Starting phenix.real_space_refine on Sun Aug 24 07:42:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sux_40779/08_2025/8sux_40779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sux_40779/08_2025/8sux_40779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sux_40779/08_2025/8sux_40779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sux_40779/08_2025/8sux_40779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sux_40779/08_2025/8sux_40779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sux_40779/08_2025/8sux_40779.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.114 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 P 12 5.49 5 S 90 5.16 5 C 11434 2.51 5 N 3200 2.21 5 O 3365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18101 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3032 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3010 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 357} Chain breaks: 2 Chain: "C" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3019 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2934 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 349} Chain breaks: 2 Chain: "E" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3019 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2963 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.18, per 1000 atoms: 0.23 Number of scatterers: 18101 At special positions: 0 Unit cell: (129.92, 116.48, 136.64, 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 90 16.00 P 12 15.00 O 3365 8.00 N 3200 7.00 C 11434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 756.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 23 sheets defined 43.5% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 53 through 58 removed outlier: 6.763A pdb=" N ALA A 56 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 58 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.818A pdb=" N LEU A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 66 " --> pdb=" O LYS A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 66' Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 118 through 136 removed outlier: 3.810A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.750A pdb=" N LEU A 157 " --> pdb=" O THR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.703A pdb=" N PHE A 177 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 180 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 217 removed outlier: 3.733A pdb=" N PHE A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 251 removed outlier: 4.249A pdb=" N LEU A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.688A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 302 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 355 through 360 removed outlier: 4.516A pdb=" N THR A 359 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'B' and resid 35 through 53 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.684A pdb=" N LEU B 58 " --> pdb=" O ASP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 118 through 136 removed outlier: 3.728A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.598A pdb=" N LEU B 157 " --> pdb=" O THR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 184 removed outlier: 3.769A pdb=" N PHE B 177 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 180 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 217 removed outlier: 3.777A pdb=" N PHE B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 247 removed outlier: 3.971A pdb=" N GLN B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.708A pdb=" N ILE B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 302 " --> pdb=" O CYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'C' and resid 34 through 46 removed outlier: 3.571A pdb=" N THR C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.613A pdb=" N ILE C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 6.697A pdb=" N ALA C 56 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.547A pdb=" N LEU C 72 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.596A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 193 through 217 removed outlier: 3.734A pdb=" N TRP C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 217 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 221 Processing helix chain 'C' and resid 224 through 251 removed outlier: 4.052A pdb=" N LEU C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN C 248 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 262 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 302 removed outlier: 4.096A pdb=" N ARG C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 333 through 342 Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.915A pdb=" N VAL C 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'D' and resid 36 through 53 Proline residue: D 49 - end of helix removed outlier: 3.836A pdb=" N GLY D 53 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 60 removed outlier: 3.725A pdb=" N LEU D 58 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 60 " --> pdb=" O SER D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 118 through 137 removed outlier: 3.549A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 181 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 192 through 217 removed outlier: 3.895A pdb=" N PHE