Starting phenix.real_space_refine on Mon Aug 25 09:47:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c5y_16444/08_2025/8c5y_16444.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5y_16444/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8c5y_16444/08_2025/8c5y_16444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5y_16444/08_2025/8c5y_16444.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c5y_16444/08_2025/8c5y_16444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5y_16444/08_2025/8c5y_16444.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.02, per 1000 atoms: 0.20 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: 1.28 Conformation dependent library (CDL) restraints added in 417.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.53 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: 2.24 Time building geometry restraints manager: 1.70 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 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: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.500 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG E 38 TYR 0.020 0.002 TYR B 177 PHE 0.020 0.002 PHE C 42 TRP 0.021 0.002 TRP I 117 HIS 0.010 0.002 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00450 (15426) covalent geometry : angle 0.70761 (20745) hydrogen bonds : bond 0.15083 ( 707) hydrogen bonds : angle 6.43456 ( 1974) metal coordination : bond 0.02491 ( 16) metal coordination : angle 3.14276 ( 12) *********************** 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 : 0.361 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: 0.1060 time to fit residues: 35.8869 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 : 0.511 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN B 162 ASN C 64 GLN E 30 ASN F 64 GLN K 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.213988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.169375 restraints weight = 18372.508| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.29 r_work: 0.3532 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15442 Z= 0.214 Angle : 0.654 9.064 20757 Z= 0.348 Chirality : 0.050 0.174 2317 Planarity : 0.004 0.054 2638 Dihedral : 5.619 82.200 2076 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.58 % Favored : 96.20 % Rotamer: Outliers : 1.16 % Allowed : 8.34 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.19), residues: 1844 helix: 1.57 (0.21), residues: 543 sheet: -0.37 (0.22), residues: 531 loop : -0.95 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 342 TYR 0.017 0.002 TYR G 215 PHE 0.022 0.002 PHE C 42 TRP 0.015 0.002 TRP D 336 HIS 0.006 0.002 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00535 (15426) covalent geometry : angle 0.65027 (20745) hydrogen bonds : bond 0.05285 ( 707) hydrogen bonds : angle 5.17284 ( 1974) metal coordination : bond 0.01605 ( 16) metal coordination : angle 2.79946 ( 12) *********************** 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 206 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.626 Fit side-chains REVERT: C 88 ASP cc_start: 0.8638 (t0) cc_final: 0.8390 (t0) REVERT: D 210 TYR cc_start: 0.8771 (m-80) cc_final: 0.8278 (m-80) REVERT: E 68 ASP cc_start: 0.7467 (p0) cc_final: 0.7250 (p0) REVERT: E 80 ASP cc_start: 0.7699 (t70) cc_final: 0.7320 (t0) REVERT: H 149 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7772 (mm-40) REVERT: J 222 LYS cc_start: 0.7278 (ttmt) cc_final: 0.6448 (tmtt) REVERT: K 181 MET cc_start: 0.3420 (mmm) cc_final: 0.2739 (mtp) REVERT: L 41 MET cc_start: 0.6461 (pmm) cc_final: 0.5318 (mpp) REVERT: L 93 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7545 (p0) outliers start: 19 outliers final: 12 residues processed: 199 average time/residue: 0.0983 time to fit residues: 30.3949 Evaluate side-chains 178 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 335 SER 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 249 ILE Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain 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 161 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 172 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 160 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 H 149 GLN K 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.209543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.154989 restraints weight = 18768.928| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.63 