Starting phenix.real_space_refine on Sat Apr 13 01:15:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhq_16066/04_2024/8bhq_16066_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhq_16066/04_2024/8bhq_16066.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhq_16066/04_2024/8bhq_16066_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhq_16066/04_2024/8bhq_16066_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhq_16066/04_2024/8bhq_16066_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhq_16066/04_2024/8bhq_16066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhq_16066/04_2024/8bhq_16066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhq_16066/04_2024/8bhq_16066_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhq_16066/04_2024/8bhq_16066_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 85 5.16 5 C 8940 2.51 5 N 2290 2.21 5 O 2485 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27215 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QR3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QR3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QR3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QR3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QR3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.26, per 1000 atoms: 0.41 Number of scatterers: 27215 At special positions: 0 Unit cell: (93.09, 95.23, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 O 2485 8.00 N 2290 7.00 C 8940 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 19.76 Conformation dependent library (CDL) restraints added in 2.7 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 19 sheets defined 36.9% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 91 through 96 removed outlier: 4.193A pdb=" N SER A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.555A pdb=" N VAL A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 removed outlier: 3.620A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 313 Processing helix chain 'A' and resid 318 through 417 removed outlier: 3.549A pdb=" N LYS A 393 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 91 through 96 removed outlier: 4.193A pdb=" N SER B 95 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 234 through 249 removed outlier: 3.555A pdb=" N VAL B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 removed outlier: 3.621A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 313 Processing helix chain 'B' and resid 318 through 417 removed outlier: 3.549A pdb=" N LYS B 393 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 91 through 96 removed outlier: 4.193A pdb=" N SER C 95 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 181 No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 234 through 249 removed outlier: 3.554A pdb=" N VAL C 246 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 276 removed outlier: 3.620A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 313 Processing helix chain 'C' and resid 318 through 417 removed outlier: 3.548A pdb=" N LYS C 393 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 91 through 96 removed outlier: 4.192A pdb=" N SER D 95 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 181 No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 234 through 249 removed outlier: 3.556A pdb=" N VAL D 246 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TRP D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 removed outlier: 3.620A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 313 Processing helix chain 'D' and resid 318 through 417 removed outlier: 3.549A pdb=" N LYS D 393 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 91 through 96 removed outlier: 4.194A pdb=" N SER E 95 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 181 No H-bonds generated for 'chain 'E' and resid 178 through 181' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 234 through 249 removed outlier: 3.555A pdb=" N VAL E 246 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 276 removed outlier: 3.620A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 313 Processing helix chain 'E' and resid 318 through 417 removed outlier: 3.549A pdb=" N LYS E 393 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.903A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 133 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.938A pdb=" N