D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 217 " --> pdb=" O THR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 247 removed outlier: 3.579A pdb=" N ARG D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 302 Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 329 through 332 removed outlier: 3.672A pdb=" N GLN D 332 " --> pdb=" O ALA D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 332' Processing helix chain 'D' and resid 333 through 342 Processing helix chain 'D' and resid 353 through 359 removed outlier: 4.357A pdb=" N THR D 359 " --> pdb=" O VAL D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 363 No H-bonds generated for 'chain 'D' and resid 361 through 363' Processing helix chain 'E' and resid 35 through 46 Processing helix chain 'E' and resid 47 through 53 removed outlier: 3.722A pdb=" N ILE E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY E 53 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.607A pdb=" N ALA E 66 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 118 through 137 removed outlier: 3.629A pdb=" N ALA E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 192 through 215 removed outlier: 4.002A pdb=" N PHE E 196 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 215 " --> pdb=" O GLN E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 219 removed outlier: 6.262A pdb=" N SER E 219 " --> pdb=" O GLU E 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 219' Processing helix chain 'E' and resid 220 through 247 removed outlier: 5.120A pdb=" N VAL E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG E 227 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE E 235 " --> pdb=" O MET E 231 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 262 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 281 through 302 removed outlier: 3.836A pdb=" N ARG E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 333 through 342 removed outlier: 3.632A pdb=" N SER E 337 " --> pdb=" O GLN E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'F' and resid 36 through 47 Processing helix chain 'F' and resid 47 through 53 removed outlier: 3.875A pdb=" N ILE F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 66 removed outlier: 3.616A pdb=" N LEU F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA F 66 " --> pdb=" O LYS F 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 66' Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 118 through 136 removed outlier: 3.782A pdb=" N ALA F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 181 Processing helix chain 'F' and resid 192 through 217 removed outlier: 3.910A pdb=" N PHE F 196 " --> pdb=" O ASN F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 247 removed outlier: 3.670A pdb=" N GLN F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG F 230 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 281 through 302 Processing helix chain 'F' and resid 333 through 342 Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.604A pdb=" N SER F 358 " --> pdb=" O GLN F 355 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR F 359 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.550A pdb=" N LYS A 15 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A 94 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 6 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A 92 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU A 8 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS A 90 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 152 removed outlier: 6.474A pdb=" N GLY A 315 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE A 348 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 317 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N THR A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 319 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR A 26 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR A 351 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU A 28 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ARG A 366 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 27 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A 368 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 29 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N GLN A 370 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258 removed outlier: 5.417A pdb=" N ASP A 254 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER A 268 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 20 removed outlier: 5.433A pdb=" N ILE B 3 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU B 96 " --> pdb=" O ILE B 3 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 152 removed outlier: 6.365A pdb=" N GLY B 315 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE B 348 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 317 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 350 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE B 319 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR B 26 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR B 351 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU B 28 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ARG B 366 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 27 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU B 368 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B 