 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AB1, first strand: chain 'E' and resid 54 through 55 removed outlier: 8.527A pdb=" N VAL E 72 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ILE E 109 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP E 74 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL E 111 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU E 76 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY E 113 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 12.492A pdb=" N PHE E 78 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 16.443A pdb=" N SER E 115 " --> pdb=" O PHE E 78 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE E 97 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL E 114 " --> pdb=" O GLN E 95 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN E 95 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LYS E 116 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU E 93 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 13 removed outlier: 6.573A pdb=" N ARG F 67 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE F 86 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE F 69 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS F 80 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ILE F 79 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE F 52 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET F 41 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL F 35 " --> pdb=" O MET F 41 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP F 43 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 186 through 187 removed outlier: 6.343A pdb=" N THR G 186 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ARG G 203 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N GLU G 314 " --> pdb=" O ASP G 338 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP G 338 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL G 316 " --> pdb=" O TRP G 336 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP G 336 " --> pdb=" O VAL G 316 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG G 318 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU G 329 " --> pdb=" O TYR G 260 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG G 262 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE G 266 " --> pdb=" O ALA G 333 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N SER G 335 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY G 253 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL G 209 " --> pdb=" O GLY G 253 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP G 255 " --> pdb=" O ALA G 207 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA G 207 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 226 through 228 removed outlier: 3.601A pdb=" N VAL G 233 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 8 through 9 Processing sheet with id=AB6, first strand: chain 'H' and resid 8 through 9 removed outlier: 7.771A pdb=" N LEU H 93 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS H 116 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN H 95 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL H 114 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE H 97 " --> pdb=" O GLU H 112 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL H 72 " --> pdb=" O LYS H 107 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N ILE H 109 " --> pdb=" O VAL H 72 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TRP H 74 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL H 111 " --> pdb=" O TRP H 74 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU H 76 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLY H 113 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 12.475A pdb=" N PHE H 78 " --> pdb=" O GLY H 113 " (cutoff:3.500A) removed outlier: 16.439A pdb=" N SER H 115 " --> pdb=" O PHE H 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AB8, first strand: chain 'I' and resid 12 through 13 removed outlier: 6.451A pdb=" N VAL I 12 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N ILE I 29 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG I 71 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ALA I 83 " --> pdb=" O ARG I 71 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE I 73 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE I 81 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASN I 