MET A 48 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 153 through 160 removed outlier: 4.057A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.219A pdb=" N SER A 139 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A 110 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR A 137 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.903A pdb=" N THR B 42 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL B 173 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL B 44 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 109 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU B 141 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLY B 107 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.937A pdb=" N MET B 48 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 153 through 160 removed outlier: 4.057A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.903A pdb=" N THR C 42 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL C 173 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL C 44 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 133 " --> pdb=" O MET C 121 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 182 through 184 removed outlier: 6.937A pdb=" N MET C 48 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 153 through 160 removed outlier: 4.057A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.219A pdb=" N SER C 139 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER C 110 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR C 137 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.903A pdb=" N THR D 42 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL D 173 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL D 44 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 133 " --> pdb=" O MET D 121 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 182 through 184 removed outlier: 6.937A pdb=" N MET D 48 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 153 through 160 removed outlier: 4.057A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 107 through 111 removed outlier: 7.219A pdb=" N SER D 139 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER D 110 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR D 137 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 170 through 174 removed outlier: 6.902A pdb=" N THR E 42 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL E 173 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL E 44 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR E 133 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.936A pdb=" N MET E 48 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 153 through 160 removed outlier: 4.057A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.219A pdb=" N SER E 139 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER E 110 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR E 137 " --> pdb=" O SER E 110 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1587 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: 9.50 Time building geometry restraints manager: 20.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 5 1.23 - 1.42: 6120 1.42 - 1.62: 7905 1.62 - 1.81: 150 Bond restraints: 27595 Sorted by residual: bond pdb=" C10 QR3 D 502 " pdb=" N4 QR3 D 502 " ideal model delta sigma weight residual 1.487 1.291 0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C10 QR3 A 502 " pdb=" N4 QR3 A 502 " ideal model delta sigma weight residual 1.487 1.292 0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" C10 QR3 B 502 " pdb=" N4 QR3 B 502 " ideal model delta sigma weight residual 1.487 1.292 0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" C10 QR3 C 502 " pdb=" N4 QR3 C 502 " ideal model delta sigma weight residual 1.487 1.292 0.195 2.00e-02 2.50e+03 9.50e+01 bond pdb=" C10 QR3 E 502 " pdb=" N4 QR3 E 502 " ideal model delta sigma weight residual 1.487 1.292 0.195 2.00e-02 2.50e+03 9.46e+01 ... (remaining 27590 not shown) Histogram of bond angle deviations from ideal: 87.79 - 97.04: 20 97.04 - 106.28: 400 106.28 - 115.52: 33829 115.52 - 124.76: 14063 124.76 - 134.00: 1273 Bond angle restraints: 49585 Sorted by residual: angle pdb=" C16 QR3 E 502 " pdb=" C15 QR3 E 502 " pdb=" C20 QR3 E 502 " ideal model delta sigma weight residual 172.58 116.80 55.78 3.00e+00 1.11e-01 3.46e+02 angle pdb=" C16 