29 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 9.806A pdb=" N GLN B 370 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 77 Processing sheet with id=AA8, first strand: chain 'B' and resid 255 through 258 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 20 removed outlier: 5.212A pdb=" N ILE C 3 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU C 96 " --> pdb=" O ILE C 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 148 through 152 removed outlier: 6.285A pdb=" N GLY C 315 " --> pdb=" O GLN C 346 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE C 348 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 317 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR C 350 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 319 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR C 26 " --> pdb=" O VAL C 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 75 removed outlier: 4.437A pdb=" N ARG C 73 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU C 84 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 253 through 258 removed outlier: 5.500A pdb=" N ASP C 254 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER C 268 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER C 258 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 264 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 17 through 19 removed outlier: 3.566A pdb=" N GLY D 95 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 103 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N MET D 106 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLU D 117 " --> pdb=" O MET D 106 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP D 108 " --> pdb=" O PRO D 115 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG D 110 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 148 through 152 removed outlier: 6.300A pdb=" N GLY D 315 " --> pdb=" O GLN D 346 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE D 348 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 317 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR D 350 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE D 319 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR D 26 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ARG D 366 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE D 27 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU D 368 " --> pdb=" O ILE D 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 74 through 77 Processing sheet with id=AB7, first strand: chain 'D' and resid 253 through 258 removed outlier: 5.425A pdb=" N ASP D 254 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER D 268 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 16 through 20 removed outlier: 7.096A pdb=" N THR E 94 " --> pdb=" O ASP E 4 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU E 6 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 92 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU E 8 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS E 90 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 148 through 152 removed outlier: 6.092A pdb=" N LEU E 148 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU E 318 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU E 150 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ASP E 320 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU E 152 " --> pdb=" O ASP E 320 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY E 315 " --> pdb=" O GLN E 346 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE E 348 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL E 317 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR E 350 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE E 319 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR E 26 " --> pdb=" O VAL E 349 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 253 through 258 removed outlier: 5.341A pdb=" N ASP E 254 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER E 268 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER E 258 " --> pdb=" O GLN E 264 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN E 264 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY E 273 " --> pdb=" O HIS E 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 16 through 20 removed outlier: 6.918A pdb=" N THR F 94 " --> pdb=" O ASP F 4 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 6 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR F 92 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU F 8 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS F 90 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS F 101 " --> pdb=" O TRP F 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 148 through 152 removed outlier: 6.258A pdb=" N GLY F 315 " --> pdb=" O GLN F 346 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE F 348 " --> pdb=" O GLY F 315 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL F 317 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR F 350 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE F 319 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR F 26 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR F 351 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU F 28 " --> pdb=" O THR F 351 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ARG F 366 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE F 27 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU F 368 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL F 29 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AC5, first strand: chain 'F' and resid 253 through 258 removed outlier: 5.442A pdb=" N ASP F 254 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER F 268 " --> pdb=" O ASP F 254 " (cutoff:3.500A) 794 hydrogen bonds defined for protein. 