Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 15 03:34:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5y_16444/10_2023/8c5y_16444.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5y_16444/10_2023/8c5y_16444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5y_16444/10_2023/8c5y_16444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5y_16444/10_2023/8c5y_16444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5y_16444/10_2023/8c5y_16444.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5y_16444/10_2023/8c5y_16444.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15078 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 44 5.16 5 C 9708 2.51 5 N 2578 2.21 5 O 2864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 93": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 15198 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1420 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain: "B" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "C" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "D" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "G" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "H" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "I" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "J" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "K" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "L" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 897 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 298 SG CYS A 218 100.781 38.199 19.306 1.00 68.58 S ATOM 320 SG CYS A 221 102.966 36.183 21.518 1.00 72.25 S ATOM 442 SG CYS A 236 104.291 37.387 18.089 1.00 70.22 S ATOM 4099 SG CYS D 218 14.845 41.257 86.768 1.00 66.19 S ATOM 4121 SG CYS D 221 12.614 41.978 83.900 1.00 70.31 S ATOM 4243 SG CYS D 236 12.969 44.566 86.746 1.00 66.39 S ATOM 7900 SG CYS G 218 53.699 92.519 19.295 1.00 69.53 S ATOM 7922 SG CYS G 221 51.510 94.158 21.868 1.00 70.11 S ATOM 8044 SG CYS G 236 49.929 92.234 18.956 1.00 73.49 S ATOM 11701 SG CYS J 218 140.233 89.729 86.412 1.00 67.67 S ATOM 11723 SG CYS J 221 142.425 88.387 83.618 1.00 74.25 S ATOM 11845 SG CYS J 236 141.756 86.268 86.751 1.00 71.09 S Time building chain proxies: 8.00, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 5.44 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 239 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 218 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 221 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 236 " pdb=" ZN D 500 " pdb="ZN ZN D 500 " - pdb=" ND1 HIS D 239 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 221 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 218 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 236 " pdb=" ZN G 500 " pdb="ZN ZN G 500 " - pdb=" NE2 HIS G 239 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 218 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 221 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 236 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 239 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 218 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 221 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 236 " Number of angles added : 12 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 22 sheets defined 34.8% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.646A pdb=" N ILE A 193 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 3.736A pdb=" N GLU A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.513A pdb=" N ILE A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.533A pdb=" N PHE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 removed outlier: 3.709A pdb=" N ILE A 311 " --> pdb=" O TYR A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 80 through 87 removed outlier: 3.669A pdb=" N LYS B 83 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 150 removed outlier: 3.648A pdb=" N HIS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 166 through 181 removed outlier: 4.241A pdb=" N LEU B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 removed outlier: 3.727A pdb=" N ILE C 19 " --> pdb=" O ILE C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 114 Proline residue: C 109 - end of helix removed outlier: 4.251A pdb=" N GLY C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 277 through 291 removed outlier: 3.587A pdb=" N ILE D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 306 Processing helix chain 'D' and resid 307 through 311 removed outlier: 4.217A pdb=" N ILE D 310 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE D 311 " --> pdb=" O TYR D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 307 through 311' Processing helix chain 'D' and resid 340 through 356 removed outlier: 4.016A pdb=" N GLU D 344 " --> pdb=" O ASP D 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 17 removed outlier: 3.609A pdb=" N ILE E 15 " --> pdb=" O TYR E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 86 removed outlier: 4.214A pdb=" N ALA E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 86' Processing helix chain 'E' and resid 118 through 150 removed outlier: 4.335A pdb=" N GLU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR E 150 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 167 through 181 removed outlier: 3.932A pdb=" N GLU E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET E 181 " --> pdb=" O TYR E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 114 Proline residue: F 109 - end of helix removed outlier: 3.686A pdb=" N GLY F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 193 Processing helix chain 'G' and resid 267 through 275 Processing helix chain 'G' and resid 277 through 291 removed outlier: 3.522A pdb=" N SER G 291 " --> pdb=" O GLU G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 307 removed outlier: 3.562A pdb=" N PHE G 307 " --> pdb=" O ALA G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 311 removed outlier: 3.663A pdb=" N ILE G 311 " --> pdb=" O TYR G 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 308 through 311' Processing helix chain 'G' and resid 340 through 356 Processing helix chain 'H' and resid 11 through 18 Processing helix chain 'H' and resid 80 through 87 removed outlier: 3.543A pdb=" N LYS H 83 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 150 removed outlier: 3.883A pdb=" N HIS H 136 " --> pdb=" O GLU H 132 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU H 145 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE H 146 " --> pdb=" O ILE H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 166 through 181 removed outlier: 4.339A pdb=" N LEU H 170 " --> pdb=" O GLU H 166 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU H 171 " --> pdb=" O GLU H 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 19 removed outlier: 3.531A pdb=" N ILE I 19 " --> pdb=" O ILE I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 114 Proline residue: I 109 - end of helix removed outlier: 3.955A pdb=" N GLY I 113 " --> pdb=" O PRO I 109 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 193 Processing helix chain 'J' and resid 267 through 275 Processing helix chain 'J' and resid 277 through 291 removed outlier: 3.592A pdb=" N ILE J 281 " --> pdb=" O SER J 277 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER J 291 " --> pdb=" O GLU J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 306 Processing helix chain 'J' and resid 340 through 356 Processing helix chain 'K' and resid 11 through 17 removed outlier: 3.802A pdb=" N ILE K 15 " --> pdb=" O TYR K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 86 removed outlier: 4.233A pdb=" N ALA K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS K 86 " --> pdb=" O THR K 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 81 through 86' Processing helix chain 'K' and resid 118 through 150 removed outlier: 3.523A pdb=" N TRP K 122 " --> pdb=" O HIS K 118 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU K 145 " --> pdb=" O LYS K 141 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE K 146 " --> pdb=" O ILE K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 167 through 181 removed outlier: 4.019A pdb=" N GLU K 171 " --> pdb=" O GLU K 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 19 Processing helix chain 'L' and resid 94 through 114 Proline residue: L 109 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 187 removed outlier: 6.307A pdb=" N THR A 186 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ARG A 203 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLU A 314 " --> pdb=" O ASP A 338 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP A 338 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 316 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TRP A 336 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ARG A 318 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N TYR A 260 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N LEU A 331 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 262 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA A 333 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A 264 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N SER A 335 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N PHE A 266 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N GLU A 337 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 245 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR A 215 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET A 247 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 213 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A 249 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG A 211 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASP A 251 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL A 209 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 253 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 228 removed outlier: 3.584A pdb=" N VAL A 233 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 8 through 9 Processing sheet with id=AA4, first strand: chain 'B' and resid 8 through 9 removed outlier: 7.526A pdb=" N LEU B 93 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS B 116 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN B 95 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 114 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 97 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS B 107 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TRP B 74 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE B 78 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 11.398A pdb=" N GLY B 113 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.525A pdb=" N VAL C 12 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ILE C 29 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG C 71 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ALA C 83 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 73 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE C 81 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASN C 75 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE C 79 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N ILE C 79 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE C 52 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 81 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 34 " --> pdb=" O TRP C 43 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP C 45 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL C 32 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 186 through 187 removed outlier: 6.292A pdb=" N THR D 186 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ARG D 203 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL D 316 " --> pdb=" O TRP D 336 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TRP D 336 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ARG D 318 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N TYR D 260 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LEU D 331 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG D 262 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA D 333 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR D 264 " --> pdb=" O ALA D 333 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER D 335 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N PHE D 266 " --> pdb=" O SER D 335 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N GLU D 337 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY D 253 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL D 209 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASP D 255 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA D 207 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 226 through 228 removed outlier: 3.565A pdb=" N VAL D 233 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AB1, first strand: chain 'E' and resid 54 through 55 removed outlier: 8.527A pdb=" N VAL E 72 