QR3 A 502 " pdb=" C15 QR3 A 502 " pdb=" C20 QR3 A 502 " ideal model delta sigma weight residual 172.58 116.82 55.76 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C16 QR3 C 502 " pdb=" C15 QR3 C 502 " pdb=" C20 QR3 C 502 " ideal model delta sigma weight residual 172.58 116.84 55.74 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C16 QR3 B 502 " pdb=" C15 QR3 B 502 " pdb=" C20 QR3 B 502 " ideal model delta sigma weight residual 172.58 116.85 55.73 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C16 QR3 D 502 " pdb=" C15 QR3 D 502 " pdb=" C20 QR3 D 502 " ideal model delta sigma weight residual 172.58 116.85 55.73 3.00e+00 1.11e-01 3.45e+02 ... (remaining 49580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 12694 18.12 - 36.24: 256 36.24 - 54.37: 147 54.37 - 72.49: 43 72.49 - 90.61: 15 Dihedral angle restraints: 13155 sinusoidal: 7025 harmonic: 6130 Sorted by residual: dihedral pdb=" C14 QR3 B 502 " pdb=" C15 QR3 B 502 " pdb=" C16 QR3 B 502 " pdb=" C17 QR3 B 502 " ideal model delta sinusoidal sigma weight residual -169.79 -79.18 -90.61 1 3.00e+01 1.11e-03 1.08e+01 dihedral pdb=" C14 QR3 D 502 " pdb=" C15 QR3 D 502 " pdb=" C16 QR3 D 502 " pdb=" C17 QR3 D 502 " ideal model delta sinusoidal sigma weight residual -169.79 -79.18 -90.61 1 3.00e+01 1.11e-03 1.08e+01 dihedral pdb=" C14 QR3 C 502 " pdb=" C15 QR3 C 502 " pdb=" C16 QR3 C 502 " pdb=" C17 QR3 C 502 " ideal model delta sinusoidal sigma weight residual -169.79 -79.20 -90.59 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 13152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1301 0.025 - 0.050: 532 0.050 - 0.074: 182 0.074 - 0.099: 64 0.099 - 0.124: 81 Chirality restraints: 2160 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 205 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 205 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 205 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 2157 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 QR3 D 502 " -0.094 2.00e-02 2.50e+03 1.30e-01 1.70e+02 pdb=" C14 QR3 D 502 " -0.064 2.00e-02 2.50e+03 pdb=" C20 QR3 D 502 " -0.067 2.00e-02 2.50e+03 pdb=" N5 QR3 D 502 " 0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QR3 A 502 " 0.094 2.00e-02 2.50e+03 1.30e-01 1.69e+02 pdb=" C14 QR3 A 502 " 0.064 2.00e-02 2.50e+03 pdb=" C20 QR3 A 502 " 0.066 2.00e-02 2.50e+03 pdb=" N5 QR3 A 502 " -0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QR3 E 502 " 0.094 2.00e-02 2.50e+03 1.30e-01 1.69e+02 pdb=" C14 QR3 E 502 " 0.064 2.00e-02 2.50e+03 pdb=" C20 QR3 E 502 " 0.066 2.00e-02 2.50e+03 pdb=" N5 QR3 E 502 " -0.224 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 3589 2.28 - 2.86: 60987 2.86 - 3.44: 64890 3.44 - 4.02: 92604 4.02 - 4.60: 142671 Nonbonded interactions: 364741 Sorted by model distance: nonbonded pdb=" OE1 GLU A 253 " pdb=" H GLU A 253 " model vdw 1.695 1.850 nonbonded pdb=" OE1 GLU C 253 " pdb=" H GLU C 253 " model vdw 1.696 1.850 nonbonded pdb=" OE1 GLU B 253 " pdb=" H GLU B 253 " model vdw 1.697 1.850 nonbonded pdb=" OE1 GLU E 253 " pdb=" H GLU E 253 " model vdw 1.697 1.850 nonbonded pdb=" OE1 GLU D 253 " pdb=" H GLU D 253 " model vdw 1.697 1.850 ... (remaining 364736 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.400 Extract box with map and model: 5.300 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 82.570 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.130 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.007 0.196 14180 Z= 0.462 Angle : 1.377 55.782 19310 Z= 0.478 Chirality : 0.038 0.124 2160 Planarity : 0.007 0.130 2395 Dihedral : 8.529 90.611 5145 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 2.16 (0.21), residues: 1670 helix: 3.31 (0.22), residues: 560 sheet: 0.66 (0.28), residues: 385 loop : 0.42 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 414 HIS 0.003 0.001 HIS D 195 PHE 0.005 0.001 PHE C 68 TYR 0.005 0.001 TYR D 285 ARG 0.002 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 ASP cc_start: 0.7065 (m-30) cc_final: 0.6861 (m-30) REVERT: E 58 ASP cc_start: 0.7847 (m-30) cc_final: 0.7645 (m-30) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.7590 time to fit residues: 271.2142 Evaluate side-chains 149 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14180 Z= 0.166 Angle : 0.487 4.796 19310 Z= 0.254 Chirality : 0.040 0.146 2160 Planarity : 0.004 0.035 2395 