r_work: 0.3420 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15442 Z= 0.187 Angle : 0.609 8.388 20757 Z= 0.326 Chirality : 0.050 0.169 2317 Planarity : 0.004 0.040 2638 Dihedral : 5.452 77.418 2076 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.42 % Favored : 96.37 % Rotamer: Outliers : 1.66 % Allowed : 10.79 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.19), residues: 1844 helix: 1.68 (0.21), residues: 543 sheet: -0.49 (0.22), residues: 538 loop : -1.05 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 38 TYR 0.016 0.001 TYR J 341 PHE 0.021 0.002 PHE C 42 TRP 0.015 0.001 TRP F 117 HIS 0.006 0.002 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00466 (15426) covalent geometry : angle 0.60598 (20745) hydrogen bonds : bond 0.04849 ( 707) hydrogen bonds : angle 4.93371 ( 1974) metal coordination : bond 0.01420 ( 16) metal coordination : angle 2.51721 ( 12) *********************** 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 204 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7517 (t0) cc_final: 0.7254 (t0) REVERT: D 210 TYR cc_start: 0.8719 (m-80) cc_final: 0.8161 (m-80) REVERT: E 80 ASP cc_start: 0.7956 (t70) cc_final: 0.7610 (t0) REVERT: E 121 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7706 (tmm) REVERT: E 181 MET cc_start: 0.2138 (tpt) cc_final: 0.1166 (mmm) REVERT: G 293 LEU cc_start: 0.8389 (mp) cc_final: 0.8038 (mt) REVERT: H 149 GLN cc_start: 0.7956 (mm110) cc_final: 0.7548 (mm-40) REVERT: J 222 LYS cc_start: 0.7267 (ttmt) cc_final: 0.6407 (tmtt) REVERT: J 337 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7165 (tm-30) REVERT: K 181 MET cc_start: 0.3456 (mmm) cc_final: 0.2926 (mtp) REVERT: L 41 MET cc_start: 0.6363 (pmm) cc_final: 0.5238 (mpp) outliers start: 27 outliers final: 15 residues processed: 194 average time/residue: 0.1025 time to fit residues: 30.8055 Evaluate side-chains 171 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 E residue 121 MET Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 140 optimal weight: 0.9980 chunk 181 optimal weight: 0.0370 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN K 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.213429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.158402 restraints weight = 18606.315| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.53 r_work: 0.3504 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15442 Z= 0.106 Angle : 0.522 8.509 20757 Z= 0.279 Chirality : 0.047 0.149 2317 Planarity : 0.003 0.040 2638 Dihedral : 4.798 74.712 2074 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.09 % Favored : 96.69 % Rotamer: Outliers : 1.53 % Allowed : 12.32 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.19), residues: 1844 helix: 1.98 (0.21), residues: 543 sheet: -0.57 (0.23), residues: 514 loop : -0.84 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.009 0.001 TYR G 215 PHE 0.014 0.001 PHE C 42 TRP 0.017 0.001 TRP C 117 HIS 0.005 0.001 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00238 (15426) covalent geometry : angle 0.51926 (20745) hydrogen bonds : bond 0.03643 ( 707) hydrogen bonds : angle 4.57598 ( 1974) metal coordination : bond 0.01212 ( 16) metal coordination : angle 2.16875 ( 12) *********************** 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 214 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7319 (t0) cc_final: 0.7109 (t0) REVERT: B 149 GLN cc_start: 0.7691 (mm110) cc_final: 0.7439 (mm-40) REVERT: D 210 TYR cc_start: 0.8663 (m-80) cc_final: 0.8032 (m-80) REVERT: E 80 ASP cc_start: 0.7918 (t70) cc_final: 0.7512 (t0) REVERT: E 121 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7619 (tmm) REVERT: F 41 MET cc_start: 0.6211 (mmm) cc_final: 0.4991 (pmm) REVERT: G 293 LEU cc_start: 0.8360 (mp) cc_final: 0.8008 (mt) REVERT: I 91 ASP cc_start: 0.7794 (p0) cc_final: 0.7585 (p0) REVERT: J 222 LYS cc_start: 0.7220 (ttmt) cc_final: 0.6332 (tmtt) REVERT: J 341 TYR cc_start: 0.6476 (m-80) cc_final: 0.6242 (m-80) REVERT: L 41 MET cc_start: 0.6306 (pmm) cc_final: 0.5366 (mpp) outliers start: 25 outliers final: 12 residues processed: 203 average time/residue: 0.1010 time to fit residues: 31.7824 Evaluate side-chains 163 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 MET 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 358 MET Chi-restraints excluded: chain H residue 146 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 74 