2139 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5995 1.34 - 1.46: 3260 1.46 - 1.57: 9049 1.57 - 1.69: 20 1.69 - 1.81: 156 Bond restraints: 18480 Sorted by residual: bond pdb=" CB ARG A 285 " pdb=" CG ARG A 285 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" CB VAL C 291 " pdb=" CG2 VAL C 291 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.73e-01 bond pdb=" CA GLN F 78 " pdb=" CB GLN F 78 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.69e-01 bond pdb=" CG1 ILE B 212 " pdb=" CD1 ILE B 212 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.40e-01 bond pdb=" CB PRO D 88 " pdb=" CG PRO D 88 " ideal model delta sigma weight residual 1.506 1.538 -0.032 3.90e-02 6.57e+02 6.61e-01 ... (remaining 18475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 24900 2.54 - 5.08: 126 5.08 - 7.62: 12 7.62 - 10.16: 2 10.16 - 12.70: 1 Bond angle restraints: 25041 Sorted by residual: angle pdb=" C LEU E 305 " pdb=" N GLN E 306 " pdb=" CA GLN E 306 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" CA LEU A 124 " pdb=" CB LEU A 124 " pdb=" CG LEU A 124 " ideal model delta sigma weight residual 116.30 129.00 -12.70 3.50e+00 8.16e-02 1.32e+01 angle pdb=" C LEU D 305 " pdb=" N GLN D 306 " pdb=" CA GLN D 306 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C ARG F 77 " pdb=" N GLN F 78 " pdb=" CA GLN F 78 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C LEU F 305 " pdb=" N GLN F 306 " pdb=" CA GLN F 306 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.95e+00 ... (remaining 25036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9965 17.92 - 35.85: 1030 35.85 - 53.77: 183 53.77 - 71.69: 59 71.69 - 89.62: 26 Dihedral angle restraints: 11263 sinusoidal: 4721 harmonic: 6542 Sorted by residual: dihedral pdb=" CA LEU E 245 " pdb=" C LEU E 245 " pdb=" N THR E 246 " pdb=" CA THR E 246 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LEU D 305 " pdb=" C LEU D 305 " pdb=" N GLN D 306 " pdb=" CA GLN D 306 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR C 246 " pdb=" C THR C 246 " pdb=" N GLN C 247 " pdb=" CA GLN C 247 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 11260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1566 0.029 - 0.057: 771 0.057 - 0.086: 276 0.086 - 0.115: 122 0.115 - 0.143: 34 Chirality restraints: 2769 Sorted by residual: chirality pdb=" CA ILE A 91 " pdb=" N ILE A 91 " pdb=" C ILE A 91 " pdb=" CB ILE A 91 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE E 91 " pdb=" N ILE E 91 " pdb=" C ILE E 91 " pdb=" CB ILE E 91 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA VAL C 266 " pdb=" N VAL C 266 " pdb=" C VAL C 266 " pdb=" CB VAL C 266 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 2766 not shown) Planarity restraints: 3195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 327 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO D 328 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 328 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 328 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 48 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO E 49 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 49 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 49 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 30 " -0.032 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO C 31 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 31 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 31 " -0.028 5.00e-02 4.00e+02 ... (remaining 3192 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 438 2.71 - 3.26: 16908 3.26 - 3.81: 26793 3.81 - 4.35: 34009 4.35 - 4.90: 59820 Nonbonded interactions: 137968 Sorted by model distance: nonbonded pdb=" OG1 THR B 37 " pdb=" O3G ATP B 501 " model vdw 2.166 3.040 nonbonded pdb=" O CYS E 244 " pdb=" OG SER E 337 " model vdw 2.185 3.040 nonbonded pdb=" OG1 THR D 37 " pdb=" O3G ATP D 501 " model vdw 2.194 3.040 nonbonded pdb=" O PRO C 147 " pdb=" OH TYR C 183 " model vdw 2.195 3.040 nonbonded pdb=" O SER A 178 " pdb=" OG SER A 181 " model vdw 2.205 3.040 ... (remaining 137963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'B' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'C' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'D' and resid 1 through 382) selection = (chain 'E' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'F' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) } 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: 0.010 Normalize map: mean=0, sd=1: 1.140 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.210 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 : 0.003 0.034 18480 Z= 0.143 Angle : 0.534 12.705 25041 Z= 0.292 Chirality : 0.042 0.143 2769 Planarity : 0.005 0.051 3195 Dihedral : 15.607 89.617 6999 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.17), residues: 2201 helix: 1.08 (0.19), residues: 765 sheet: -0.27 (0.22), residues: 503 loop : -1.22 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.012 0.001 TYR B 200 PHE 0.032 0.001 PHE C 296 TRP 0.021 0.002 TRP F 199 HIS 0.006 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00328 (18480) covalent geometry : angle 0.53403 (25041) hydrogen bonds : bond 0.15644 ( 794) hydrogen bonds : angle 5.49794 ( 2139) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.689 Fit side-chains REVERT: A 15 LYS cc_start: 0.8214 (tttt) cc_final: 0.7928 (tttm) REVERT: A 41 ASP cc_start: 0.7138 (m-30) cc_final: 0.6861 (m-30) REVERT: A 57 SER cc_start: 0.7928 (p) cc_final: 0.7575 (m) REVERT: A 59 TYR cc_start: 0.7908 (m-80) cc_final: 0.7486 (m-80) REVERT: A 63 LYS cc_start: 0.7663 (mttm) cc_final: 0.7226 (mtpt) REVERT: A 110 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6626 (ttm170) REVERT: A 129 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 133 LYS cc_start: 0.7446 (ttpp) cc_final: 0.6113 (mmtt) REVERT: A 134 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6911 (mtm-85) REVERT: A 137 GLU cc_start: 0.6876 (tt0) cc_final: 0.6376 (mt-10) REVERT: A 231 MET cc_start: 0.8323 (mtm) cc_final: 0.7927 (mtp) REVERT: A 256 GLU cc_start: 0.8507 (pt0) cc_final: 0.8224 (pt0) REVERT: A 290 MET cc_start: 0.8130 (ttp) cc_final: 0.7860 (ttm) REVERT: A 334 ILE cc_start: 0.8008 (tt) cc_final: 0.7681 (pt) REVERT: A 361 LYS cc_start: 0.8340 (mttm) cc_final: 0.7501 (ptmm) REVERT: A 362 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7848 (ttp80) REVERT: A 377 LYS cc_start: 0.7202 (mtpt) cc_final: 0.6429 (tptp) REVERT: B 1 MET cc_start: 0.5957 (ptp) cc_final: 0.5400 (mtm) REVERT: B 18 ASP cc_start: 0.7731 (m-30) cc_final: 0.7521 (m-30) REVERT: B 70 GLU cc_start: 0.7511 (mp0) cc_final: 0.7063 (mt-10) REVERT: B 110 ARG cc_start: 0.7278 (ttm110) cc_final: 0.6614 (ttm170) REVERT: B 129 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6927 (mt-10) REVERT: B 133 LYS cc_start: 0.7408 (ttmm) cc_final: 0.6255 (mmtt) REVERT: B 154 THR cc_start: 0.8675 (m) cc_final: 0.8465 (p) REVERT: B 236 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6587 (mt0) REVERT: B 256 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6134 (mp0) REVERT: B 262 ASN cc_start: 0.8253 (t0) cc_final: 0.7876 (m-40) REVERT: B 290 MET cc_start: 0.8058 (ttp) cc_final: 0.7798 (ttm) REVERT: B 312 LYS cc_start: 0.7930 (mttm) cc_final: 0.7688 (mttt) REVERT: B 324 MET cc_start: 0.7373 (mtm) cc_final: 0.6366 (mmm) REVERT: B 362 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8007 (ttp80) REVERT: B 373 ASN cc_start: 0.7983 (m-40) cc_final: 0.7697 (m-40) REVERT: C 5 LYS cc_start: 0.7977 (tttp) cc_final: 0.7432 (tptm) REVERT: C 16 GLN cc_start: 0.7819 (tt0) cc_final: 0.7393 (tm130) REVERT: C 23 GLU cc_start: 0.6883 (tt0) cc_final: 0.6519 (tt0) REVERT: C 77 ARG cc_start: 0.7082 (mtt-85) cc_final: 0.6404 (mtm-85) REVERT: C 78 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7101 (tp-100) REVERT: C 110 ARG cc_start: 0.7126 (mtt-85) cc_final: 0.6696 (mmt180) REVERT: C 145 GLU cc_start: 0.6566 (pm20) cc_final: 0.6296 (pt0) REVERT: C 244 CYS cc_start: 0.7147 (t) cc_final: 0.6535 (m) REVERT: C 361 LYS cc_start: 0.7879 (mttm) cc_final: 0.7446 (ptpp) REVERT: C 377 LYS cc_start: 0.7643 (mtmm) cc_final: 0.6845 (tmtt) REVERT: D 214 GLN cc_start: 0.6932 (tt0) cc_final: 0.6729 (tt0) REVERT: D 233 GLU cc_start: 0.5402 (mt-10) cc_final: 0.4980 (mm-30) REVERT: D 314 GLN cc_start: 0.7924 (mt0) cc_final: 0.7600 (mt0) REVERT: E 5 LYS cc_start: 0.7494 (ptmt) cc_final: 0.6781 (ptpt) REVERT: E 16 GLN cc_start: 0.7990 (pt0) cc_final: 0.7567 (pm20) REVERT: E 75 ILE cc_start: 0.8055 (pt) cc_final: 0.7496 (mp) REVERT: E 77 ARG cc_start: 0.7277 (mtp180) cc_final: 0.6489 (mtm-85) REVERT: E 84 GLU cc_start: 0.7338 (tp30) cc_final: 0.6637 (mm-30) REVERT: E 106 MET cc_start: 0.7704 (ttm) cc_final: 0.7324 (tmm) REVERT: E 112 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6989 (mp0) REVERT: E 312 LYS cc_start: 0.7460 (mmtp) cc_final: 0.6836 (mttp) REVERT: E 324 MET cc_start: 0.8167 (ttp) cc_final: 0.7852 (ttm) REVERT: E 363 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7596 (mp0) REVERT: E 377 LYS cc_start: 0.7385 (mttp) cc_final: 0.6513 (mptt) REVERT: F 4 ASP cc_start: 0.7947 (m-30) cc_final: 0.7642 (m-30) REVERT: F 214 GLN cc_start: 0.6411 (tm-30) cc_final: 0.6105 (tt0) REVERT: F 261 HIS cc_start: 0.7727 (m90) cc_final: 0.5828 (t70) REVERT: F 262 ASN cc_start: 0.7332 (t0) cc_final: 0.6957 (t0) REVERT: F 267 MET cc_start: 0.8641 (mtt) cc_final: 0.8199 (mmt) REVERT: F 278 SER cc_start: 0.8407 (t) cc_final: 0.8054 (p) REVERT: F 323 ASP cc_start: 0.7517 (p0) cc_final: 0.7238 (p0) outliers start: 0 outliers final: 1 residues processed: 405 average time/residue: 0.6166 time to fit residues: 276.3031 Evaluate side-chains 262 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0770 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS A 236 GLN A 253 HIS ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN B 210 HIS B 263 GLN B 314 GLN D 130 GLN D 302 ASN D 332 GLN E 130 GLN F 302 ASN F 307 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.205293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143937 restraints weight = 16952.112| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.63 r_work: 0.3203 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 