Starting phenix.real_space_refine on Sun May 25 16:23:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c5y_16444/05_2025/8c5y_16444.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5y_16444/05_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_16444/05_2025/8c5y_16444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5y_16444/05_2025/8c5y_16444.map" model { file = "/net/cci-nas-00/data/ceres_data/8c5y_16444/05_2025/8c5y_16444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5y_16444/05_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-5687/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: 8.96, per 1000 atoms: 0.59 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 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: 1.93 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: 4.98 Time building geometry restraints manager: 3.95 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.460 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.310 ------------------------------------------------------------------------------- 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 : 1.778 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: 0.2468 time to fit residues: 83.0688 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 : 1.811 ------------------------------------------------------------------------------- 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 = 18580.436| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 1.95 r_work: 0.3622 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 1.926 Fit side-chains REVERT: C 88 ASP cc_start: 0.8559 (t0) cc_final: 0.8320 (t0) REVERT: D 210 TYR cc_start: 0.8704 (m-80) cc_final: 0.8235 (m-80) REVERT: E 80 ASP cc_start: 0.7652 (t70) cc_final: 0.7273 (t0) REVERT: H 149 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7740 (mm-40) REVERT: J 222 LYS cc_start: 0.7273 (ttmt) cc_final: 0.6458 (tmtt) REVERT: K 181 MET cc_start: 0.3575 (mmm) cc_final: 0.2843 (mtp) REVERT: L 41 MET cc_start: 0.6393 (pmm) cc_final: 0.5322 (mpp) REVERT: L 93 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7394 (p0) outliers start: 16 outliers final: 9 residues processed: 202 average time/residue: 0.2444 time to fit residues: 75.4814 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 : 1.718 ------------------------------------------------------------------------------- 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: 0.2980 chunk 105 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 40.0000 chunk 40 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.217323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.178167 restraints weight = 18527.334| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.14 r_work: 0.3582 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.003 0.042 15442 Z= 0.140 Angle : 0.567 8.219 20757 Z= 0.304 Chirality : 0.048 0.175 2317 Planarity : 0.003 0.040 2638 Dihedral : 5.306 80.389 2076 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.09 % Favored : 96.69 % Rotamer: Outliers : 1.29 % Allowed : 10.06 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.19), residues: 1844 helix: 1.76 (0.21), residues: 543 sheet: -0.32 (0.23), residues: 517 loop : -0.87 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 117 HIS 0.005 0.001 HIS K 136 PHE 0.017 0.001 PHE C 42 TYR 0.014 0.001 TYR J 341 ARG 0.003 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 707) hydrogen bonds : angle 4.81751 ( 1974) metal coordination : bond 0.01365 ( 16) metal coordination : angle 2.37699 ( 12) covalent geometry : bond 0.00335 (15426) covalent geometry : angle 0.56448 (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 205 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7484 (t0) cc_final: 0.7247 (t0) REVERT: B 175 GLU cc_start: 0.8371 (tp30) cc_final: 0.8125 (tp30) REVERT: D 210 TYR cc_start: 0.8677 (m-80) cc_final: 0.8133 (m-80) REVERT: E 80 ASP cc_start: 0.7835 (t70) cc_final: 0.7467 (t0) REVERT: E 181 MET cc_start: 0.2371 (tpt) cc_final: 0.1216 (mmt) REVERT: G 293 LEU cc_start: 0.8362 (mp) cc_final: 0.8006 (mt) REVERT: H 149 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7522 (mm-40) REVERT: J 222 LYS cc_start: 0.7240 (ttmt) cc_final: 0.6429 (tmtt) REVERT: K 181 MET cc_start: 0.3385 (mmm) cc_final: 0.2882 (mtp) REVERT: L 41 MET cc_start: 0.6338 (pmm) cc_final: 0.5362 (mmm) outliers start: 21 outliers final: 12 residues processed: 196 average time/residue: 0.2331 time to fit residues: 70.6955 Evaluate side-chains 171 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain D residue 248 THR 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 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: 0.9980 chunk 53 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4461 r_free = 0.4461 