Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 11:15:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/04_2023/6m68_30116.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/04_2023/6m68_30116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/04_2023/6m68_30116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/04_2023/6m68_30116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/04_2023/6m68_30116.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/04_2023/6m68_30116.pdb" } resolution = 4.6 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 ------------------------------------------------------------------------------- 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= 0.028 sd= 0.157 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 9975 2.51 5 N 2303 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14938 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "B" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "C" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "D" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "E" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "F" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "G" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Time building chain proxies: 7.45, per 1000 atoms: 0.50 Number of scatterers: 14938 At special positions: 0 Unit cell: (113.4, 113.4, 116.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2590 8.00 N 2303 7.00 C 9975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 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: 5.86 Conformation dependent library (CDL) restraints added in 2.3 seconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 69.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 removed outlier: 4.483A pdb=" N ILE A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 44 " --> pdb=" O CYS A 40 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.601A pdb=" N LEU A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.595A pdb=" N ALA A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.407A pdb=" N HIS A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 107 " --> pdb=" O TRP A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 108 through 129 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 156 removed outlier: 3.644A pdb=" N ASP A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 207 through 238 removed outlier: 4.234A pdb=" N ILE A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.176A pdb=" N ASN A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.752A pdb=" N VAL A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 328 through 336 removed outlier: 4.188A pdb=" N ASN A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 59 removed outlier: 4.484A pdb=" N ILE B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 44 " --> pdb=" O CYS B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.601A pdb=" N LEU B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 50 " --> pdb=" O PRO B 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.595A pdb=" N ALA B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 4.408A pdb=" N HIS B 106 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 107 " --> pdb=" O TRP B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 107' Processing helix chain 'B' and resid 108 through 129 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 156 removed outlier: 3.645A pdb=" N ASP B 147 " --> pdb=" O MET B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 207 through 238 removed outlier: 4.234A pdb=" N ILE B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 276 through 286 removed outlier: 4.175A pdb=" N ASN B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.753A pdb=" N VAL B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 316 Processing helix chain 'B' and resid 317 through 320 Processing helix chain 'B' and resid 328 through 336 removed outlier: 4.187A pdb=" N ASN B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 59 removed outlier: 4.483A pdb=" N ILE C 41 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 44 " --> pdb=" O CYS C 40 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.601A pdb=" N LEU C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 50 " --> pdb=" O PRO C 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.596A pdb=" N ALA C 78 " --> pdb=" O TRP C 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.408A pdb=" N HIS C 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 107 " --> pdb=" O TRP C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 108 through 129 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 156 removed outlier: 3.644A pdb=" N ASP C 147 " --> pdb=" O MET C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 207 through 238 removed outlier: 4.234A pdb=" N ILE C 211 " --> pdb=" O ASN C 207 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 276 through 286 removed outlier: 4.176A pdb=" N ASN C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 3.753A pdb=" N VAL C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 