18480 Z= 0.260 Angle : 0.738 11.952 25041 Z= 0.381 Chirality : 0.049 0.187 2769 Planarity : 0.007 0.097 3195 Dihedral : 9.339 82.227 2549 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.16 % Allowed : 10.52 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2201 helix: 0.61 (0.18), residues: 788 sheet: -0.44 (0.22), residues: 498 loop : -1.31 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 44 TYR 0.019 0.002 TYR B 159 PHE 0.036 0.002 PHE A 296 TRP 0.026 0.002 TRP F 158 HIS 0.015 0.002 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00640 (18480) covalent geometry : angle 0.73766 (25041) hydrogen bonds : bond 0.07027 ( 794) hydrogen bonds : angle 4.85404 ( 2139) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 18 ASP cc_start: 0.8157 (m-30) cc_final: 0.7954 (m-30) REVERT: A 59 TYR cc_start: 0.8207 (m-80) cc_final: 0.7702 (m-80) REVERT: A 63 LYS cc_start: 0.8190 (mttm) cc_final: 0.7769 (mtpt) REVERT: A 110 ARG cc_start: 0.7618 (ttm110) cc_final: 0.7071 (ttm170) REVERT: A 133 LYS cc_start: 0.7956 (ttpp) cc_final: 0.6676 (mmtt) REVERT: A 134 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.7345 (mtm-85) REVERT: A 248 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8257 (tt0) REVERT: A 267 MET cc_start: 0.9274 (mtp) cc_final: 0.8973 (mtm) REVERT: A 312 LYS cc_start: 0.8543 (mttp) cc_final: 0.8315 (mttt) REVERT: A 334 ILE cc_start: 0.8475 (tt) cc_final: 0.8082 (pt) REVERT: B 110 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7064 (ttt180) REVERT: B 129 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7622 (mt-10) REVERT: B 133 LYS cc_start: 0.7762 (ttmm) cc_final: 0.6712 (mmtt) REVERT: B 236 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7515 (mt0) REVERT: B 262 ASN cc_start: 0.8803 (t0) cc_final: 0.8419 (m-40) REVERT: B 324 MET cc_start: 0.8047 (mtm) cc_final: 0.7520 (mmm) REVERT: B 336 GLN cc_start: 0.8298 (tp-100) cc_final: 0.8043 (tp40) REVERT: B 373 ASN cc_start: 0.8256 (m-40) cc_final: 0.8053 (m-40) REVERT: C 16 GLN cc_start: 0.8129 (tt0) cc_final: 0.7462 (tm-30) REVERT: C 77 ARG cc_start: 0.7950 (mtt-85) cc_final: 0.6926 (mtm-85) REVERT: C 110 ARG cc_start: 0.7455 (mtt-85) cc_final: 0.6878 (mtp85) REVERT: C 112 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6829 (mp0) REVERT: C 145 GLU cc_start: 0.6482 (pm20) cc_final: 0.5488 (mm-30) REVERT: C 190 THR cc_start: 0.6987 (m) cc_final: 0.6732 (p) REVERT: C 192 ASN cc_start: 0.6333 (p0) cc_final: 0.5935 (p0) REVERT: C 244 CYS cc_start: 0.6989 (t) cc_final: 0.6243 (m) REVERT: C 336 GLN cc_start: 0.6542 (mm110) cc_final: 0.6287 (mm110) REVERT: C 361 LYS cc_start: 0.7549 (mttm) cc_final: 0.6990 (ptpp) REVERT: C 377 LYS cc_start: 0.7319 (mtmm) cc_final: 0.6034 (tppt) REVERT: D 106 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5845 (tpp) REVERT: D 120 MET cc_start: 0.5225 (tpp) cc_final: 0.4980 (ttt) REVERT: D 262 ASN cc_start: 0.8219 (t0) cc_final: 0.7733 (t0) REVERT: D 271 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6751 (mt0) REVERT: D 355 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6566 (mp10) REVERT: E 5 LYS cc_start: 0.7262 (ptmt) cc_final: 0.6331 (ptpt) REVERT: E 16 GLN cc_start: 0.8191 (pt0) cc_final: 0.7957 (pt0) REVERT: E 77 ARG cc_start: 0.7960 (mtp180) cc_final: 0.6794 (mtm-85) REVERT: E 106 MET cc_start: 0.8102 (ttm) cc_final: 0.7417 (tmm) REVERT: E 112 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7005 (mp0) REVERT: E 300 LYS cc_start: 0.5410 (OUTLIER) cc_final: 0.4879 (mtmt) REVERT: E 324 MET cc_start: 0.7429 (ttp) cc_final: 0.7193 (ttm) REVERT: E 363 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7323 (mp0) REVERT: E 377 LYS cc_start: 0.7135 (mttp) cc_final: 0.6795 (mttt) REVERT: F 4 ASP cc_start: 0.7709 (m-30) cc_final: 0.7374 (m-30) REVERT: F 5 LYS cc_start: 0.7635 (pttp) cc_final: 0.7003 (ptpp) REVERT: F 6 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7382 (tm) REVERT: F 70 GLU cc_start: 0.6099 (mp0) cc_final: 0.5684 (mt-10) REVERT: F 106 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.6185 (tpp) REVERT: F 195 GLN cc_start: 0.7148 (mp10) cc_final: 0.6637 (mt0) REVERT: F 214 GLN cc_start: 0.6929 (tm-30) cc_final: 0.6578 (tt0) REVERT: F 262 ASN cc_start: 0.8252 (t0) cc_final: 0.7874 (t0) REVERT: F 267 MET cc_start: 0.8865 (mtt) cc_final: 0.8544 (mtt) REVERT: F 278 SER cc_start: 0.8547 (t) cc_final: 0.8194 (p) REVERT: F 355 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.6967 (mt0) outliers start: 42 outliers final: 15 residues processed: 292 average time/residue: 0.5821 time to fit residues: 188.5758 Evaluate side-chains 253 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 148 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 179 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 130 GLN ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN C 130 GLN D 302 ASN D 344 GLN F 302 ASN F 307 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.206202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.145506 restraints weight = 17181.399| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.65 r_work: 0.3217 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18480 Z= 0.173 Angle : 0.595 8.656 25041 Z= 0.314 Chirality : 0.043 0.154 2769 Planarity : 0.005 0.052 3195 Dihedral : 8.605 81.204 2547 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.57 % Allowed : 13.96 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.17), residues: 2201 helix: 0.87 (0.19), residues: 781 sheet: -0.51 (0.22), residues: 503 loop : -1.26 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 362 TYR 0.012 0.001 TYR B 159 PHE 0.024 0.002 PHE A 296 TRP 0.022 0.002 TRP D 199 HIS 0.010 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00406 (18480) covalent geometry : angle 0.59465 (25041) hydrogen bonds : bond 0.05761 ( 794) hydrogen bonds : angle 4.60568 ( 2139) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 0.638 Fit side-chains REVERT: A 59 TYR cc_start: 0.8251 (m-80) cc_final: 0.7801 (m-80) REVERT: A 63 LYS cc_start: 0.8186 (mttm) cc_final: 0.7758 (mtpt) REVERT: A 110 ARG cc_start: 0.7578 (ttm110) cc_final: 0.6987 (ttm170) REVERT: A 133 LYS cc_start: 0.7957 (ttpp) cc_final: 0.6564 (mmtt) REVERT: A 134 ARG cc_start: 0.7544 (mmm-85) cc_final: 0.7107 (mtm-85) REVERT: A 231 MET cc_start: 0.8652 (mtm) cc_final: 0.8087 (mtp) REVERT: A 248 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8231 (tt0) REVERT: A 312 LYS cc_start: 0.8410 (mttp) cc_final: 0.8175 (mttt) REVERT: A 334 ILE cc_start: 0.8483 (tt) cc_final: 0.8147 (pt) REVERT: A 362 ARG cc_start: 0.8447 (ptm-80) cc_final: 0.8231 (ptm-80) REVERT: B 110 ARG cc_start: 0.7647 (ttm110) cc_final: 0.7019 (ttt180) REVERT: B 129 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7509 (mt-10) REVERT: B 133 LYS cc_start: 0.7741 (ttmm) cc_final: 0.6627 (mmtt) REVERT: B 236 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7539 (mt0) REVERT: B 262 ASN cc_start: 0.8818 (t0) cc_final: 0.8406 (m-40) REVERT: B 312 LYS cc_start: 0.8374 (mttp) cc_final: 0.8162 (mttt) REVERT: B 324 MET cc_start: 0.8048 (mtm) cc_final: 0.7471 (mmm) REVERT: B 336 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7945 (tp40) REVERT: C 16 GLN cc_start: 0.8093 (tt0) cc_final: 0.7433 (tm-30) REVERT: C 77 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.6670 (mtm-85) REVERT: C 110 ARG cc_start: 0.7462 (mtt-85) cc_final: 0.6903 (mtp85) REVERT: C 112 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6719 (mp0) REVERT: C 145 GLU cc_start: 0.6578 (pm20) cc_final: 0.5509 (mm-30) REVERT: C 190 THR cc_start: 0.6763 (m) cc_final: 0.6481 (p) REVERT: C 244 CYS cc_start: 0.6749 (t) cc_final: 0.6067 (m) REVERT: C 336 GLN cc_start: 0.6438 (mm110) cc_final: 0.6171 (mm110) REVERT: C 361 LYS cc_start: 0.7575 (mttm) cc_final: 0.7039 (ptpp) REVERT: D 106 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5919 (tpp) REVERT: D 120 MET cc_start: 0.5589 (tpp) cc_final: 0.5052 (mtt) REVERT: D 247 GLN cc_start: 0.7110 (tt0) cc_final: 0.6863 (tt0) REVERT: D 262 ASN cc_start: 0.8014 (t0) cc_final: 0.7750 (t0) REVERT: D 267 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8456 (tpp) REVERT: D 271 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6791 (mt0) REVERT: E 77 ARG cc_start: 0.7949 (mtp180) cc_final: 0.6679 (mtm-85) REVERT: E 106 MET cc_start: 0.8078 (ttm) cc_final: 0.7360 (tmm) REVERT: E 110 ARG cc_start: 0.7521 (ttm110) cc_final: 0.6759 (mtp85) REVERT: E 112 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6931 (mp0) REVERT: E 300 LYS cc_start: 0.5334 (OUTLIER) cc_final: 0.4684 (mtmt) REVERT: E 363 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7220 (mp0) REVERT: E 377 LYS cc_start: 0.7113 (mttp) cc_final: 0.6102 (mtmt) REVERT: F 4 ASP cc_start: 0.7745 (m-30) cc_final: 0.7424 (m-30) REVERT: F 6 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7336 (tm) REVERT: F 106 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.6203 (tpp) REVERT: F 120 MET cc_start: 0.5588 (tpp) cc_final: 0.5251 (ttt) REVERT: F 195 GLN cc_start: 0.7110 (mp10) cc_final: 0.6437 (mt0) REVERT: F 214 GLN cc_start: 0.6822 (tm-30) cc_final: 0.6456 (tt0) REVERT: F 256 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7745 (pt0) REVERT: F 262 ASN cc_start: 0.7969 (t0) cc_final: 0.7744 (t0) REVERT: F 267 MET cc_start: 0.8827 (mtt) cc_final: 0.8498 (mtt) REVERT: F 271 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6650 (mt0) REVERT: F 278 SER cc_start: 0.8411 (t) cc_final: 0.8078 (p) REVERT: F 355 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.6903 (mt0) outliers start: 50 outliers final: 15 residues processed: 273 average time/residue: 0.5785 time to fit residues: 175.1198 Evaluate side-chains 250 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 195 optimal weight: 0.7980 chunk 211 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS C 130 GLN C 352 HIS D 192 ASN D 302 ASN E 375 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.204836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144002 restraints weight = 17211.587| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.67 r_work: 0.3189 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18480 Z= 0.196 Angle : 0.619 7.896 25041 Z= 0.324 Chirality : 0.044 0.154 2769 Planarity : 0.005 0.061 3195 Dihedral : 8.263 81.538 2547 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.70 % Allowed : 14.48 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.17), residues: 2201 helix: 0.81 (0.19), residues: 781 sheet: -0.60 (0.22), residues: 503 loop : -1.27 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 362 TYR 0.016 0.002 TYR B 159 PHE 0.028 0.002 PHE A 296 TRP 0.022 0.002 TRP D 199 HIS 0.012 0.001 