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 63 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN K 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.210809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153708 restraints weight = 18553.970| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.65 r_work: 0.3446 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15442 Z= 0.149 Angle : 0.569 10.321 20757 Z= 0.302 Chirality : 0.049 0.174 2317 Planarity : 0.003 0.041 2638 Dihedral : 4.877 72.642 2074 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.47 % Favored : 96.31 % Rotamer: Outliers : 1.72 % Allowed : 13.92 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.19), residues: 1844 helix: 2.00 (0.21), residues: 543 sheet: -0.62 (0.22), residues: 553 loop : -0.86 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 71 TYR 0.017 0.001 TYR E 41 PHE 0.018 0.002 PHE C 42 TRP 0.015 0.001 TRP I 117 HIS 0.005 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00365 (15426) covalent geometry : angle 0.56696 (20745) hydrogen bonds : bond 0.04229 ( 707) hydrogen bonds : angle 4.62908 ( 1974) metal coordination : bond 0.01162 ( 16) metal coordination : angle 2.13918 ( 12) *********************** 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 191 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7375 (t0) cc_final: 0.7164 (t0) REVERT: A 271 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: B 149 GLN cc_start: 0.7760 (mm110) cc_final: 0.7465 (mm-40) REVERT: D 210 TYR cc_start: 0.8682 (m-80) cc_final: 0.8015 (m-80) REVERT: E 80 ASP cc_start: 0.7983 (t70) cc_final: 0.7623 (t0) REVERT: E 121 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7636 (tmm) REVERT: E 181 MET cc_start: 0.1596 (tpt) cc_final: 0.0674 (mmm) REVERT: F 41 MET cc_start: 0.6375 (mmm) cc_final: 0.5208 (pmm) REVERT: F 56 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.4927 (mm-30) REVERT: H 149 GLN cc_start: 0.7877 (mm110) cc_final: 0.7497 (mm-40) REVERT: I 91 ASP cc_start: 0.7819 (p0) cc_final: 0.7601 (p0) REVERT: J 222 LYS cc_start: 0.7211 (ttmt) cc_final: 0.6352 (tmtt) REVERT: J 341 TYR cc_start: 0.6644 (m-80) cc_final: 0.6208 (m-80) REVERT: K 63 LYS cc_start: 0.8334 (pttt) cc_final: 0.8106 (pttt) REVERT: L 41 MET cc_start: 0.6301 (pmm) cc_final: 0.5374 (mpp) outliers start: 28 outliers final: 15 residues processed: 180 average time/residue: 0.0885 time to fit residues: 24.9389 Evaluate side-chains 169 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU 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 358 MET Chi-restraints excluded: chain H residue 24 GLU 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 156 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN ** 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 = 0.4427 r_free = 0.4427 target = 0.207023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.151755 restraints weight = 18471.337| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.53 r_work: 0.3401 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15442 Z= 0.248 Angle : 0.651 9.109 20757 Z= 0.344 Chirality : 0.051 0.169 2317 Planarity : 0.004 0.040 2638 Dihedral : 5.202 70.423 2074 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.23 % Favored : 95.55 % Rotamer: Outliers : 1.90 % Allowed : 15.02 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.19), residues: 1844 helix: 1.71 (0.21), residues: 528 sheet: -0.75 (0.22), residues: 511 loop : -0.96 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 8 TYR 0.014 0.002 TYR B 127 PHE 0.024 0.002 PHE C 42 TRP 0.012 0.001 TRP I 117 HIS 0.007 0.002 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00628 (15426) covalent geometry : angle 0.64878 (20745) hydrogen bonds : bond 0.05253 ( 707) hydrogen bonds : angle 4.85621 ( 1974) metal coordination : bond 0.01040 ( 16) metal coordination : angle 2.43698 ( 12) *********************** 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 184 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: B 149 GLN cc_start: 0.8020 (mm110) cc_final: 0.7748 (mm-40) REVERT: D 210 TYR cc_start: 0.8748 (m-80) cc_final: 0.8155 (m-80) REVERT: D 358 MET cc_start: 0.3620 (mpp) cc_final: 0.3364 (mmt) REVERT: E 80 ASP cc_start: 0.8096 (t70) cc_final: 0.7814 (t0) REVERT: E 121 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7625 (tmm) REVERT: E 181 MET cc_start: 0.1032 (tpt) cc_final: 0.0780 (mmm) REVERT: F 41 MET cc_start: 