75 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE I 79 " --> pdb=" O ASN I 75 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ILE I 79 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE I 52 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE I 81 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS I 34 " --> pdb=" O TRP I 43 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP I 45 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL I 32 " --> pdb=" O ASP I 45 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.583A pdb=" N THR J 186 " --> pdb=" O GLU J 201 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ARG J 203 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL J 316 " --> pdb=" O TRP J 336 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP J 336 " --> pdb=" O VAL J 316 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARG J 318 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N TYR J 260 " --> pdb=" O LEU J 329 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N LEU J 331 " --> pdb=" O TYR J 260 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG J 262 " --> pdb=" O LEU J 331 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA J 333 " --> pdb=" O ARG J 262 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR J 264 " --> pdb=" O ALA J 333 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER J 335 " --> pdb=" O THR J 264 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N PHE J 266 " --> pdb=" O SER J 335 " (cutoff:3.500A) removed outlier: 11.028A pdb=" N GLU J 337 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE J 245 " --> pdb=" O TYR J 215 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR J 215 " --> pdb=" O ILE J 245 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N MET J 247 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU J 213 " --> pdb=" O MET J 247 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE J 249 " --> pdb=" O ARG J 211 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG J 211 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASP J 251 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL J 209 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY J 253 " --> pdb=" O ALA J 207 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 226 through 227 Processing sheet with id=AC2, first strand: chain 'K' and resid 19 through 21 Processing sheet with id=AC3, first strand: chain 'K' and resid 54 through 55 removed outlier: 8.718A pdb=" N VAL K 72 " --> pdb=" O LYS K 107 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N ILE K 109 " --> pdb=" O VAL K 72 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP K 74 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL K 111 " --> pdb=" O TRP K 74 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU K 76 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLY K 113 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 12.441A pdb=" N PHE K 78 " --> pdb=" O GLY K 113 " (cutoff:3.500A) removed outlier: 16.511A pdb=" N SER K 115 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE K 109 " --> pdb=" O ALA K 101 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA K 101 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL K 111 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS K 99 " --> pdb=" O VAL K 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 12 through 13 removed outlier: 6.490A pdb=" N VAL L 12 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE L 29 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG L 67 " --> pdb=" O ILE L 86 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE L 86 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE L 69 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS L 80 " --> pdb=" O ILE L 73 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN L 75 " --> pdb=" O GLY L 78 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY L 78 " --> pdb=" O ASN L 75 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ILE L 79 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE L 52 " --> pdb=" O ILE L 79 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE L 81 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET L 41 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL L 35 " --> pdb=" O MET L 41 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP L 43 " --> pdb=" O ILE L 33 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 1974 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: 5.20 Time building geometry restraints manager: 5.