target = 0.210800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.154863 restraints weight = 18490.298| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.50 r_work: 0.3457 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15442 Z= 0.153 Angle : 0.571 8.645 20757 Z= 0.303 Chirality : 0.048 0.169 2317 Planarity : 0.003 0.041 2638 Dihedral : 5.169 87.809 2074 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.15 % Favored : 96.64 % Rotamer: Outliers : 1.72 % Allowed : 11.65 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 1844 helix: 1.88 (0.21), residues: 543 sheet: -0.60 (0.22), residues: 513 loop : -0.85 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 117 HIS 0.006 0.001 HIS K 136 PHE 0.019 0.002 PHE C 42 TYR 0.015 0.001 TYR J 341 ARG 0.003 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 707) hydrogen bonds : angle 4.74457 ( 1974) metal coordination : bond 0.01279 ( 16) metal coordination : angle 2.25430 ( 12) covalent geometry : bond 0.00373 (15426) covalent geometry : angle 0.56826 (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 205 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7459 (t0) cc_final: 0.7239 (t0) REVERT: D 210 TYR cc_start: 0.8667 (m-80) cc_final: 0.8025 (m-80) REVERT: E 80 ASP cc_start: 0.7908 (t70) cc_final: 0.7509 (t0) REVERT: E 121 MET cc_start: 0.7994 (tmm) cc_final: 0.7767 (tmm) REVERT: H 149 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7505 (mm-40) REVERT: J 222 LYS cc_start: 0.7252 (ttmt) cc_final: 0.6378 (tmtt) REVERT: K 63 LYS cc_start: 0.8327 (pttt) cc_final: 0.8104 (pttt) REVERT: L 41 MET cc_start: 0.6281 (pmm) cc_final: 0.5302 (mpp) outliers start: 28 outliers final: 16 residues processed: 194 average time/residue: 0.2561 time to fit residues: 76.1018 Evaluate side-chains 165 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.863 ------------------------------------------------------------------------------- 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 D residue 248 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.212545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.165142 restraints weight = 18703.697| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.52 r_work: 0.3489 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15442 Z= 0.112 Angle : 0.536 10.007 20757 Z= 0.284 Chirality : 0.048 0.179 2317 Planarity : 0.003 0.042 2638 Dihedral : 4.873 69.926 2074 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.09 % Favored : 96.69 % Rotamer: Outliers : 1.41 % Allowed : 13.86 % 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: 0.12 (0.19), residues: 1844 helix: 2.02 (0.21), residues: 543 sheet: -0.55 (0.22), residues: 513 loop : -0.81 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 117 HIS 0.004 0.001 HIS E 136 PHE 0.014 0.001 PHE C 42 TYR 0.009 0.001 TYR D 215 ARG 0.002 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 707) hydrogen bonds : angle 4.55954 ( 1974) metal coordination : bond 0.01164 ( 16) metal coordination : angle 2.06119 ( 12) covalent geometry : bond 0.00257 (15426) covalent geometry : angle 0.53369 (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 189 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.663 Fit side-chains revert: symmetry clash REVERT: D 210 TYR cc_start: 0.8689 (m-80) cc_final: 0.8122 (m-80) REVERT: E 121 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7580 (tmm) REVERT: E 181 MET cc_start: 0.1895 (tpt) cc_final: 0.0806 (mmm) REVERT: F 41 MET cc_start: 0.5874 (mmm) cc_final: 0.4972 (pmm) REVERT: H 59 GLU cc_start: 0.6583 (tm-30) cc_final: 0.6229 (tm-30) REVERT: H 149 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7656 (mm-40) REVERT: J 222 LYS cc_start: 0.7279 (ttmt) cc_final: 0.6363 (tmtt) REVERT: J 341 TYR cc_start: 0.6650 (m-80) cc_final: 0.6278 (m-80) REVERT: J 358 MET cc_start: 0.3277 (mmt) cc_final: 0.2868 (mmt) REVERT: L 41 MET cc_start: 0.6142 (pmm) cc_final: 0.5272 (mpp) outliers start: 23 outliers final: 13 residues processed: 178 average time/residue: 0.2483 time to fit residues: 67.5779 Evaluate side-chains 165 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 181 MET 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 G residue 247 MET Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain I residue 24 THR 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 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: 0.5980 chunk 174 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 85 optimal weight: 30.0000 chunk 106 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.206579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.153878 restraints weight = 18641.182| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.64 r_work: 0.3346 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15442 