316 Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 328 through 336 removed outlier: 4.187A pdb=" N ASN C 332 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 59 removed outlier: 4.483A pdb=" N ILE D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 44 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.601A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 50 " --> pdb=" O PRO D 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.596A pdb=" N ALA D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.407A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 107 " --> pdb=" O TRP D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 107' Processing helix chain 'D' and resid 108 through 129 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 156 removed outlier: 3.645A pdb=" N ASP D 147 " --> pdb=" O MET D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 207 through 238 removed outlier: 4.234A pdb=" N ILE D 211 " --> pdb=" O ASN D 207 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR D 234 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 254 Processing helix chain 'D' and resid 269 through 274 Processing helix chain 'D' and resid 276 through 286 removed outlier: 4.176A pdb=" N ASN D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 removed outlier: 3.752A pdb=" N VAL D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 316 Processing helix chain 'D' and resid 317 through 320 Processing helix chain 'D' and resid 328 through 336 removed outlier: 4.187A pdb=" N ASN D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 59 removed outlier: 4.483A pdb=" N ILE E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY E 44 " --> pdb=" O CYS E 40 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.601A pdb=" N LEU E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 removed outlier: 3.596A pdb=" N ALA E 78 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 removed outlier: 4.408A pdb=" N HIS E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS E 107 " --> pdb=" O TRP E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 107' Processing helix chain 'E' and resid 108 through 129 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 156 removed outlier: 3.645A pdb=" N ASP E 147 " --> pdb=" O MET E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 207 through 238 removed outlier: 4.235A pdb=" N ILE E 211 " --> pdb=" O ASN E 207 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG E 217 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 222 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR E 234 " --> pdb=" O TYR E 230 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 254 Processing helix chain 'E' and resid 269 through 274 Processing helix chain 'E' and resid 276 through 286 removed outlier: 4.176A pdb=" N ASN E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 3.753A pdb=" N VAL E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 316 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 328 through 336 removed outlier: 4.187A pdb=" N ASN E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 59 removed outlier: 4.483A pdb=" N ILE F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.601A pdb=" N LEU F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 50 " --> pdb=" O PRO F 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE F 58 " --> pdb=" O PHE F 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 removed outlier: 3.596A pdb=" N ALA F 78 " --> pdb=" O TRP F 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 removed outlier: 4.407A pdb=" N HIS F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS F 107 " --> pdb=" O TRP F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 107' Processing helix chain 'F' and resid 108 through 129 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 156 removed outlier: 3.644A pdb=" N ASP F 147 " --> pdb=" O MET F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 198 through 203 Processing helix chain 'F' and resid 207 through 238 removed outlier: 4.235A pdb=" N ILE F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU F 218 " --> pdb=" O ILE F 214 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE F 222 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR F 234 " --> pdb=" O TYR F 230 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 254 Processing helix chain 'F' and resid 269 through 274 Processing helix chain 'F' and resid 276 through 286 removed outlier: 4.176A pdb=" N ASN F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 295 removed outlier: 3.752A pdb=" N VAL F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 328 through 336 removed outlier: 4.187A pdb=" N ASN F 332 " --> pdb=" O LEU F 328 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 59 removed outlier: 4.483A pdb=" N ILE G 41 " --> pdb=" O MET G 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY G 44 " --> pdb=" O CYS G 40 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.601A pdb=" N LEU G 49 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 50 " --> pdb=" O PRO