0.6183 (mmm) cc_final: 0.5263 (pmm) REVERT: F 56 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.4717 (mm-30) REVERT: J 222 LYS cc_start: 0.7184 (ttmt) cc_final: 0.6301 (tmtt) REVERT: J 358 MET cc_start: 0.3539 (mmt) cc_final: 0.3181 (mmt) REVERT: K 63 LYS cc_start: 0.8447 (pttt) cc_final: 0.8157 (pttt) REVERT: L 41 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.5229 (mpp) outliers start: 31 outliers final: 22 residues processed: 170 average time/residue: 0.0906 time to fit residues: 24.2628 Evaluate side-chains 167 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 180 MET Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 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 93 LEU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 75 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 0.3980 chunk 134 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.210702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155414 restraints weight = 18304.863| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.64 r_work: 0.3442 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2441 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= 0.125 Angle : 0.559 12.913 20757 Z= 0.294 Chirality : 0.048 0.162 2317 Planarity : 0.003 0.040 2638 Dihedral : 4.810 68.892 2074 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.25 % Favored : 96.53 % Rotamer: Outliers : 2.21 % Allowed : 15.45 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.19), residues: 1844 helix: 1.90 (0.22), residues: 528 sheet: -0.61 (0.23), residues: 507 loop : -0.88 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.015 0.001 TYR J 341 PHE 0.015 0.001 PHE C 42 TRP 0.014 0.001 TRP C 117 HIS 0.005 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00296 (15426) covalent geometry : angle 0.55724 (20745) hydrogen bonds : bond 0.03980 ( 707) hydrogen bonds : angle 4.60812 ( 1974) metal coordination : bond 0.00995 ( 16) metal coordination : angle 2.00498 ( 12) *********************** 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 187 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7354 (t0) cc_final: 0.7076 (t0) REVERT: D 210 TYR cc_start: 0.8683 (m-80) cc_final: 0.8004 (m-80) REVERT: E 80 ASP cc_start: 0.8168 (t70) cc_final: 0.7877 (t0) REVERT: E 121 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7561 (tmm) REVERT: E 181 MET cc_start: 0.1178 (tpt) cc_final: 0.0843 (mmm) REVERT: F 41 MET cc_start: 0.6243 (mmm) cc_final: 0.5298 (pmm) REVERT: F 56 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.4955 (mm-30) REVERT: H 149 GLN cc_start: 0.7916 (mm110) cc_final: 0.7615 (mm-40) REVERT: I 103 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8128 (tt) REVERT: J 222 LYS cc_start: 0.7088 (ttmt) cc_final: 0.6261 (tmtt) REVERT: K 63 LYS cc_start: 0.8357 (pttt) cc_final: 0.8079 (pttt) REVERT: L 41 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5257 (mpp) REVERT: L 107 LEU cc_start: 0.7315 (mp) cc_final: 0.6993 (tp) outliers start: 36 outliers final: 20 residues processed: 173 average time/residue: 0.0976 time to fit residues: 26.2971 Evaluate side-chains 162 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 107 LEU 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 H residue 24 GLU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 318 ARG Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 98 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 94 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 chunk 181 optimal weight: 0.0030 chunk 42 optimal weight: 0.0030 chunk 35 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN K 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.212201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.158113 restraints weight = 18442.757| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.45 r_work: 0.3481 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15442 Z= 0.108 Angle : 0.561 23.162 20757 Z= 0.288 Chirality : 0.047 0.148 2317 Planarity : 0.003 0.039 2638 Dihedral : 4.622 62.736 2074 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.42 % Rotamer: Outliers : 1.47 % Allowed : 16.