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2970 1.33 - 1.45: 3398 1.45 - 1.57: 8982 1.57 - 1.69: 0 1.69 - 1.82: 76 Bond restraints: 15426 Sorted by residual: bond pdb=" CA ASP A 340 " pdb=" CB ASP A 340 " ideal model delta sigma weight residual 1.527 1.489 0.038 7.60e-03 1.73e+04 2.54e+01 bond pdb=" CA TYR A 341 " pdb=" CB TYR A 341 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.69e-02 3.50e+03 9.89e+00 bond pdb=" C VAL A 339 " pdb=" O VAL A 339 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.19e-02 7.06e+03 7.46e+00 bond pdb=" C TYR A 341 " pdb=" O TYR A 341 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.26e-02 6.30e+03 6.46e+00 bond pdb=" CB ASP A 340 " pdb=" CG ASP A 340 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.07e+00 ... (remaining 15421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 20688 4.02 - 8.04: 51 8.04 - 12.06: 4 12.06 - 16.08: 1 16.08 - 20.09: 1 Bond angle restraints: 20745 Sorted by residual: angle pdb=" C VAL K 117 " pdb=" N HIS K 118 " pdb=" CA HIS K 118 " ideal model delta sigma weight residual 120.69 140.78 -20.09 2.95e+00 1.15e-01 4.64e+01 angle pdb=" N TYR A 341 " pdb=" CA TYR A 341 " pdb=" C TYR A 341 " ideal model delta sigma weight residual 110.80 124.19 -13.39 2.13e+00 2.20e-01 3.95e+01 angle pdb=" O ASP A 338 " pdb=" C ASP A 338 " pdb=" N VAL A 339 " ideal model delta sigma weight residual 122.85 117.45 5.40 1.14e+00 7.69e-01 2.25e+01 angle pdb=" N GLU G 238 " pdb=" CA GLU G 238 " pdb=" C GLU G 238 " ideal model delta sigma weight residual 114.09 106.75 7.34 1.55e+00 4.16e-01 2.24e+01 angle pdb=" CA ASP A 338 " pdb=" C ASP A 338 " pdb=" N VAL A 339 " ideal model delta sigma weight residual 115.27 121.14 -5.87 1.30e+00 5.92e-01 2.04e+01 ... (remaining 20740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8403 17.93 - 35.87: 873 35.87 - 53.80: 132 53.80 - 71.73: 28 71.73 - 89.67: 11 Dihedral angle restraints: 9447 sinusoidal: 4059 harmonic: 5388 Sorted by residual: dihedral pdb=" CA MET E 5 " pdb=" C MET E 5 " pdb=" N PRO E 6 " pdb=" CA PRO E 6 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU K 10 " pdb=" C LEU K 10 " pdb=" N TYR K 11 " pdb=" CA TYR K 11 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU E 10 " pdb=" C LEU E 10 " pdb=" N TYR E 11 " pdb=" CA TYR E 11 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 9444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2290 0.130 - 0.260: 25 0.260 - 0.389: 1 0.389 - 0.519: 0 0.519 - 0.649: 1 Chirality restraints: 2317 Sorted by residual: chirality pdb=" CA TYR A 341 " pdb=" N TYR A 341 " pdb=" C TYR A 341 " pdb=" CB TYR A 341 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA ASP A 340 " pdb=" N ASP A 340 " pdb=" C ASP A 340 " pdb=" CB ASP A 340 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA LEU L 107 " pdb=" N LEU L 107 " pdb=" C LEU L 107 " pdb=" CB LEU L 107 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 2314 not shown) Planarity restraints: 2638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS G 236 " -0.049 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO G 237 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 237 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 237 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER L 90 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.23e+00 pdb=" C SER L 90 " 0.046 2.00e-02 2.50e+03 pdb=" O SER L 90 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP L 91 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 236 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A 237 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.024 5.00e-02 4.00e+02 ... (remaining 2635 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 183 2.67 - 3.23: 13651 3.23 - 3.78: 21593 3.78 - 4.34: 29055 4.34 - 4.90: 49273 Nonbonded interactions: 113755 Sorted by model distance: nonbonded pdb=" OG SER F 55 " pdb=" O ASP F 58 " model vdw 2.111 3.040 nonbonded pdb=" CG HIS G 239 " pdb="ZN ZN G 500 " model vdw 2.131 1.960 nonbonded pdb=" OD2 ASP G 251 " pdb=" NH2 ARG G 262 " model vdw 2.165 3.120 nonbonded pdb=" OD2 ASP A 251 " pdb=" NH2 ARG A 262 " model vdw 2.165 3.120 nonbonded pdb=" ND1 HIS G 239 " pdb="ZN ZN G 500 " model vdw 2.167 1.848 ... (remaining 113750 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' and (resid 184 