Dihedral : 6.081 69.520 2010 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.27 % Allowed : 4.83 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.70 (0.21), residues: 1670 helix: 2.78 (0.22), residues: 550 sheet: 0.37 (0.26), residues: 440 loop : 0.36 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.002 0.001 HIS D 195 PHE 0.009 0.001 PHE B 406 TYR 0.011 0.001 TYR D 285 ARG 0.007 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.6972 (mpp) cc_final: 0.6752 (mpp) REVERT: B 290 ASP cc_start: 0.7715 (m-30) cc_final: 0.7421 (m-30) REVERT: E 78 LEU cc_start: 0.8388 (mt) cc_final: 0.8155 (mt) outliers start: 4 outliers final: 1 residues processed: 175 average time/residue: 0.5330 time to fit residues: 141.9169 Evaluate side-chains 140 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN C 245 GLN E 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14180 Z= 0.206 Angle : 0.485 4.415 19310 Z= 0.250 Chirality : 0.040 0.148 2160 Planarity : 0.004 0.038 2395 Dihedral : 6.520 71.515 2010 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.67 % Allowed : 5.50 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.54 (0.21), residues: 1670 helix: 2.46 (0.22), residues: 555 sheet: 0.43 (0.25), residues: 490 loop : 0.31 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 414 HIS 0.003 0.001 HIS B 195 PHE 0.013 0.002 PHE A 68 TYR 0.010 0.001 TYR E 132 ARG 0.010 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8912 (mtp) cc_final: 0.8679 (mtm) REVERT: A 115 MET cc_start: 0.8398 (mmp) cc_final: 0.8128 (mmt) REVERT: B 290 ASP cc_start: 0.8051 (m-30) cc_final: 0.7773 (m-30) REVERT: D 78 LEU cc_start: 0.8380 (mt) cc_final: 0.8027 (mt) REVERT: D 267 LEU cc_start: 0.8557 (mt) cc_final: 0.8258 (mt) REVERT: D 290 ASP cc_start: 0.8090 (m-30) cc_final: 0.7730 (m-30) REVERT: E 267 LEU cc_start: 0.8566 (mt) cc_final: 0.8240 (mt) REVERT: E 290 ASP cc_start: 0.7998 (m-30) cc_final: 0.7611 (m-30) outliers start: 10 outliers final: 3 residues processed: 158 average time/residue: 0.4436 time to fit residues: 110.8207 Evaluate side-chains 134 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 95 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN E 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14180 Z= 0.263 Angle : 0.520 5.442 19310 Z= 0.268 Chirality : 0.042 0.146 2160 Planarity : 0.005 0.041 2395 Dihedral : 6.538 70.435 2010 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.21 % Allowed : 6.58 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.24 (0.21), residues: 1670 helix: 2.17 (0.22), residues: 560 sheet: 0.29 (0.25), residues: 465 loop : 0.13 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.003 0.001 HIS E 195 PHE 0.015 0.002 PHE A 68 TYR 0.013 0.001 TYR B 132 ARG 0.010 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8502 (mmp) cc_final: 0.8030 (mmt) REVERT: A 290 ASP cc_start: 0.8230 (m-30) cc_final: 0.7718 (m-30) REVERT: B 290 ASP cc_start: 0.8127 (m-30) cc_final: 0.7703 (m-30) REVERT: C 267 LEU cc_start: 0.8617 (mt) cc_final: 0.8221 (mt) REVERT: C 290 ASP cc_start: 0.8109 (m-30) cc_final: 0.7577 (m-30) REVERT: D 239 MET cc_start: 0.8744 (mmm) cc_final: 0.8294 (mmp) REVERT: D 267 LEU cc_start: 0.8542 (mt) cc_final: 0.8175 (mt) REVERT: D 290 ASP cc_start: 0.8168 (m-30) cc_final: 0.7603 (m-30) REVERT: E 267 LEU cc_start: 0.8594 (mt) cc_final: 0.8210 (mt) REVERT: E 290 ASP cc_start: 0.8061 (m-30) cc_final: 0.7466 (m-30) outliers start: 18 outliers final: 17 residues processed: 156 average time/residue: 0.4237 time to fit residues: 106.7675 Evaluate side-chains 150 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 205 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN E 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14180 Z= 0.280 Angle : 0.517 5.276 19310 Z= 0.266 Chirality : 0.041 0.150 2160 Planarity : 0.005 0.048 2395 Dihedral : 6.640 69.938 2010 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.34 % Allowed : 7.32 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1670 helix: 2.14 (0.23), residues: 555 sheet: 0.11 (0.25), residues: 465 loop : -0.14 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 414 HIS 0.003 0.001 HIS E 195 PHE 0.015 0.002 PHE A 68 TYR 0.010 0.001 TYR E 132 ARG 0.007 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8507 (mmp) cc_final: 0.8120 (mmt) REVERT: A 290 ASP cc_start: 0.8227 (m-30) cc_final: 