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.19), residues: 1844 helix: 2.07 (0.22), residues: 543 sheet: -0.53 (0.23), residues: 507 loop : -0.85 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.020 0.001 TYR J 341 PHE 0.013 0.001 PHE J 252 TRP 0.016 0.001 TRP D 336 HIS 0.004 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00245 (15426) covalent geometry : angle 0.55907 (20745) hydrogen bonds : bond 0.03611 ( 707) hydrogen bonds : angle 4.50104 ( 1974) metal coordination : bond 0.00935 ( 16) metal coordination : angle 1.91604 ( 12) *********************** 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 179 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7204 (t0) cc_final: 0.6948 (t0) REVERT: B 149 GLN cc_start: 0.7759 (mm110) cc_final: 0.7371 (mm-40) REVERT: B 181 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6815 (tpp) REVERT: C 91 ASP cc_start: 0.7870 (p0) cc_final: 0.7668 (p0) REVERT: D 210 TYR cc_start: 0.8691 (m-80) cc_final: 0.8017 (m-80) REVERT: E 67 ASP cc_start: 0.7095 (m-30) cc_final: 0.6682 (m-30) REVERT: E 80 ASP cc_start: 0.8176 (t0) cc_final: 0.7887 (t0) REVERT: E 121 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7555 (tmm) REVERT: F 56 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.4984 (mm-30) REVERT: I 103 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8148 (tt) REVERT: J 222 LYS cc_start: 0.7073 (ttmt) cc_final: 0.6250 (tmtt) REVERT: J 358 MET cc_start: 0.3783 (mmt) cc_final: 0.3498 (mmt) REVERT: K 63 LYS cc_start: 0.8342 (pttt) cc_final: 0.8124 (pttt) REVERT: K 180 MET cc_start: 0.3829 (OUTLIER) cc_final: 0.2938 (mmp) REVERT: L 41 MET cc_start: 0.6047 (OUTLIER) cc_final: 0.5124 (mpp) REVERT: L 107 LEU cc_start: 0.7272 (mp) cc_final: 0.7012 (tp) outliers start: 24 outliers final: 15 residues processed: 169 average time/residue: 0.0949 time to fit residues: 24.8280 Evaluate side-chains 167 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 H residue 24 GLU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 318 ARG Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 180 MET 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 4 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.210474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.153902 restraints weight = 18386.483| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.71 r_work: 0.3430 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2633 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= 0.137 Angle : 0.571 21.869 20757 Z= 0.297 Chirality : 0.048 0.161 2317 Planarity : 0.003 0.038 2638 Dihedral : 4.627 57.865 2074 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.69 % Favored : 96.10 % Rotamer: Outliers : 1.78 % Allowed : 16.55 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.20), residues: 1844 helix: 2.02 (0.22), residues: 543 sheet: -0.52 (0.23), residues: 509 loop : -0.84 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.018 0.001 TYR J 341 PHE 0.016 0.001 PHE C 42 TRP 0.014 0.001 TRP D 336 HIS 0.005 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00331 (15426) covalent geometry : angle 0.56899 (20745) hydrogen bonds : bond 0.04029 ( 707) hydrogen bonds : angle 4.52974 ( 1974) metal coordination : bond 0.00871 ( 16) metal coordination : angle 1.87164 ( 12) *********************** 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: 29 poor density : 151 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7439 (t0) cc_final: 0.7128 (t0) REVERT: B 149 GLN cc_start: 0.7798 (mm110) cc_final: 0.7405 (mm-40) REVERT: B 181 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6860 (tpp) REVERT: D 210 TYR cc_start: 0.8697 (m-80) cc_final: 0.7968 (m-80) REVERT: E 67 ASP cc_start: 0.7164 (m-30) cc_final: 0.6744 (m-30) REVERT: E 80 ASP cc_start: 0.8215 (t0) cc_final: 0.7934 (t0) REVERT: E 121 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7552 (tmm) REVERT: E 181 MET cc_start: 0.1246 (tpt) cc_final: 0.0276 (mmt) REVERT: F 41 MET cc_start: 0.6360 (mmm) cc_final: 0.5568 (pmm) REVERT: F 56 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.4951 (mm-30) REVERT: I 103 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8118 (tt) REVERT: J 222 LYS cc_start: 0.7046 (ttmt) cc_final: 0.6218 (tmtt) REVERT: J 358 MET cc_start: 0.3907 (mmt) cc_final: 0.3671 (mmt) REVERT: K 63 LYS cc_start: 0.8366 (pttt) cc_final: 0.8156 (pttt) REVERT: K 180 MET cc_start: 0.3759 (OUTLIER) cc_final: 0.2970 (mmp) REVERT: L 41 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.5134 (mpp) REVERT: L 107 LEU cc_start: 0.7260 (mp) cc_final: 0.7005 (tp) outliers start: 29 outliers final: 20 residues processed: 167 average time/residue: 0.0913 time to fit residues: 23.8384 Evaluate side-chains 168 