G 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 58 " --> pdb=" O PHE G 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 removed outlier: 3.595A pdb=" N ALA G 78 " --> pdb=" O TRP G 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA G 86 " --> pdb=" O SER G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 removed outlier: 4.407A pdb=" N HIS G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS G 107 " --> pdb=" O TRP G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 103 through 107' Processing helix chain 'G' and resid 108 through 129 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 156 removed outlier: 3.645A pdb=" N ASP G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 207 through 238 removed outlier: 4.235A pdb=" N ILE G 211 " --> pdb=" O ASN G 207 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG G 217 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU G 218 " --> pdb=" O ILE G 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE G 222 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 254 Processing helix chain 'G' and resid 269 through 274 Processing helix chain 'G' and resid 276 through 286 removed outlier: 4.175A pdb=" N ASN G 280 " --> pdb=" O LEU G 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU G 281 " --> pdb=" O SER G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 295 removed outlier: 3.752A pdb=" N VAL G 291 " --> pdb=" O LEU G 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 316 Processing helix chain 'G' and resid 317 through 320 Processing helix chain 'G' and resid 328 through 336 removed outlier: 4.188A pdb=" N ASN G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU G 336 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.583A pdb=" N SER A 65 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.584A pdb=" N SER B 65 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.584A pdb=" N SER C 65 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.584A pdb=" N SER D 65 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.583A pdb=" N SER E 65 " --> pdb=" O LYS E 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.584A pdb=" N SER F 65 " --> pdb=" O LYS F 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.584A pdb=" N SER G 65 " --> pdb=" O LYS G 266 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1893 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: 3.86 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4364 1.34 - 1.46: 3605 1.46 - 1.58: 7256 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15309 Sorted by residual: bond pdb=" C LEU D 312 " pdb=" N PRO D 313 " ideal model delta sigma weight residual 1.335 1.379 -0.044 9.40e-03 1.13e+04 2.19e+01 bond pdb=" C LEU G 312 " pdb=" N PRO G 313 " ideal model delta sigma weight residual 1.335 1.379 -0.044 9.40e-03 1.13e+04 2.17e+01 bond pdb=" C LEU E 312 " pdb=" N PRO E 313 " ideal model delta sigma weight residual 1.335 1.379 -0.044 9.40e-03 1.13e+04 2.17e+01 bond pdb=" C LEU F 312 " pdb=" N PRO F 313 " ideal model delta sigma weight residual 1.335 1.378 -0.043 9.40e-03 1.13e+04 2.10e+01 bond pdb=" C LEU C 312 " pdb=" N PRO C 313 " ideal model delta sigma weight residual 1.335 1.378 -0.043 9.40e-03 1.13e+04 2.10e+01 ... (remaining 15304 not shown) Histogram of bond angle deviations from ideal: 101.08 - 107.67: 520 107.67 - 114.25: 8831 114.25 - 120.84: 7196 120.84 - 127.42: 4103 127.42 - 134.01: 175 Bond angle restraints: 20825 Sorted by residual: angle pdb=" N ILE A 268 " pdb=" CA ILE A 268 " pdb=" CB ILE A 268 " ideal model delta sigma weight residual 112.33 107.01 5.32 1.19e+00 7.06e-01 2.00e+01 angle pdb=" N ILE G 268 " pdb=" CA ILE G 268 " pdb=" CB ILE G 268 " ideal model delta sigma weight residual 112.33 107.02 5.31 1.19e+00 7.06e-01 1.99e+01 angle pdb=" N ILE C 268 " pdb=" CA ILE C 268 " pdb=" CB ILE C 268 " ideal model delta sigma weight residual 112.33 107.03 5.30 1.19e+00 7.06e-01 1.99e+01 angle pdb=" N ILE F 268 " pdb=" CA ILE F 268 " pdb=" CB ILE F 268 " ideal model delta sigma weight residual 112.33 107.03 5.30 1.19e+00 7.06e-01 1.99e+01 angle pdb=" N ILE E 268 " pdb=" CA ILE E 268 " pdb=" CB ILE E 268 " ideal model delta sigma weight residual 112.33 107.03 5.30 1.19e+00 7.06e-01 1.98e+01 ... (remaining 20820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.28: 6935 10.28 - 20.57: 1311 20.57 - 30.85: 573 30.85 - 41.13: 211 41.13 - 51.42: 84 Dihedral angle restraints: 9114 sinusoidal: 3563 harmonic: 5551 Sorted by residual: dihedral pdb=" CA VAL D 308 " pdb=" C VAL D 308 " pdb=" N TYR D 309 " pdb=" CA TYR D 309 " ideal model delta harmonic sigma weight residual -180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA VAL G 308 " pdb=" C VAL G 308 " pdb=" N TYR G 309 " pdb=" CA TYR G 309 " ideal model delta harmonic sigma weight residual 180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA VAL E 308 " pdb=" C VAL E 308 " pdb=" N TYR E 309 " pdb=" CA TYR E 309 " ideal model delta harmonic sigma weight residual -180.00 -156.21 -23.79 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 