0.7719 (m-30) REVERT: B 89 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5610 (mp) REVERT: B 290 ASP cc_start: 0.8133 (m-30) cc_final: 0.7723 (m-30) REVERT: B 397 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6689 (ttt) REVERT: C 267 LEU cc_start: 0.8601 (mt) cc_final: 0.8221 (mt) REVERT: C 290 ASP cc_start: 0.8153 (m-30) cc_final: 0.7625 (m-30) REVERT: D 267 LEU cc_start: 0.8555 (mt) cc_final: 0.8181 (mt) REVERT: D 290 ASP cc_start: 0.8179 (m-30) cc_final: 0.7648 (m-30) REVERT: E 267 LEU cc_start: 0.8579 (mt) cc_final: 0.8152 (mt) REVERT: E 290 ASP cc_start: 0.8120 (m-30) cc_final: 0.7723 (m-30) outliers start: 20 outliers final: 18 residues processed: 149 average time/residue: 0.4291 time to fit residues: 104.7219 Evaluate side-chains 148 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14180 Z= 0.243 Angle : 0.502 5.551 19310 Z= 0.256 Chirality : 0.041 0.148 2160 Planarity : 0.005 0.042 2395 Dihedral : 6.540 69.741 2010 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.68 % Allowed : 7.65 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1670 helix: 2.16 (0.23), residues: 555 sheet: 0.14 (0.27), residues: 415 loop : -0.30 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 414 HIS 0.003 0.001 HIS E 195 PHE 0.013 0.001 PHE B 68 TYR 0.010 0.001 TYR B 132 ARG 0.006 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8514 (mmp) cc_final: 0.8131 (mmt) REVERT: A 290 ASP cc_start: 0.8214 (m-30) cc_final: 0.7712 (m-30) REVERT: B 89 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5568 (mp) REVERT: B 290 ASP cc_start: 0.8097 (m-30) cc_final: 0.7707 (m-30) REVERT: B 397 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6716 (ttt) REVERT: C 267 LEU cc_start: 0.8613 (mt) cc_final: 0.8246 (mt) REVERT: C 290 ASP cc_start: 0.8153 (m-30) cc_final: 0.7625 (m-30) REVERT: D 290 ASP cc_start: 0.8171 (m-30) cc_final: 0.7636 (m-30) REVERT: E 267 LEU cc_start: 0.8629 (mt) cc_final: 0.8225 (mt) REVERT: E 290 ASP cc_start: 0.8193 (m-30) cc_final: 0.7697 (m-30) outliers start: 25 outliers final: 22 residues processed: 148 average time/residue: 0.4292 time to fit residues: 104.1853 Evaluate side-chains 152 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 412 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 90 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14180 Z= 0.277 Angle : 0.521 5.708 19310 Z= 0.267 Chirality : 0.041 0.150 2160 Planarity : 0.005 0.043 2395 Dihedral : 6.630 70.558 2010 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.81 % Allowed : 7.72 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1670 helix: 2.11 (0.23), residues: 555 sheet: 0.09 (0.26), residues: 425 loop : -0.45 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 114 HIS 0.004 0.001 HIS B 195 PHE 0.014 0.002 PHE B 68 TYR 0.011 0.001 TYR B 132 ARG 0.004 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8678 (mmm) cc_final: 0.8210 (mmp) REVERT: A 290 ASP cc_start: 0.8225 (m-30) cc_final: 0.7721 (m-30) REVERT: B 89 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5552 (mp) REVERT: B 290 ASP cc_start: 0.8116 (m-30) cc_final: 0.7740 (m-30) REVERT: B 397 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6824 (ttt) REVERT: C 290 ASP cc_start: 0.8143 (m-30) cc_final: 0.7615 (m-30) REVERT: D 290 ASP cc_start: 0.8176 (m-30) cc_final: 0.7928 (m-30) REVERT: E 245 GLN cc_start: 0.8235 (mt0) cc_final: 0.8015 (mt0) REVERT: E 267 LEU cc_start: 0.8632 (mt) cc_final: 0.8226 (mt) REVERT: E 290 ASP cc_start: 0.8173 (m-30) cc_final: 0.7707 (m-30) outliers start: 27 outliers final: 23 residues processed: 151 average time/residue: 0.4462 time to fit residues: 108.7392 Evaluate side-chains 154 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 412 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 0.0970 chunk 144 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14180 Z= 0.143 Angle : 0.451 5.159 19310 Z= 0.227 Chirality : 0.039 0.145 2160 Planarity : 0.004 0.041 2395 Dihedral : 6.309 68.009 2010 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.07 % Allowed : 8.72 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.03 (0.21), residues: 1670 helix: 2.37 (0.23), residues: 555 sheet: 0.10 (0.27), residues: 415 loop : -0.28 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 73 HIS 0.002 0.001 HIS E 195 PHE 0.008 0.001 PHE B 68 TYR 0.008 0.001 TYR E 