Starting phenix.real_space_refine on Sat Jan 20 10:22:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/01_2024/6m68_30116.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/01_2024/6m68_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_30116/01_2024/6m68_30116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/01_2024/6m68_30116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/01_2024/6m68_30116.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m68_30116/01_2024/6m68_30116.pdb" } resolution = 4.6 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= 0.028 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-1.21-5211/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: 8.14, per 1000 atoms: 0.54 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: 6.07 Conformation dependent library (CDL) restraints added in 3.2 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: 1.42 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: 3.70 Time building geometry restraints manager: 6.58 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: 0.730 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: 0.010 Extract box with map and model: 4.260 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 41.020 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.080 ------------------------------------------------------------------------------- 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 % Allowed : 11.44 % Favored : 88.56 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 104 HIS 0.008 0.002 HIS F 106 PHE 0.012 0.002 PHE B 263 TYR 0.017 0.002 TYR B 284 ARG 0.004 0.001 ARG C 217 *********************** 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 : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.9376 (tpp-160) cc_final: 0.8564 (mpt180) REVERT: A 121 TYR cc_start: 0.9283 (t80) cc_final: 0.9078 (t80) REVERT: A 205 ASN cc_start: 0.9455 (p0) cc_final: 0.9252 (p0) REVERT: A 318 LEU cc_start: 0.8608 (tt) cc_final: 0.8318 (mt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1744 time to fit residues: 12.1820 Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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: 0.0030 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: 4.9990 chunk 106 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 overall best weight: 1.1376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15309 Z= 0.188 Angle : 0.799 9.019 20825 Z= 0.402 Chirality : 0.047 0.201 2471 Planarity : 0.007 0.057 2520 Dihedral : 6.515 24.904 1981 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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: -3.19 (0.17), residues: 1827 helix: -1.43 (0.14), residues: 1127 sheet: None (None), residues: 0 loop : -3.20 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 127 HIS 0.002 0.001 HIS C 319 PHE 0.021 0.002 PHE E 141 TYR 0.015 0.001 TYR B 111 ARG 0.004 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 2 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 54 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.253 Fit side-chains REVERT: A 37 MET cc_start: 0.8988 (ttt) cc_final: 0.8717 (ttp) REVERT: A 75 ARG cc_start: 0.9288 (tpp-160) cc_final: 0.8388 (mtt90) REVERT: A 121 TYR cc_start: 0.9394 (t80) cc_final: 0.9153 (t80) REVERT: A 141 PHE cc_start: 0.9287 (t80) cc_final: 0.9035 (t80) REVERT: A 145 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9267 (mt-10) REVERT: A 205 ASN cc_start: 0.9517 (p0) cc_final: 0.9302 (p0) REVERT: A 273 PHE cc_start: 0.9199 (m-10) cc_final: 0.8661 (m-80) REVERT: A 331 TYR cc_start: 0.8026 (t80) cc_final: 0.7315 (m-10) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1425 time to fit residues: 9.0187 Evaluate side-chains 30 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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: 0.0020 chunk 51 optimal weight: 0.0970 chunk 137 optimal weight: 4.9990 chunk 112 optimal weight: 0.0170 chunk 45 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 0.4980 chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 overall best weight: 0.3226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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: 0.7954 moved from start: 0.4602 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= 0.176 Angle : 0.736 6.664 20825 Z= 0.369 Chirality : 0.046 0.171 2471 Planarity : 0.006 0.051 2520 Dihedral : 5.972 27.049 1981 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.41 % Allowed : 3.32 % Favored : 96.27 % 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: -0.89 (0.15), residues: 1134 sheet: -1.22 (0.57), residues: 84 loop : -2.82 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.004 0.001 HIS G 319 PHE 0.010 0.001 PHE D 67 TYR 0.012 0.001 TYR D 325 ARG 0.001 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 3 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 46 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 TYR cc_start: 0.9363 (t80) cc_final: 0.9097 (t80) REVERT: D 125 LEU cc_start: 0.9722 (tp) cc_final: 0.9174 (pp) REVERT: D 145 GLU cc_start: 0.9603 (mt-10) cc_final: 0.9243 (mt-10) REVERT: D 273 PHE cc_start: 0.9012 (m-10) cc_final: 0.8569 (m-80) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1503 time to fit residues: 8.0948 Evaluate side-chains 26 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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: 6.9990 chunk 124 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 175 optimal weight: 0.0370 chunk 86 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 0.0020 overall best weight: 1.