9111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1242 0.036 - 0.072: 792 0.072 - 0.107: 274 0.107 - 0.143: 111 0.143 - 0.179: 52 Chirality restraints: 2471 Sorted by residual: chirality pdb=" CA LEU A 101 " pdb=" N LEU A 101 " pdb=" C LEU A 101 " pdb=" CB LEU A 101 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CA LEU B 101 " pdb=" N LEU B 101 " pdb=" C LEU B 101 " pdb=" CB LEU B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA LEU G 101 " pdb=" N LEU G 101 " pdb=" C LEU G 101 " pdb=" CB LEU G 101 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 2468 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO C 124 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 123 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO A 124 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 123 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO G 124 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO G 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 124 " 0.046 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 752 2.72 - 3.27: 15541 3.27 - 3.81: 24514 3.81 - 4.36: 29248 4.36 - 4.90: 44640 Nonbonded interactions: 114695 Sorted by model distance: nonbonded pdb=" O PHE F 72 " pdb=" OG SER G 71 " model vdw 2.175 2.440 nonbonded pdb=" O PHE A 72 " pdb=" OG SER B 71 " model vdw 2.224 2.440 nonbonded pdb=" O PHE E 72 " pdb=" OG SER F 71 " model vdw 2.235 2.440 nonbonded pdb=" OG SER A 71 " pdb=" O PHE G 72 " model vdw 2.285 2.440 nonbonded pdb=" O GLU A 310 " pdb=" OG1 THR A 314 " model vdw 2.293 2.440 ... (remaining 114690 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.920 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 37.880 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 0.045 15309 Z= 0.311 Angle : 0.998 8.669 20825 Z= 0.551 Chirality : 0.055 0.179 2471 Planarity : 0.009 0.081 2520 Dihedral : 14.609 48.948 5460 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer Outliers : 0.00 % 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: -5.56 (0.13), residues: 1827 helix: -3.55 (0.09), residues: 1183 sheet: None (None), residues: 0 loop : -3.65 (0.18), residues: 644 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1704 time to fit residues: 11.7897 Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.211 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.0010 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 0.0870 chunk 142 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 0.0970 chunk 106 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 15309 Z= 0.203 Angle : 0.807 10.241 20825 Z= 0.408 Chirality : 0.047 0.195 2471 Planarity : 0.007 0.054 2520 Dihedral : 6.407 24.432 1981 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 0.41 % 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: -3.35 (0.17), residues: 1827 helix: -1.58 (0.14), residues: 1120 sheet: None (None), residues: 0 loop : -3.21 (0.20), residues: 707 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.1325 time to fit residues: 7.9023 Evaluate side-chains 27 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 0.0070 chunk 137 optimal weight: 0.0030 chunk 112 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.6810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 15309 Z= 0.189 Angle : 0.732 6.673 20825 Z= 0.363 Chirality : 0.045 0.167 2471 Planarity : 0.006 0.045 2520 Dihedral : 5.816 23.459 1981 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 0.41 % 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: -2.38 (0.19), residues: 1827 helix: -0.83 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -2.73 (0.21), residues: 728 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.345 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.1522 time to fit residues: 8.4319 Evaluate side-chains 26 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 4.9990 chunk 124 optimal weight: 0.0970 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 0.0670 chunk 79 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 86 optimal weight: 0.4980 chunk 157 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15309 Z= 0.175 Angle : 0.729 6.661 20825 Z= 0.365 Chirality : 0.045 0.158 2471 Planarity : 0.005 0.044 2520 Dihedral : 5.215 18.461 1981 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer Outliers : 0.00 % 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: -2.17 (0.19), residues: 1827 helix: -0.57 (0.16), residues: 1071 sheet: -1.83 (0.63), residues: 84 loop : -2.77 (0.23), residues: 672 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1358 time to fit residues: 7.2794 Evaluate side-chains 28 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.286 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.0470 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 157 optimal weight: 0.0010 chunk 44 optimal weight: 6.9990 overall best weight: 2.