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ILE E 109 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP E 74 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL E 111 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU E 76 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY E 113 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 12.492A pdb=" N PHE E 78 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 16.443A pdb=" N SER E 115 " --> pdb=" O PHE E 78 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE E 97 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL E 114 " --> pdb=" O GLN E 95 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN E 95 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LYS E 116 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU E 93 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 13 removed outlier: 6.573A pdb=" N ARG F 67 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE F 86 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE F 69 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS F 80 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ILE F 79 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE F 52 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET F 41 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL F 35 " --> pdb=" O MET F 41 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP F 43 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 186 through 187 removed outlier: 6.343A pdb=" N THR G 186 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ARG G 203 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N GLU G 314 " --> pdb=" O ASP G 338 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP G 338 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL G 316 " --> pdb=" O TRP G 336 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP G 336 " --> pdb=" O VAL G 316 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG G 318 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU G 329 " --> pdb=" O TYR G 260 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG G 262 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE G 266 " --> pdb=" O ALA G 333 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N SER G 335 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY G 253 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL G 209 " --> pdb=" O GLY G 253 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP G 255 " --> pdb=" O ALA G 207 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA G 207 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 226 through 228 removed outlier: 3.601A pdb=" N VAL G 233 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 8 through 9 Processing sheet with id=AB6, first strand: chain 'H' and resid 8 through 9 removed outlier: 7.771A pdb=" N LEU H 93 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS H 116 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN H 95 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL H 114 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE H 97 " --> pdb=" O GLU H 112 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL H 72 " --> pdb=" O LYS H 107 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N ILE H 109 " --> pdb=" O VAL H 72 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TRP H 74 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL H 111 " --> pdb=" O TRP H 74 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU H 76 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLY H 113 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 12.475A pdb=" N PHE H 78 " --> pdb=" O GLY H 113 " (cutoff:3.500A) removed outlier: 16.439A pdb=" N SER H 115 " --> pdb=" O PHE H 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AB8, first strand: chain 'I' and resid 12 through 13 removed outlier: 6.451A pdb=" N VAL I 12 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N ILE I 29 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG I 71 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ALA I 83 " --> pdb=" O ARG I 71 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE I 73 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE I 81 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASN I 75 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE I 79 " --> pdb=" O ASN I 75 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ILE I 79 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE I 52 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE I 81 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS I 34 " --> pdb=" O TRP I 43 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP I 45 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL I 32 " --> pdb=" O ASP I 45 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.583A pdb=" N THR J 186 " --> pdb=" O GLU J 201 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ARG J 203 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL J 316 " --> pdb=" O TRP J 336 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP J 336 " --> pdb=" O VAL J 316 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARG J 318 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N TYR J 260 " --> pdb=" O LEU J 329 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N LEU J 331 " --> pdb=" O TYR J 260 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG J 262 " --> pdb=" O LEU J 331 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA J 333 " --> pdb=" O ARG J 262 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR J 264 " --> pdb=" O ALA J 333 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER J 335 " --> pdb=" O THR J 264 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N PHE J 266 " --> pdb=" O SER J 335 " (cutoff:3.500A) removed outlier: 11.028A pdb=" N GLU J 337 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE J 245 " --> pdb=" O TYR J 215 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR J 215 " --> pdb=" O ILE J 245 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N MET J 247 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU J 213 " --> pdb=" O MET J 247 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE J 249 " --> pdb=" O ARG J 211 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG J 211 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASP J 251 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL J 209 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY J 253 " --> pdb=" O ALA J 207 