Z= 0.224 Angle : 0.628 9.062 20757 Z= 0.333 Chirality : 0.050 0.163 2317 Planarity : 0.004 0.041 2638 Dihedral : 5.070 67.157 2074 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.18 % Favored : 95.61 % Rotamer: Outliers : 2.02 % Allowed : 14.96 % Favored : 83.02 % 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: -0.14 (0.19), residues: 1844 helix: 1.82 (0.21), residues: 543 sheet: -0.76 (0.22), residues: 556 loop : -0.93 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 117 HIS 0.006 0.002 HIS E 136 PHE 0.024 0.002 PHE C 42 TYR 0.014 0.002 TYR B 127 ARG 0.004 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 707) hydrogen bonds : angle 4.81619 ( 1974) metal coordination : bond 0.01117 ( 16) metal coordination : angle 2.33940 ( 12) covalent geometry : bond 0.00569 (15426) covalent geometry : angle 0.62546 (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 192 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7630 (t0) cc_final: 0.7350 (t0) REVERT: D 210 TYR cc_start: 0.8714 (m-80) cc_final: 0.8140 (m-80) REVERT: D 358 MET cc_start: 0.3564 (mpp) cc_final: 0.3335 (mmt) REVERT: E 80 ASP cc_start: 0.8126 (t70) cc_final: 0.7821 (t0) REVERT: E 121 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7719 (tmm) REVERT: F 41 MET cc_start: 0.6066 (mmm) cc_final: 0.4984 (pmm) REVERT: F 56 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.4791 (mm-30) REVERT: H 59 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6449 (tm-30) REVERT: H 149 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7868 (mm-40) REVERT: J 222 LYS cc_start: 0.7236 (ttmt) cc_final: 0.6381 (tmtt) REVERT: L 41 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5293 (mpp) outliers start: 33 outliers final: 23 residues processed: 176 average time/residue: 0.2429 time to fit residues: 65.5208 Evaluate side-chains 172 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 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 59 GLU Chi-restraints excluded: chain H residue 93 LEU 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 63 LYS Chi-restraints excluded: chain K residue 93 LEU 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 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: 2.9990 chunk 42 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 135 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.210954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.163422 restraints weight = 18538.511| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.52 r_work: 0.3459 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15442 Z= 0.124 Angle : 0.554 13.166 20757 Z= 0.292 Chirality : 0.048 0.165 2317 Planarity : 0.003 0.040 2638 Dihedral : 4.805 66.906 2074 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.15 % Favored : 96.64 % Rotamer: Outliers : 2.02 % Allowed : 15.27 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1844 helix: 1.97 (0.22), residues: 543 sheet: -0.67 (0.22), residues: 553 loop : -0.87 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 117 HIS 0.005 0.001 HIS K 136 PHE 0.015 0.001 PHE C 42 TYR 0.012 0.001 TYR K 61 ARG 0.002 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 707) hydrogen bonds : angle 4.58429 ( 1974) metal coordination : bond 0.01011 ( 16) metal coordination : angle 2.01051 ( 12) covalent geometry : bond 0.00295 (15426) covalent geometry : angle 0.55251 (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 194 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7467 (t0) cc_final: 0.7195 (t0) REVERT: B 181 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6429 (ptt) REVERT: D 210 TYR cc_start: 0.8694 (m-80) cc_final: 0.8118 (m-80) REVERT: E 80 ASP cc_start: 0.8080 (t70) cc_final: 0.7785 (t0) REVERT: E 121 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7511 (tmm) REVERT: E 181 MET cc_start: 0.1793 (tpt) cc_final: 0.0908 (mmm) REVERT: F 41 MET cc_start: 0.6151 (mmm) cc_final: 0.5238 (pmm) REVERT: F 56 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.4814 (mm-30) REVERT: H 59 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6163 (tm-30) REVERT: H 149 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7716 (mm-40) REVERT: J 222 LYS cc_start: 0.7171 (ttmt) cc_final: 0.6318 (tmtt) REVERT: J 358 MET cc_start: 0.3838 (mmt) cc_final: 0.3565 (mmt) REVERT: L 41 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5180 (mpp) outliers start: 33 outliers final: 22 residues processed: 178 average time/residue: 0.2374 time to fit residues: 64.7361 Evaluate side-chains 175 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.625 ------------------------------------------------------------------------------- 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 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 249 