through 358 or resid 500)) selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = (chain 'C' and resid 8 through 117) selection = (chain 'F' and resid 8 through 117) selection = (chain 'I' and resid 8 through 117) selection = chain 'L' } 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.200 Process input model: 43.160 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.005 0.069 15442 Z= 0.203 Angle : 0.711 20.095 20757 Z= 0.394 Chirality : 0.052 0.649 2317 Planarity : 0.004 0.075 2638 Dihedral : 14.436 89.668 5991 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.42 % Favored : 96.26 % Rotamer: Outliers : 0.18 % Allowed : 0.37 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 1844 helix: 1.50 (0.22), residues: 533 sheet: -0.26 (0.22), residues: 530 loop : -0.78 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 117 HIS 0.010 0.002 HIS G 239 PHE 0.020 0.002 PHE C 42 TYR 0.020 0.002 TYR B 177 ARG 0.006 0.001 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.15083 ( 707) hydrogen bonds : angle 6.43456 ( 1974) metal coordination : bond 0.02491 ( 16) metal coordination : angle 3.14276 ( 12) covalent geometry : bond 0.00450 (15426) covalent geometry : angle 0.70761 (20745) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 1.706 Fit side-chains REVERT: C 88 ASP cc_start: 0.8074 (t0) cc_final: 0.7836 (t0) REVERT: D 348 ILE cc_start: 0.6639 (pt) cc_final: 0.6104 (pt) REVERT: E 80 ASP cc_start: 0.7101 (t70) cc_final: 0.6837 (t0) REVERT: E 181 MET cc_start: 0.2334 (tpt) cc_final: 0.1397 (mmt) REVERT: J 222 LYS cc_start: 0.6414 (ttmt) cc_final: 0.6144 (tmtt) outliers start: 3 outliers final: 1 residues processed: 221 average time/residue: 0.2513 time to fit residues: 84.9057 Evaluate side-chains 169 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 93 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.0870 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 87 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN C 64 GLN E 30 ASN F 64 GLN K 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.217068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.179947 restraints weight = 18580.434| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 1.95 r_work: 0.3617 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15442 Z= 0.186 Angle : 0.630 8.839 20757 Z= 0.336 Chirality : 0.050 0.170 2317 Planarity : 0.004 0.054 2638 Dihedral : 5.511 78.155 2076 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.31 % Favored : 96.48 % Rotamer: Outliers : 0.98 % Allowed : 8.22 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1844 helix: 1.61 (0.21), residues: 543 sheet: -0.38 (0.22), residues: 534 loop : -0.88 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 336 HIS 0.006 0.002 HIS K 136 PHE 0.021 0.002 PHE C 42 TYR 0.014 0.002 TYR G 215 ARG 0.004 0.000 ARG D 342 Details of bonding type rmsd hydrogen bonds : bond 0.05028 ( 707) hydrogen bonds : angle 5.12896 ( 1974) metal coordination : bond 0.01571 ( 16) metal coordination : angle 2.71662 ( 12) covalent geometry : bond 0.00459 (15426) covalent geometry : angle 0.62653 (20745) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 1.822 Fit side-chains REVERT: C 88 ASP cc_start: 0.8567 (t0) cc_final: 0.8321 (t0) REVERT: D 210 TYR cc_start: 0.8696 (m-80) cc_final: 0.8229 (m-80) REVERT: E 80 ASP cc_start: 0.7669 (t70) cc_final: 0.7289 (t0) REVERT: H 149 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7735 (mm-40) REVERT: J 222 LYS cc_start: 0.7268 (ttmt) cc_final: 0.6457 (tmtt) REVERT: K 181 MET cc_start: 0.3586 (mmm) cc_final: 0.2852 (mtp) REVERT: L 41 MET cc_start: 0.6403 (pmm) cc_final: 0.5327 (mpp) REVERT: L 93 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7386 (p0) outliers start: 16 outliers final: 9 residues processed: 202 average time/residue: 0.2505 time to fit residues: 77.4314 Evaluate side-chains 170 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 93 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 40.0000 chunk 40 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN E 30 ASN K 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.210200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.153490 restraints weight = 18702.963| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.58 r_work: 0.3437 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15442 Z= 0.181 Angle : 0.604 8.059 20757 Z= 0.323 Chirality : 0.049 0.176 2317 Planarity : 0.004 