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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: 0.7977 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15309 Z= 0.166 Angle : 0.709 6.396 20825 Z= 0.353 Chirality : 0.044 0.152 2471 Planarity : 0.005 0.044 2520 Dihedral : 5.561 23.007 1981 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: -2.02 (0.20), residues: 1827 helix: -0.50 (0.16), residues: 1106 sheet: -2.21 (0.56), residues: 84 loop : -2.63 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 127 HIS 0.002 0.001 HIS G 106 PHE 0.011 0.001 PHE A 141 TYR 0.010 0.001 TYR F 325 ARG 0.002 0.000 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 4 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 40 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 125 LEU cc_start: 0.9714 (tp) cc_final: 0.9211 (pp) REVERT: D 141 PHE cc_start: 0.9226 (t80) cc_final: 0.8964 (t80) REVERT: D 145 GLU cc_start: 0.9585 (mt-10) cc_final: 0.9286 (mt-10) REVERT: D 273 PHE cc_start: 0.9083 (m-10) cc_final: 0.8580 (m-80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1311 time to fit residues: 6.3521 Evaluate side-chains 28 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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: 5.9990 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 157 optimal weight: 0.0980 chunk 44 optimal weight: 0.0050 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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: 0.7925 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15309 Z= 0.145 Angle : 0.673 6.613 20825 Z= 0.334 Chirality : 0.043 0.161 2471 Planarity : 0.005 0.039 2520 Dihedral : 5.209 17.275 1981 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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: -0.35 (0.15), residues: 1113 sheet: -2.51 (0.57), residues: 84 loop : -2.49 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 127 HIS 0.001 0.000 HIS C 134 PHE 0.015 0.001 PHE F 129 TYR 0.023 0.001 TYR A 121 ARG 0.003 0.000 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 5 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 44 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 MET cc_start: 0.8852 (ttp) cc_final: 0.8405 (tmm) REVERT: D 125 LEU cc_start: 0.9738 (tp) cc_final: 0.9393 (pp) REVERT: D 141 PHE cc_start: 0.9233 (t80) cc_final: 0.8982 (t80) REVERT: D 145 GLU cc_start: 0.9568 (mt-10) cc_final: 0.9258 (mt-10) REVERT: D 273 PHE cc_start: 0.9037 (m-10) cc_final: 0.8675 (m-80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1450 time to fit residues: 7.5440 Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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: 3.9990 chunk 158 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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: 0.7958 moved from start: 0.5672 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= 0.164 Angle : 0.680 6.586 20825 Z= 0.335 Chirality : 0.044 0.150 2471 Planarity : 0.006 0.085 2520 Dihedral : 5.228 20.458 1981 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -1.50 (0.20), residues: 1827 helix: -0.16 (0.16), residues: 1155 sheet: -2.82 (0.58), residues: 84 loop : -2.26 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 104 HIS 0.001 0.000 HIS C 134 PHE 0.010 0.001 PHE C 109 TYR 0.008 0.001 TYR G 111 ARG 0.003 0.001 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 6 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 40 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 MET cc_start: 0.8859 (ttp) cc_final: 0.8372 (tmm) REVERT: D 125 LEU cc_start: 0.9773 (tp) cc_final: 0.9449 (pp) REVERT: D 273 PHE cc_start: 0.9098 (m-10) cc_final: 0.8742 (m-80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1235 time to fit residues: 6.0140 Evaluate side-chains 31 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 4.9990 chunk 100 optimal weight: 0.0670 chunk 128 optimal weight: 0.4980 chunk 99 optimal weight: 0.0980 chunk 148 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 109 optimal weight: 0.0970 chunk 106 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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: 0.7878 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15309 Z= 0.144 Angle : 0.688 6.615 20825 Z= 0.330 Chirality : 0.043 0.144 2471 Planarity : 0.005 0.047 2520 Dihedral : 5.009 18.356 1981 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -1.47 (0.20), residues: 1827 helix: -0.06 (0.15), residues: 1155 sheet: -2.47 (0.54), residues: 84 loop : -2.50 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 127 HIS 0.001 0.000 HIS B 319 PHE 0.014 0.001 PHE A 54 TYR 0.007 0.001 TYR F 325 ARG 0.012 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 7 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 40 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 125 LEU cc_start: 0.9771 (tp) cc_final: 0.9447 (pp) REVERT: D 273 PHE cc_start: 0.9023 (m-10) cc_final: 0.8783 (m-80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1338 time to fit residues: 6.4685 Evaluate side-chains 