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 107 LEU 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 H residue 24 GLU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 318 ARG Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 121 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 161 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 176 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4465 r_free = 0.4465 target = 0.211177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155469 restraints weight = 18407.553| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.62 r_work: 0.3462 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2747 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= 0.124 Angle : 0.558 21.091 20757 Z= 0.290 Chirality : 0.048 0.154 2317 Planarity : 0.003 0.038 2638 Dihedral : 4.560 54.722 2074 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.47 % Favored : 96.31 % Rotamer: Outliers : 1.78 % Allowed : 16.68 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.20), residues: 1844 helix: 2.01 (0.22), residues: 547 sheet: -0.50 (0.23), residues: 507 loop : -0.77 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.012 0.001 TYR E 41 PHE 0.015 0.001 PHE C 42 TRP 0.016 0.001 TRP D 336 HIS 0.005 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00296 (15426) covalent geometry : angle 0.55615 (20745) hydrogen bonds : bond 0.03842 ( 707) hydrogen bonds : angle 4.49403 ( 1974) metal coordination : bond 0.00814 ( 16) metal coordination : angle 1.78574 ( 12) ********************** 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 178 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7281 (t0) cc_final: 0.6978 (t0) REVERT: B 149 GLN cc_start: 0.7832 (mm110) cc_final: 0.7475 (mm-40) REVERT: B 181 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.7010 (tpp) REVERT: D 210 TYR cc_start: 0.8713 (m-80) cc_final: 0.8005 (m-80) REVERT: E 80 ASP cc_start: 0.8192 (t0) cc_final: 0.7927 (t0) REVERT: E 121 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7556 (tmm) REVERT: F 41 MET cc_start: 0.6388 (mmm) cc_final: 0.5570 (pmm) REVERT: F 56 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.4923 (mm-30) REVERT: I 91 ASP cc_start: 0.7761 (p0) cc_final: 0.7524 (p0) REVERT: I 103 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8138 (tt) REVERT: J 222 LYS cc_start: 0.7019 (ttmt) cc_final: 0.6202 (tmtt) REVERT: J 358 MET cc_start: 0.4214 (mmt) cc_final: 0.3971 (mmt) REVERT: K 180 MET cc_start: 0.3816 (OUTLIER) cc_final: 0.3043 (mmp) REVERT: L 41 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.5131 (mpp) REVERT: L 107 LEU cc_start: 0.7284 (mp) cc_final: 0.7059 (tp) outliers start: 29 outliers final: 20 residues processed: 167 average time/residue: 0.0958 time to fit residues: 25.0721 Evaluate side-chains 171 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain 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 H residue 24 GLU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 318 ARG Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 180 MET 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 47 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 126 optimal weight: 0.0570 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.209762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.149260 restraints weight = 18552.790| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.47 r_work: 0.3445 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15442 Z= 0.125 Angle : 0.562 20.496 20757 Z= 0.292 Chirality : 0.048 0.162 2317 Planarity : 0.003 0.038 2638 Dihedral : 4.546 52.090 2074 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.63 % Favored : 96.15 % Rotamer: Outliers : 1.96 % Allowed : 16.74 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.20), residues: 1844 helix: 2.01 (0.22), residues: 547 sheet: -0.49 (0.23), residues: 507 loop : -0.74 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.013 0.001 TYR E 41 PHE 0.015 0.001 PHE C 42 TRP 0.015 0.001 TRP D 336 HIS 0.005 0.001 HIS K 136 Details of bonding type rmsd covalent geometry : bond 0.00299 (15426) covalent geometry : angle 0.56077 (20745) hydrogen bonds : bond 0.03864 ( 707) hydrogen bonds : angle 4.48238 ( 1974) metal coordination : bond 0.00775 ( 16) metal coordination : angle 1.76285 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3231.16 seconds wall clock time: 55 minutes 55.84 seconds (3355.84 seconds total)