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 226 through 227 Processing sheet with id=AC2, first strand: chain 'K' and resid 19 through 21 Processing sheet with id=AC3, first strand: chain 'K' and resid 54 through 55 removed outlier: 8.718A pdb=" N VAL K 72 " --> pdb=" O LYS K 107 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N ILE K 109 " --> pdb=" O VAL K 72 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP K 74 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL K 111 " --> pdb=" O TRP K 74 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU K 76 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLY K 113 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 12.441A pdb=" N PHE K 78 " --> pdb=" O GLY K 113 " (cutoff:3.500A) removed outlier: 16.511A pdb=" N SER K 115 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE K 109 " --> pdb=" O ALA K 101 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA K 101 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL K 111 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS K 99 " --> pdb=" O VAL K 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 12 through 13 removed outlier: 6.490A pdb=" N VAL L 12 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE L 29 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG L 67 " --> pdb=" O ILE L 86 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE L 86 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE L 69 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS L 80 " --> pdb=" O ILE L 73 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN L 75 " --> pdb=" O GLY L 78 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY L 78 " --> pdb=" O ASN L 75 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ILE L 79 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE L 52 " --> pdb=" O ILE L 79 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE L 81 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET L 41 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL L 35 " --> pdb=" O MET L 41 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP L 43 " --> pdb=" O ILE L 33 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.01 Time building geometry restraints manager: 5.85 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: 100.18 - 108.30: 502 108.30 - 116.42: 10042 116.42 - 124.54: 9963 124.54 - 132.66: 208 132.66 - 140.78: 30 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 2.440 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 2.520 nonbonded pdb=" OD2 ASP A 251 " pdb=" NH2 ARG A 262 " model vdw 2.165 2.520 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 184 through 358 or resid 500)) selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = (chain 'C' and resid 8 through 117) selection = (chain 'F' and resid 8 through 117) selection = (chain 'I' and resid 8 through 117) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 12.510 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 42.150 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.640 ------------------------------------------------------------------------------- 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 : 0.004 0.053 15426 Z= 0.291 Angle : 0.708 20.095 20745 Z= 0.394 Chirality : 0.052 0.649 2317 Planarity : 0.004 0.075 2638 Dihedral : 14.436 89.668 5991 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.42 % Favored : 96.26 % Rotamer: Outliers : 0.18 % Allowed : 0.37 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 1844 helix: 1.50 (0.22), residues: 533 sheet: -0.26 (0.22), residues: 530 loop : -0.78 (0.22), residues: 781 *********************** 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 fitting. rotamer outliers: 3 poor density : 219 time to evaluate : 1.915 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 221 average time/residue: 0.2457 time to fit residues: 82.5668 Evaluate side-chains 166 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1309 time to fit residues: 2.7213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 94 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN E 30 ASN F 64 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15426 Z= 0.274 Angle : 0.607 8.907 20745 Z= 0.325 Chirality : 0.049 0.171 2317 Planarity : 0.004 0.051 2638 Dihedral : 5.310 75.655 2074 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.20 % Favored : 96.53 % Rotamer: Outliers : 1.04 % Allowed : 8.89 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 1844 helix: 1.66 (0.21), residues: 543 sheet: -0.33 (0.22), residues: 559 loop : -0.82 (0.22), residues: 742 *********************** 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 204 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.821 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 200 average time/residue: 0.2462 time to fit residues: 76.2257 Evaluate side-chains 169 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1390 time to fit residues: 5.4214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN H 149 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15426 Z= 0.375 Angle : 0.639 8.581 20745 Z= 0.342 Chirality : 0.051 0.181 2317 Planarity : 0.004 0.041 2638 Dihedral : 5.511 86.149 2074 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.96 % Favored : 95.82 % Rotamer: Outliers : 1.47 % Allowed : 11.34 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 1844 helix: 1.64 (0.21), residues: 543 sheet: -0.65 (0.22), residues: 547 loop : -0.97 (0.22), residues: 754 *********************** 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 197 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 185 average time/residue: 0.2505 time to fit residues: 70.7027 Evaluate side-chains 169 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1372 time to fit residues: 5.1681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN H 149 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15426 Z= 0.263 Angle : 0.577 8.236 20745 Z= 0.307 Chirality : 0.049 0.172 2317 Planarity : 0.004 0.041 2638 Dihedral : 5.119 71.981 2074 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.69 % Favored : 96.10 % Rotamer: Outliers : 1.16 % Allowed : 13.18 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1844 helix: 1.81 (0.21), residues: 543 sheet: -0.66 (0.23), residues: 506 loop : -0.94 (0.21), residues: 795 *********************** 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 189 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 1.589 