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15309 Z= 0.194 Angle : 0.725 7.780 20825 Z= 0.366 Chirality : 0.045 0.149 2471 Planarity : 0.005 0.039 2520 Dihedral : 5.301 21.554 1981 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer Outliers : 0.00 % 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: -1.93 (0.19), residues: 1827 helix: -0.46 (0.15), residues: 1113 sheet: -2.24 (0.57), residues: 84 loop : -2.53 (0.24), residues: 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1444 time to fit residues: 7.1047 Evaluate side-chains 29 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.4980 chunk 158 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 103 optimal weight: 0.4980 chunk 43 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15309 Z= 0.167 Angle : 0.687 7.106 20825 Z= 0.343 Chirality : 0.044 0.150 2471 Planarity : 0.004 0.043 2520 Dihedral : 5.124 20.297 1981 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer Outliers : 0.00 % 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: -1.73 (0.19), residues: 1827 helix: -0.31 (0.15), residues: 1162 sheet: -2.13 (0.54), residues: 84 loop : -2.58 (0.25), residues: 581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1313 time to fit residues: 6.5165 Evaluate side-chains 28 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 chunk 148 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 109 optimal weight: 0.0040 chunk 106 optimal weight: 0.0570 chunk 80 optimal weight: 4.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15309 Z= 0.146 Angle : 0.668 7.262 20825 Z= 0.324 Chirality : 0.044 0.149 2471 Planarity : 0.004 0.041 2520 Dihedral : 4.837 15.739 1981 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 0.00 % 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: -1.45 (0.20), residues: 1827 helix: 0.07 (0.16), residues: 1078 sheet: -1.40 (0.53), residues: 84 loop : -2.62 (0.23), residues: 665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1317 time to fit residues: 7.1831 Evaluate side-chains 29 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 15309 Z= 0.157 Angle : 0.682 7.243 20825 Z= 0.329 Chirality : 0.044 0.145 2471 Planarity : 0.004 0.042 2520 Dihedral : 4.764 14.851 1981 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer Outliers : 0.00 % 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: -1.82 (0.20), residues: 1827 helix: -0.44 (0.15), residues: 1190 sheet: -1.28 (0.53), residues: 84 loop : -2.73 (0.24), residues: 553 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1264 time to fit residues: 6.5021 Evaluate side-chains 29 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.251 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.0270 chunk 168 optimal weight: 8.9990 chunk 153 optimal weight: 0.2980 chunk 163 optimal weight: 0.0770 chunk 98 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 15309 Z= 0.153 Angle : 0.691 7.668 20825 Z= 0.328 Chirality : 0.044 0.147 2471 Planarity : 0.004 0.041 2520 Dihedral : 4.592 14.643 1981 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer Outliers : 0.00 % 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: -1.69 (0.19), residues: 1827 helix: -0.24 (0.15), residues: 1148 sheet: -0.63 (0.58), residues: 84 loop : -2.89 (0.23), residues: 595 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1224 time to fit residues: 6.8385 Evaluate side-chains 28 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.262 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 111 optimal weight: 0.0980 chunk 88 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 15309 Z= 0.229 Angle : 0.740 7.390 20825 Z= 0.361 Chirality : 0.047 0.136 2471 Planarity : 0.005 0.040 2520 Dihedral : 4.975 18.480 1981 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer Outliers : 0.00 % 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: -1.95 (0.19), residues: 1827 helix: -0.56 (0.15), residues: 1218 sheet: -2.84 (0.46), residues: 84 loop : -2.55 (0.27), residues: 525 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1123 time to fit residues: 5.9059 Evaluate side-chains 29 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 5.9990 chunk 153 optimal weight: 0.0270 chunk 44 optimal weight: 8.9990 chunk 133 optimal weight: 0.0010 chunk 21 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.8050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.063366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.050383 restraints weight = 15246.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051652 restraints weight = 9621.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.052512 restraints weight = 6927.544| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 15309 Z= 0.230 Angle : 0.744 7.455 20825 Z= 0.361 Chirality : 0.046 0.146 2471 Planarity : 0.005 0.040 2520 Dihedral : 5.128 18.934 1981 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer Outliers : 0.00 % 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: -1.98 (0.19), residues: 1827 helix: -0.58 (0.14), residues: 1183 sheet: -3.45 (0.50), residues: 84 loop : -2.33 (0.27), residues: 560 =============================================================================== Job complete usr+sys time: 1949.18 seconds wall clock time: 37 minutes 7.50 seconds (2227.50 seconds total)