0.041 2638 Dihedral : 5.493 87.987 2076 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.42 % Favored : 96.37 % Rotamer: Outliers : 1.41 % Allowed : 10.48 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 1844 helix: 1.68 (0.21), residues: 543 sheet: -0.46 (0.22), residues: 541 loop : -0.96 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 117 HIS 0.006 0.002 HIS K 136 PHE 0.020 0.002 PHE C 42 TYR 0.015 0.001 TYR G 215 ARG 0.003 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 707) hydrogen bonds : angle 4.92974 ( 1974) metal coordination : bond 0.01417 ( 16) metal coordination : angle 2.46782 ( 12) covalent geometry : bond 0.00450 (15426) covalent geometry : angle 0.60151 (20745) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.739 Fit side-chains revert: symmetry clash REVERT: D 210 TYR cc_start: 0.8702 (m-80) cc_final: 0.8124 (m-80) REVERT: E 80 ASP cc_start: 0.7919 (t70) cc_final: 0.7473 (t0) REVERT: E 121 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7696 (tmm) REVERT: E 181 MET cc_start: 0.2280 (tpt) cc_final: 0.1229 (mmm) REVERT: F 12 VAL cc_start: 0.6948 (t) cc_final: 0.6627 (p) REVERT: H 149 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7583 (mm-40) REVERT: J 222 LYS cc_start: 0.7246 (ttmt) cc_final: 0.6417 (tmtt) REVERT: J 337 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7148 (tm-30) REVERT: K 181 MET cc_start: 0.3337 (mmm) cc_final: 0.2774 (mtp) REVERT: L 41 MET cc_start: 0.6386 (pmm) cc_final: 0.5358 (mmm) outliers start: 23 outliers final: 14 residues processed: 189 average time/residue: 0.2500 time to fit residues: 73.9714 Evaluate side-chains 171 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.210693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.154826 restraints weight = 18475.806| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.60 r_work: 0.3446 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15442 Z= 0.150 Angle : 0.563 8.769 20757 Z= 0.302 Chirality : 0.048 0.167 2317 Planarity : 0.004 0.041 2638 Dihedral : 5.088 73.860 2074 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.42 % Rotamer: Outliers : 1.72 % Allowed : 11.83 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1844 helix: 1.87 (0.21), residues: 543 sheet: -0.63 (0.22), residues: 513 loop : -0.90 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 117 HIS 0.006 0.001 HIS K 136 PHE 0.018 0.002 PHE C 42 TYR 0.016 0.001 TYR J 341 ARG 0.003 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 707) hydrogen bonds : angle 4.74081 ( 1974) metal coordination : bond 0.01263 ( 16) metal coordination : angle 2.26508 ( 12) covalent geometry : bond 0.00367 (15426) covalent geometry : angle 0.56065 (20745) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 2.682 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7432 (t0) cc_final: 0.7206 (t0) REVERT: D 210 TYR cc_start: 0.8716 (m-80) cc_final: 0.8149 (m-80) REVERT: E 80 ASP cc_start: 0.7991 (t70) cc_final: 0.7589 (t0) REVERT: E 121 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7651 (tmm) REVERT: H 149 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7567 (mm-40) REVERT: J 222 LYS cc_start: 0.7299 (ttmt) cc_final: 0.6389 (tmtt) REVERT: L 41 MET cc_start: 0.6233 (pmm) cc_final: 0.5235 (mpp) outliers start: 28 outliers final: 15 residues processed: 184 average time/residue: 0.3352 time to fit residues: 97.9041 Evaluate side-chains 164 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.211388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147634 restraints weight = 18685.604| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.66 r_work: 0.3440 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15442 Z= 0.127 Angle : 0.545 8.753 20757 Z= 0.290 Chirality : 0.048 0.177 2317 Planarity : 0.003 0.040 2638 Dihedral : 4.874 74.879 2074 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.42 % Rotamer: Outliers : 1.72 % Allowed : 13.55 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 1844 helix: 2.00 (0.22), residues: 543 sheet: -0.55 (0.23), residues: 507 loop : -0.85 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 117 HIS 0.005 0.001 HIS E 136 PHE 0.016 0.001 PHE J 252 TYR 0.011 0.001 TYR G 215 ARG 0.002 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 707) hydrogen bonds : angle 4.60855 ( 1974) metal coordination : bond 0.01163 ( 16) metal coordination : angle 2.10339 ( 12) covalent geometry : bond 0.00301 (15426) covalent