132 ARG 0.004 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8497 (mmt) cc_final: 0.8029 (mmt) REVERT: A 290 ASP cc_start: 0.8181 (m-30) cc_final: 0.7689 (m-30) REVERT: B 89 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5680 (mp) REVERT: B 397 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6750 (ttt) REVERT: C 290 ASP cc_start: 0.8102 (m-30) cc_final: 0.7575 (m-30) REVERT: D 290 ASP cc_start: 0.8117 (m-30) cc_final: 0.7602 (m-30) REVERT: E 245 GLN cc_start: 0.8195 (mt0) cc_final: 0.7981 (mt0) REVERT: E 267 LEU cc_start: 0.8459 (mt) cc_final: 0.8021 (mt) outliers start: 16 outliers final: 13 residues processed: 151 average time/residue: 0.4339 time to fit residues: 106.8263 Evaluate side-chains 145 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 14180 Z= 0.234 Angle : 0.495 5.651 19310 Z= 0.251 Chirality : 0.040 0.147 2160 Planarity : 0.005 0.042 2395 Dihedral : 6.487 70.136 2010 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.14 % Allowed : 9.40 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1670 helix: 2.30 (0.23), residues: 555 sheet: 0.06 (0.26), residues: 415 loop : -0.39 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 414 HIS 0.003 0.001 HIS E 195 PHE 0.012 0.001 PHE B 68 TYR 0.010 0.001 TYR E 132 ARG 0.003 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8534 (mmt) cc_final: 0.7953 (mmt) REVERT: A 290 ASP cc_start: 0.8211 (m-30) cc_final: 0.7729 (m-30) REVERT: B 89 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5720 (mp) REVERT: B 290 ASP cc_start: 0.8169 (m-30) cc_final: 0.7742 (m-30) REVERT: B 397 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6922 (ttt) REVERT: C 290 ASP cc_start: 0.8153 (m-30) cc_final: 0.7633 (m-30) REVERT: D 290 ASP cc_start: 0.8176 (m-30) cc_final: 0.7656 (m-30) REVERT: E 245 GLN cc_start: 0.8209 (mt0) cc_final: 0.7988 (mt0) REVERT: E 267 LEU cc_start: 0.8637 (mt) cc_final: 0.8223 (mt) REVERT: E 290 ASP cc_start: 0.8164 (m-30) cc_final: 0.7713 (m-30) outliers start: 17 outliers final: 15 residues processed: 146 average time/residue: 0.4418 time to fit residues: 103.3546 Evaluate side-chains 145 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14180 Z= 0.148 Angle : 0.452 5.184 19310 Z= 0.227 Chirality : 0.039 0.146 2160 Planarity : 0.004 0.041 2395 Dihedral : 6.293 68.201 2010 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.07 % Allowed : 9.53 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.05 (0.21), residues: 1670 helix: 2.46 (0.23), residues: 555 sheet: 0.08 (0.26), residues: 415 loop : -0.31 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 73 HIS 0.002 0.001 HIS E 195 PHE 0.009 0.001 PHE B 68 TYR 0.008 0.001 TYR E 132 ARG 0.003 0.000 ARG A 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8510 (mmt) cc_final: 0.8014 (mmt) REVERT: A 290 ASP cc_start: 0.8194 (m-30) cc_final: 0.7707 (m-30) REVERT: B 89 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5653 (mp) REVERT: B 290 ASP cc_start: 0.8093 (m-30) cc_final: 0.7678 (m-30) REVERT: B 397 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6884 (ttt) REVERT: C 290 ASP cc_start: 0.8103 (m-30) cc_final: 0.7590 (m-30) REVERT: D 290 ASP cc_start: 0.8122 (m-30) cc_final: 0.7613 (m-30) REVERT: E 245 GLN cc_start: 0.8206 (mt0) cc_final: 0.7994 (mt0) REVERT: E 267 LEU cc_start: 0.8558 (mt) cc_final: 0.8116 (mt) outliers start: 16 outliers final: 13 residues processed: 145 average time/residue: 0.4388 time to fit residues: 103.3746 Evaluate side-chains 143 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105511 restraints weight = 55857.181| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.12 r_work: 0.3174 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 14180 Z= 0.171 Angle : 0.463 5.300 19310 Z= 0.233 Chirality : 0.039 0.146 2160 Planarity : 0.004 0.041 2395 Dihedral : 6.336 68.656 2010 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.14 % Allowed : 9.53 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.04 (0.21), residues: 1670 helix: 2.47 (0.23), residues: 555 sheet: 0.09 (0.26), residues: 415 loop : -0.35 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 73 HIS 0.002 0.001 HIS E 195 PHE 0.009 0.001 PHE B 68 TYR 0.009 0.001 TYR E 132 ARG 0.003 0.000 ARG A 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5007.68 seconds wall clock time: 92 minutes 14.28 seconds (5534.28 seconds total)