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 59 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 60 THR Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain K residue 93 LEU 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 98 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 74 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.205525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147075 restraints weight = 18460.424| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.64 r_work: 0.3362 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15442 Z= 0.247 Angle : 0.673 22.517 20757 Z= 0.349 Chirality : 0.051 0.163 2317 Planarity : 0.004 0.039 2638 Dihedral : 5.064 59.965 2074 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.50 % Favored : 95.28 % Rotamer: Outliers : 2.15 % Allowed : 15.76 % Favored : 82.10 % 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: -0.31 (0.19), residues: 1844 helix: 1.66 (0.22), residues: 528 sheet: -0.90 (0.21), residues: 580 loop : -0.90 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 117 HIS 0.006 0.002 HIS E 136 PHE 0.024 0.002 PHE C 42 TYR 0.018 0.002 TYR E 41 ARG 0.004 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.05217 ( 707) hydrogen bonds : angle 4.84577 ( 1974) metal coordination : bond 0.00930 ( 16) metal coordination : angle 2.16102 ( 12) covalent geometry : bond 0.00628 (15426) covalent geometry : angle 0.67127 (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 189 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 1.809 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7565 (t0) cc_final: 0.7297 (t0) REVERT: B 181 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6386 (ptt) REVERT: E 80 ASP cc_start: 0.8121 (t70) cc_final: 0.7827 (t0) REVERT: E 121 MET cc_start: 0.7956 (tmm) cc_final: 0.7628 (tmm) REVERT: F 41 MET cc_start: 0.6123 (mmm) cc_final: 0.5239 (pmm) REVERT: F 56 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.4840 (mm-30) REVERT: H 59 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: H 149 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7861 (mm-40) REVERT: J 222 LYS cc_start: 0.7137 (ttmt) cc_final: 0.6279 (tmtt) REVERT: J 318 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5233 (mmt90) REVERT: J 358 MET cc_start: 0.4195 (mmt) cc_final: 0.3963 (mmt) REVERT: K 121 MET cc_start: 0.7347 (tpt) cc_final: 0.6911 (tpt) REVERT: L 41 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5244 (mpp) outliers start: 35 outliers final: 22 residues processed: 175 average time/residue: 0.2562 time to fit residues: 68.4006 Evaluate side-chains 169 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 E residue 93 LEU Chi-restraints excluded: chain E residue 115 SER 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 249 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 59 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 60 THR Chi-restraints excluded: chain K residue 63 LYS 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: 0.7980 chunk 82 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.209286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145882 restraints weight = 18415.702| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.85 r_work: 0.3392 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2644 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= 0.120 Angle : 0.566 21.878 20757 Z= 0.294 Chirality : 0.048 0.165 2317 Planarity : 0.003 0.038 2638 Dihedral : 4.707 57.382 2074 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.52 % Favored : 96.26 % Rotamer: Outliers : 1.84 % Allowed : 16.31 % 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: 0.05 (0.19), residues: 1844 helix: 2.01 (0.22), residues: 543 sheet: -0.62 (0.23), residues: 507 loop : -0.88 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 336 HIS 0.005 0.001 HIS E 136 PHE 0.014 0.001 PHE C 42 TYR 0.015 0.001 TYR E 41 ARG 0.002 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 707) hydrogen bonds : angle 4.55178 ( 1974) metal coordination : bond 0.00893 ( 16) metal coordination : angle 1.83314 ( 12) covalent geometry : bond 0.00282 (15426) covalent geometry : angle 0.56456 (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 180 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7549 (t0) cc_final: 0.7244 (t0) REVERT: B 149 GLN cc_start: 0.7778 (mm110) cc_final: 0.7493 (mm-40) REVERT: B 181 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6188 (ptt) REVERT: C 91 ASP cc_start: 0.7982 (p0) cc_final: 0.7762 (p0) REVERT: D 210 TYR cc_start: 0.8717 (m-80) cc_final: 0.8064 (m-80) REVERT: E 80 ASP cc_start: 0.8208 (t70) cc_final: 0.7906 (t0) REVERT: E 121 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7470 (tmm) REVERT: F 56 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5122 (mm-30) REVERT: H 59 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6720 (tm-30) REVERT: H 149 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7619 (mm-40) REVERT: J 222 LYS cc_start: 0.6974 (ttmt) cc_final: 0.6156 (tmtt) REVERT: J 358 MET cc_start: 0.4609 (mmt) cc_final: 0.4394 (mmt) REVERT: L 41 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5275 (mpp) outliers start: 30 outliers final: 20 residues processed: 166 average time/residue: 0.2579 time to fit residues: 64.7363 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 : 1.666 ------------------------------------------------------------------------------- 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 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 214 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 146 ILE 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 60 THR 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: 0.7980 chunk 151 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.208513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.149383 restraints weight = 18570.233| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.53 r_work: 0.3428 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15442 Z= 0.135 Angle : 0.586 21.096 20757 Z= 0.303 Chirality : 0.048 0.153 2317 Planarity : 0.003 0.038 2638 Dihedral : 4.665 54.222 2074 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.85 % Favored : 95.93 % Rotamer: Outliers : 1.53 % Allowed : 17.23 % 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: 0.07 (0.20), residues: 1844 helix: 1.98 (0.21), residues: 543 sheet: -0.58 (0.23), residues: 507 loop : -0.84 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 336 HIS 0.005 0.001 HIS K 136 PHE 0.016 0.001 PHE C 42 TYR 0.017 0.001 TYR J 341 ARG 0.002 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 707) hydrogen bonds : angle 4.58487 ( 1974) metal coordination : bond 0.00834 ( 16) metal coordination : angle 1.82614 ( 12) covalent geometry : bond 0.00326 (15426) covalent geometry : angle 0.58480 (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 172 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7444 (t0) cc_final: 0.7174 (t0) REVERT: B 149 GLN cc_start: 0.7811 (mm110) cc_final: 0.7510 (mm-40) REVERT: D 210 TYR cc_start: 0.8663 (m-80) cc_final: 0.8003 (m-80) REVERT: E 80 ASP cc_start: 0.8261 (t70) cc_final: 0.7905 (t0) REVERT: E 121 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7495 (tmm) REVERT: F 41 MET cc_start: 0.6209 (mmm) cc_final: 0.5336 (pmm) REVERT: F 56 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.4985 (mm-30) REVERT: H 59 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: H 149 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7622 (mm-40) REVERT: J 222 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6230 (tmtt) REVERT: J 358 MET cc_start: 0.4696 (mmt) cc_final: 0.4485 (mmt) REVERT: L 41 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5124 (mpp) REVERT: L 107 LEU cc_start: 0.7293 (mp) cc_final: 0.6799 (tp) outliers start: 25 outliers final: 19 residues processed: 161 average time/residue: 0.2440 time to fit residues: 60.8896 Evaluate side-chains 166 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 134 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 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 249 ILE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 59 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 60 THR 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: 0.9990 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.208408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.158542 restraints weight = 18397.253| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.64 r_work: 0.3387 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15442 Z= 0.143 Angle : 0.578 20.542 20757 Z= 0.301 Chirality : 0.048 0.158 2317 Planarity : 0.003 0.038 2638 Dihedral : 4.668 52.255 2074 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.42 % Rotamer: Outliers : 1.59 % Allowed : 17.17 % 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: 0.08 (0.20), residues: 1844 helix: 1.99 (0.21), residues: 543 sheet: -0.58 (0.23), residues: 507 loop : -0.83 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 336 HIS 0.005 0.001 HIS K 136 PHE 0.017 0.001 PHE C 42 TYR 0.017 0.001 TYR J 341 ARG 0.002 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 707) hydrogen bonds : angle 4.56990 ( 1974) metal coordination : bond 0.00757 ( 16) metal coordination : angle 1.79165 ( 12) covalent geometry : bond 0.00349 (15426) covalent geometry : angle 0.57668 (20745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7433.83 seconds wall clock time: 129 minutes 26.26 seconds (7766.26 seconds total)