geometry : angle 0.54279 (20745) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7468 (t0) cc_final: 0.7196 (t0) REVERT: D 210 TYR cc_start: 0.8653 (m-80) cc_final: 0.7969 (m-80) REVERT: E 80 ASP cc_start: 0.8006 (t70) cc_final: 0.7630 (t0) REVERT: E 121 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7605 (tmm) REVERT: E 181 MET cc_start: 0.1636 (tpt) cc_final: 0.0746 (mmm) REVERT: F 41 MET cc_start: 0.6030 (mmm) cc_final: 0.4920 (pmm) REVERT: F 56 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5072 (mm-30) REVERT: H 149 GLN cc_start: 0.7867 (mm110) cc_final: 0.7624 (mm-40) REVERT: J 222 LYS cc_start: 0.7193 (ttmt) cc_final: 0.6306 (tmtt) REVERT: J 341 TYR cc_start: 0.6512 (m-80) cc_final: 0.6037 (m-80) REVERT: K 63 LYS cc_start: 0.8314 (pttt) cc_final: 0.8065 (pttt) REVERT: L 41 MET cc_start: 0.6331 (pmm) cc_final: 0.5394 (mpp) outliers start: 28 outliers final: 17 residues processed: 187 average time/residue: 0.2384 time to fit residues: 68.9342 Evaluate side-chains 171 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 103 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN E 162 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.203172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.159244 restraints weight = 18661.019| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.26 r_work: 0.3387 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.075 15442 Z= 0.422 Angle : 0.811 9.451 20757 Z= 0.429 Chirality : 0.057 0.248 2317 Planarity : 0.006 0.061 2638 Dihedral : 5.727 74.216 2074 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.53 % Favored : 94.25 % Rotamer: Outliers : 2.76 % Allowed : 14.41 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1844 helix: 1.29 (0.21), residues: 528 sheet: -1.10 (0.21), residues: 577 loop : -1.11 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 122 HIS 0.008 0.002 HIS K 136 PHE 0.032 0.003 PHE I 42 TYR 0.023 0.002 TYR G 215 ARG 0.008 0.001 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.06601 ( 707) hydrogen bonds : angle 5.21562 ( 1974) metal coordination : bond 0.01378 ( 16) metal coordination : angle 2.82213 ( 12) covalent geometry : bond 0.01081 (15426) covalent geometry : angle 0.80882 (20745) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 1.854 Fit side-chains revert: symmetry clash REVERT: A 343 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.8138 (ttm-80) REVERT: D 210 TYR cc_start: 0.8799 (m-80) cc_final: 0.8332 (m-80) REVERT: E 80 ASP cc_start: 0.8093 (t70) cc_final: 0.7814 (t0) REVERT: E 81 ASP cc_start: 0.8651 (m-30) cc_final: 0.8353 (m-30) REVERT: E 121 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7648 (tmm) REVERT: F 41 MET cc_start: 0.5818 (mmm) cc_final: 0.5041 (pmm) REVERT: F 56 GLU cc_start: 0.5819 (OUTLIER) cc_final: 0.4664 (mm-30) REVERT: J 222 LYS cc_start: 0.7275 (ttmt) cc_final: 0.6333 (tmtt) REVERT: J 318 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6155 (mmt90) REVERT: J 358 MET cc_start: 0.3905 (mmt) cc_final: 0.3699 (mmt) REVERT: L 41 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5248 (mmm) outliers start: 45 outliers final: 32 residues processed: 187 average time/residue: 0.2755 time to fit residues: 77.9896 Evaluate side-chains 187 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 318 ARG Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 133 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 148 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.210127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152181 restraints weight = 18526.359| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.65 r_work: 0.3443 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15442 Z= 0.122 Angle : 0.562 9.204 20757 Z= 0.300 Chirality : 0.048 0.191 2317 Planarity : 0.003 0.042 2638 Dihedral : 5.079 78.497 2074 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.20 % Favored : 96.58 % Rotamer: Outliers : 1.66 % Allowed : 16.49 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1844 helix: 1.74 (0.21), residues: 529 sheet: -0.80 (0.22), residues: 513 loop : -0.95 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 117 HIS 0.004 0.001 HIS E 136 PHE 0.016 0.001 PHE I 42 TYR 0.016 0.001 TYR E 61 ARG 0.003 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 707) hydrogen bonds : angle 4.66582 ( 1974) metal coordination : bond 0.01071 ( 16) metal coordination : angle 2.09497 ( 12) covalent geometry : bond 