28 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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: 0.6980 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 111 optimal weight: 0.1980 chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 0.0970 chunk 16 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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: 0.7927 moved from start: 0.6203 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= 0.168 Angle : 0.701 7.560 20825 Z= 0.337 Chirality : 0.045 0.162 2471 Planarity : 0.005 0.046 2520 Dihedral : 5.042 17.107 1981 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -1.62 (0.20), residues: 1827 helix: -0.35 (0.15), residues: 1197 sheet: -2.44 (0.54), residues: 84 loop : -2.28 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 104 HIS 0.002 0.001 HIS G 106 PHE 0.016 0.001 PHE D 54 TYR 0.007 0.001 TYR C 325 ARG 0.006 0.001 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 8 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 38 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 MET cc_start: 0.8918 (ttp) cc_final: 0.8531 (tmm) REVERT: D 125 LEU cc_start: 0.9776 (tp) cc_final: 0.9463 (pp) REVERT: D 273 PHE cc_start: 0.9061 (m-10) cc_final: 0.8794 (m-80) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1268 time to fit residues: 5.8267 Evaluate side-chains 26 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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: 8.9990 chunk 168 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 0.0000 chunk 71 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 147 optimal weight: 0.0670 chunk 154 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 overall best weight: 0.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15309 Z= 0.146 Angle : 0.683 7.434 20825 Z= 0.322 Chirality : 0.044 0.139 2471 Planarity : 0.005 0.046 2520 Dihedral : 4.760 17.572 1981 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.41 % Allowed : 1.24 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.42 (0.20), residues: 1827 helix: -0.05 (0.15), residues: 1162 sheet: -1.30 (0.61), residues: 70 loop : -2.62 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 104 HIS 0.001 0.000 HIS G 106 PHE 0.009 0.001 PHE C 109 TYR 0.015 0.001 TYR B 121 ARG 0.003 0.001 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 9 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 38 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 MET cc_start: 0.8755 (ttp) cc_final: 0.8496 (tmm) REVERT: D 125 LEU cc_start: 0.9784 (tp) cc_final: 0.9479 (mt) REVERT: D 273 PHE cc_start: 0.9005 (m-10) cc_final: 0.8738 (m-80) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.1324 time to fit residues: 6.0808 Evaluate side-chains 26 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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: 2.9990 chunk 172 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 111 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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: 0.6639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15309 Z= 0.150 Angle : 0.683 6.829 20825 Z= 0.324 Chirality : 0.044 0.136 2471 Planarity : 0.005 0.044 2520 Dihedral : 4.992 19.925 1981 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -1.29 (0.20), residues: 1827 helix: -0.09 (0.15), residues: 1190 sheet: -0.97 (0.63), residues: 70 loop : -2.39 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 104 HIS 0.002 0.001 HIS G 106 PHE 0.007 0.001 PHE C 109 TYR 0.006 0.001 TYR B 325 ARG 0.008 0.001 ARG F 217 ********************** REFINEMENT MACRO_CYCLE 10 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 35 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 MET cc_start: 0.8856 (ttp) cc_final: 0.8536 (tmm) REVERT: D 125 LEU cc_start: 0.9683 (tp) cc_final: 0.9408 (pp) REVERT: D 273 PHE cc_start: 0.9004 (m-10) cc_final: 0.8762 (m-80) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1148 time to fit residues: 5.0566 Evaluate side-chains 25 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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: 7.9990 chunk 153 optimal weight: 6.9990 chunk 44 optimal weight: 0.0030 chunk 133 optimal weight: 0.0770 chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 148 optimal weight: 0.0020 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 10.0000 overall best weight: 0.1356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.069503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056249 restraints weight = 14299.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057702 restraints weight = 9025.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.058696 restraints weight = 6423.551| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15309 Z= 0.140 Angle : 0.702 7.204 20825 Z= 0.326 Chirality : 0.044 0.136 2471 Planarity : 0.005 0.047 2520 Dihedral : 4.807 18.490 1981 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.26 (0.20), residues: 1827 helix: 0.16 (0.16), residues: 1162 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 74 HIS 0.000 0.000 HIS G 106 PHE 0.007 0.001 PHE D 109 TYR 0.028 0.001 TYR C 121 ARG 0.007 0.001 ARG G 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2078.44 seconds wall clock time: 39 minutes 20.71 seconds (2360.71 seconds total)