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 180 average time/residue: 0.2408 time to fit residues: 66.9597 Evaluate side-chains 166 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1378 time to fit residues: 5.0863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15426 Z= 0.180 Angle : 0.534 9.984 20745 Z= 0.284 Chirality : 0.048 0.172 2317 Planarity : 0.003 0.041 2638 Dihedral : 4.844 70.237 2074 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.63 % Favored : 96.15 % Rotamer: Outliers : 1.10 % Allowed : 14.16 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 1844 helix: 2.02 (0.22), residues: 543 sheet: -0.58 (0.23), residues: 505 loop : -0.88 (0.21), residues: 796 *********************** 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 fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 184 average time/residue: 0.2402 time to fit residues: 68.9245 Evaluate side-chains 156 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1444 time to fit residues: 4.7639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 14 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15426 Z= 0.158 Angle : 0.523 8.411 20745 Z= 0.278 Chirality : 0.047 0.161 2317 Planarity : 0.003 0.041 2638 Dihedral : 4.690 69.163 2074 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.09 % Favored : 96.69 % Rotamer: Outliers : 0.55 % Allowed : 15.76 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1844 helix: 2.12 (0.22), residues: 543 sheet: -0.53 (0.23), residues: 511 loop : -0.84 (0.22), residues: 790 *********************** 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 173 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 168 average time/residue: 0.2581 time to fit residues: 66.3051 Evaluate side-chains 158 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1414 time to fit residues: 3.8979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 9.9990 chunk 20 optimal weight: 0.0770 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 162 ASN H 149 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15426 Z= 0.159 Angle : 0.529 16.651 20745 Z= 0.277 Chirality : 0.047 0.165 2317 Planarity : 0.003 0.042 2638 Dihedral : 4.628 63.630 2074 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.47 % Favored : 96.31 % Rotamer: Outliers : 0.74 % Allowed : 16.13 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 1844 helix: 2.18 (0.22), residues: 543 sheet: -0.52 (0.22), residues: 514 loop : -0.85 (0.21), residues: 787 *********************** 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 173 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.820 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 169 average time/residue: 0.2512 time to fit residues: 65.4259 Evaluate side-chains 151 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2050 time to fit residues: 4.5817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15426 Z= 0.230 Angle : 0.582 18.304 20745 Z= 0.301 Chirality : 0.048 0.159 2317 Planarity : 0.003 0.041 2638 Dihedral : 4.663 58.367 2074 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.80 % Favored : 95.93 % Rotamer: Outliers : 0.55 % Allowed : 17.23 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 1844 helix: 2.07 (0.22), residues: 543 sheet: -0.53 (0.22), residues: 511 loop : -0.85 (0.21), residues: 790 *********************** 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 166 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 1.716 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 159 average time/residue: 0.2419 time to fit residues: 60.1373 Evaluate side-chains 157 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1361 time to fit residues: 3.4692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 149 optimal weight: 0.3980 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15426 Z= 0.241 Angle : 0.590 20.702 20745 Z= 0.306 Chirality : 0.048 0.169 2317 Planarity : 0.003 0.040 2638 Dihedral : 4.705 55.260 2074 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.69 % Favored : 96.10 % Rotamer: Outliers : 0.25 % Allowed : 17.90 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1844 helix: 2.09 (0.22), residues: 544 sheet: -0.55 (0.23), residues: 505 loop : -0.87 (0.21), residues: 795 *********************** 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 163 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 1.854 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 160 average time/residue: 0.2476 time to fit residues: 61.3944 Evaluate side-chains 156 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1285 time to fit residues: 3.1435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 183 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN H 149 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15426 Z= 0.224 Angle : 0.582 20.175 20745 Z= 0.302 Chirality : 0.048 0.154 2317 Planarity : 0.003 0.039 2638 Dihedral : 4.644 53.552 2074 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.69 % Favored : 96.04 % Rotamer: Outliers : 0.25 % Allowed : 18.09 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1844 helix: 2.10 (0.22), residues: 544 sheet: -0.50 (0.23), residues: 520 loop : -0.83 (0.22), residues: 780 ********************** 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 155 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.655 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 153 average time/residue: 0.2488 time to fit residues: 59.4520 Evaluate side-chains 153 residues out of total 1631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1413 time to fit residues: 3.5715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 18 optimal weight: 0.0020 chunk 26 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.211459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150553 restraints weight = 18651.274| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.63 r_work: 0.3479 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15426 Z= 0.149 Angle : 0.540 19.681 20745 Z= 0.280 Chirality : 0.047 0.147 2317 Planarity : 0.003 0.038 2638 Dihedral : 4.446 51.618 2074 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.25 % Favored : 96.53 % Rotamer: Outliers : 0.18 % Allowed : 18.09 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1844 helix: 2.18 (0.22), residues: 548 sheet: -0.46 (0.22), residues: 530 loop : -0.71 (0.22), residues: 766 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2944.46 seconds wall clock time: 54 minutes 20.14 seconds (3260.14 seconds total)