0.00282 (15426) covalent geometry : angle 0.55963 (20745) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7362 (t0) cc_final: 0.7055 (t0) REVERT: C 91 ASP cc_start: 0.8032 (p0) cc_final: 0.7819 (p0) REVERT: D 210 TYR cc_start: 0.8715 (m-80) cc_final: 0.8151 (m-80) REVERT: E 80 ASP cc_start: 0.8189 (t0) cc_final: 0.7921 (t0) REVERT: E 121 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7500 (tmm) REVERT: F 41 MET cc_start: 0.6176 (mmm) cc_final: 0.5154 (pmm) REVERT: F 56 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.4938 (mm-30) REVERT: H 149 GLN cc_start: 0.7975 (mm110) cc_final: 0.7642 (mm-40) REVERT: J 222 LYS cc_start: 0.7096 (ttmt) cc_final: 0.6241 (tmtt) REVERT: J 358 MET cc_start: 0.4393 (mmt) cc_final: 0.3915 (mmt) REVERT: K 63 LYS cc_start: 0.8338 (pttt) cc_final: 0.8051 (pttt) REVERT: K 121 MET cc_start: 0.7123 (tpt) cc_final: 0.6889 (tpt) REVERT: L 41 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5242 (mpp) outliers start: 27 outliers final: 17 residues processed: 179 average time/residue: 0.2612 time to fit residues: 70.9975 Evaluate side-chains 157 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain J residue 318 ARG Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 74 optimal weight: 0.2980 chunk 179 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 112 optimal weight: 0.2980 chunk 125 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN K 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.211825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.163360 restraints weight = 18330.464| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.28 r_work: 0.3498 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15442 Z= 0.119 Angle : 0.557 9.067 20757 Z= 0.297 Chirality : 0.048 0.154 2317 Planarity : 0.003 0.040 2638 Dihedral : 4.915 86.346 2074 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.96 % Favored : 95.82 % Rotamer: Outliers : 1.78 % Allowed : 16.55 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.00 (0.20), residues: 1844 helix: 1.95 (0.21), residues: 544 sheet: -0.64 (0.22), residues: 547 loop : -0.90 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP I 117 HIS 0.004 0.001 HIS K 136 PHE 0.014 0.001 PHE I 42 TYR 0.020 0.001 TYR J 341 ARG 0.002 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 707) hydrogen bonds : angle 4.56092 ( 1974) metal coordination : bond 0.00962 ( 16) metal coordination : angle 1.97737 ( 12) covalent geometry : bond 0.00276 (15426) covalent geometry : angle 0.55513 (20745) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7295 (t0) cc_final: 0.7028 (t0) REVERT: D 210 TYR cc_start: 0.8681 (m-80) cc_final: 0.8063 (m-80) REVERT: E 80 ASP cc_start: 0.8192 (t0) cc_final: 0.7929 (t0) REVERT: E 121 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7489 (tmm) REVERT: E 181 MET cc_start: 0.1407 (tpt) cc_final: 0.0512 (mmt) REVERT: F 41 MET cc_start: 0.6200 (mmm) cc_final: 0.5341 (pmm) REVERT: J 222 LYS cc_start: 0.7118 (ttmt) cc_final: 0.6270 (tmtt) REVERT: J 358 MET cc_start: 0.4509 (mmt) cc_final: 0.4063 (mmt) REVERT: K 63 LYS cc_start: 0.8328 (pttt) cc_final: 0.8041 (pttt) REVERT: L 41 MET cc_start: 0.6093 (OUTLIER) cc_final: 0.5222 (mpp) outliers start: 29 outliers final: 19 residues processed: 173 average time/residue: 0.2567 time to fit residues: 68.7538 Evaluate side-chains 163 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN H 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.207994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150618 restraints weight = 18378.912| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.53 r_work: 0.3403 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15442 Z= 0.184 Angle : 0.620 15.248 20757 Z= 0.326 Chirality : 0.049 0.165 2317 Planarity : 0.004 0.040 2638 Dihedral : 4.939 63.427 2074 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.90 % Favored : 95.88 % Rotamer: Outliers : 1.72 % Allowed : 17.04 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1844 helix: 1.86 (0.21), residues: 544 sheet: -0.69 (0.22), residues: 547 loop : -0.94 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 117 HIS 0.006 0.002 HIS K 136 PHE 0.021 0.002 PHE I 42 TYR 0.018 0.002 TYR E 61 ARG 0.003 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 707) hydrogen bonds : angle 4.69538 ( 1974) metal coordination : bond 0.00920 ( 16) metal coordination : angle 2.01560 ( 12) covalent geometry : bond 0.00461 (15426) covalent geometry : angle 0.61779 (20745) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7460 (t0) cc_final: 0.7103 (t0) REVERT: D 210 TYR cc_start: 0.8721 (m-80) cc_final: 0.8108 (m-80) REVERT: E 80 ASP cc_start: 0.8231 (t0) cc_final: 0.7988 (t0) REVERT: E 121 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7581 (tmm) REVERT: E 181 MET cc_start: 0.1094 (tpt) cc_final: 0.0393 (mmm) REVERT: F 56 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.4813 (mm-30) REVERT: J 222 LYS cc_start: 0.7058 (ttmt) cc_final: 0.6203 (tmtt) REVERT: K 63 LYS cc_start: 0.8399 (pttt) cc_final: 0.8115 (pttt) REVERT: L 41 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5171 (mpp) outliers start: 28 outliers final: 22 residues processed: 167 average time/residue: 0.2424 time to fit residues: 63.0473 Evaluate side-chains 166 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 180 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS B 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.207775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150012 restraints weight = 18460.552| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.57 r_work: 0.3416 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 2.255 15442 Z= 0.375 Angle : 0.627 19.557 20757 Z= 0.327 Chirality : 0.050 0.158 2317 Planarity : 0.004 0.041 2638 Dihedral : 4.905 57.115 2074 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.34 % Favored : 95.44 % Rotamer: Outliers : 1.84 % Allowed : 17.23 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.20), residues: 1844 helix: 1.85 (0.21), residues: 544 sheet: -0.73 (0.22), residues: 549 loop : -0.94 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 117 HIS 0.006 0.002 HIS K 136 PHE 0.020 0.002 PHE I 42 TYR 0.021 0.002 TYR E 61 ARG 0.003 0.000 ARG A 318 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 707) hydrogen bonds : angle 4.70243 ( 1974) metal coordination : bond 0.56372 ( 16) metal coordination : angle 1.95855 ( 12) covalent geometry : bond 0.00472 (15426) covalent geometry : angle 0.62589 (20745) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7454 (t0) cc_final: 0.7107 (t0) REVERT: B 181 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6491 (ptt) REVERT: D 210 TYR cc_start: 0.8727 (m-80) cc_final: 0.8113 (m-80) REVERT: E 80 ASP cc_start: 0.8285 (t0) cc_final: 0.8051 (t0) REVERT: E 121 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7556 (tmm) REVERT: F 41 MET cc_start: 0.6137 (mmm) cc_final: 0.5344 (pmm) REVERT: F 56 GLU cc_start: 0.5819 (OUTLIER) cc_final: 0.4867 (mm-30) REVERT: J 222 LYS cc_start: 0.7052 (ttmt) cc_final: 0.6177 (tmtt) REVERT: K 63 LYS cc_start: 0.8380 (pttt) cc_final: 0.8088 (pttt) REVERT: L 41 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5148 (mpp) outliers start: 30 outliers final: 22 residues processed: 158 average time/residue: 0.2869 time to fit residues: 72.0162 Evaluate side-chains 165 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain J residue 318 ARG Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 183 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 180 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN H 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.209880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144440 restraints weight = 18289.919| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 4.06 r_work: 0.3405 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.586 15442 Z= 0.160 Angle : 0.610 19.196 20757 Z= 0.309 Chirality : 0.048 0.151 2317 Planarity : 0.003 0.042 2638 Dihedral : 4.708 55.843 2074 Min Nonbonded Distance : 1.442 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.52 % Favored : 96.26 % Rotamer: Outliers : 1.66 % Allowed : 17.66 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1844 helix: 2.01 (0.21), residues: 544 sheet: -0.63 (0.22), residues: 547 loop : -0.87 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 117 HIS 0.043 0.003 HIS A 239 PHE 0.015 0.001 PHE I 42 TYR 0.017 0.001 TYR E 61 ARG 0.003 0.000 ARG A 318 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 707) hydrogen bonds : angle 4.53185 ( 1974) metal coordination : bond 0.14828 ( 16) metal coordination : angle 7.73493 ( 12) covalent geometry : bond 0.00321 (15426) covalent geometry : angle 0.58104 (20745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8704.94 seconds wall clock time: 155 minutes 40.24 seconds (9340.24 seconds total)