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00476 (18480) covalent geometry : angle 0.61902 (25041) hydrogen bonds : bond 0.05950 ( 794) hydrogen bonds : angle 4.58511 ( 2139) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 231 time to evaluate : 0.590 Fit side-chains REVERT: A 59 TYR cc_start: 0.8244 (m-80) cc_final: 0.7722 (m-80) REVERT: A 63 LYS cc_start: 0.8227 (mttm) cc_final: 0.7806 (mtpt) REVERT: A 110 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7063 (ttt180) REVERT: A 133 LYS cc_start: 0.7975 (ttpp) cc_final: 0.6478 (mmtt) REVERT: A 134 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7256 (mtm-85) REVERT: A 231 MET cc_start: 0.8639 (mtm) cc_final: 0.8049 (mtp) REVERT: A 248 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8245 (tt0) REVERT: A 334 ILE cc_start: 0.8483 (tt) cc_final: 0.8181 (pt) REVERT: B 110 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7051 (ttt180) REVERT: B 129 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7524 (mt-10) REVERT: B 133 LYS cc_start: 0.7711 (ttmm) cc_final: 0.6620 (mmtt) REVERT: B 231 MET cc_start: 0.8625 (mtt) cc_final: 0.8075 (mtp) REVERT: B 236 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7459 (mt0) REVERT: B 312 LYS cc_start: 0.8410 (mttp) cc_final: 0.8189 (mttt) REVERT: B 324 MET cc_start: 0.8066 (mtm) cc_final: 0.7534 (mmm) REVERT: B 336 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7993 (tp40) REVERT: C 5 LYS cc_start: 0.7246 (tttp) cc_final: 0.6760 (tttm) REVERT: C 16 GLN cc_start: 0.7969 (tt0) cc_final: 0.7449 (tm-30) REVERT: C 77 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.6613 (mtm-85) REVERT: C 110 ARG cc_start: 0.7684 (mtt-85) cc_final: 0.6857 (mtp85) REVERT: C 112 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6771 (mp0) REVERT: C 145 GLU cc_start: 0.6593 (pm20) cc_final: 0.5673 (mm-30) REVERT: C 190 THR cc_start: 0.6898 (m) cc_final: 0.6608 (p) REVERT: C 244 CYS cc_start: 0.6932 (t) cc_final: 0.6158 (m) REVERT: C 336 GLN cc_start: 0.6446 (mm110) cc_final: 0.6164 (mm110) REVERT: C 361 LYS cc_start: 0.7550 (mttm) cc_final: 0.6926 (mtmm) REVERT: D 85 MET cc_start: 0.6838 (mmm) cc_final: 0.6558 (tpt) REVERT: D 106 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.6093 (tpp) REVERT: D 120 MET cc_start: 0.5465 (tpp) cc_final: 0.5137 (mtt) REVERT: D 195 GLN cc_start: 0.7135 (mp10) cc_final: 0.6694 (mt0) REVERT: D 247 GLN cc_start: 0.7210 (tt0) cc_final: 0.6942 (tt0) REVERT: D 262 ASN cc_start: 0.8100 (t0) cc_final: 0.7688 (t0) REVERT: D 267 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8454 (tpp) REVERT: D 271 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6711 (mt0) REVERT: D 355 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6394 (mt0) REVERT: E 77 ARG cc_start: 0.7886 (mtp180) cc_final: 0.6591 (mtm-85) REVERT: E 84 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7438 (mm-30) REVERT: E 106 MET cc_start: 0.8097 (ttm) cc_final: 0.7344 (tmm) REVERT: E 110 ARG cc_start: 0.7573 (ttm110) cc_final: 0.6775 (mtp85) REVERT: E 112 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6872 (mp0) REVERT: E 300 LYS cc_start: 0.5344 (OUTLIER) cc_final: 0.4666 (mtmt) REVERT: E 324 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7512 (ttm) REVERT: E 363 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7214 (mp0) REVERT: E 377 LYS cc_start: 0.7341 (mttp) cc_final: 0.6237 (mtmt) REVERT: F 4 ASP cc_start: 0.7767 (m-30) cc_final: 0.7459 (m-30) REVERT: F 5 LYS cc_start: 0.7744 (pttp) cc_final: 0.7060 (ptpp) REVERT: F 6 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7421 (tm) REVERT: F 68 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6424 (mtp85) REVERT: F 106 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.6271 (tpp) REVERT: F 195 GLN cc_start: 0.7253 (mp10) cc_final: 0.6560 (mt0) REVERT: F 214 GLN cc_start: 0.6888 (tm-30) cc_final: 0.6461 (tt0) REVERT: F 256 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7806 (pt0) REVERT: F 262 ASN cc_start: 0.8049 (t0) cc_final: 0.7753 (t0) REVERT: F 271 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6625 (mt0) REVERT: F 278 SER cc_start: 0.8435 (t) cc_final: 0.8108 (p) REVERT: F 336 GLN cc_start: 0.7076 (tp40) cc_final: 0.6158 (pt0) REVERT: F 355 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7062 (mt0) outliers start: 72 outliers final: 31 residues processed: 282 average time/residue: 0.6047 time to fit residues: 189.0784 Evaluate side-chains 273 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 162 optimal weight: 0.0970 chunk 113 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 263 GLN C 130 GLN D 192 ASN D 375 ASN F 307 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.205821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.146774 restraints weight = 17231.246| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.86 r_work: 0.3173 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18480 Z= 0.157 Angle : 0.570 9.537 25041 Z= 0.301 Chirality : 0.042 0.150 2769 Planarity : 0.005 0.056 3195 Dihedral : 8.086 82.916 2547 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.29 % Allowed : 15.91 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.17), residues: 2201 helix: 0.97 (0.19), residues: 781 sheet: -0.60 (0.21), residues: 507 loop : -1.23 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 362 TYR 0.015 0.001 TYR B 159 PHE 0.029 0.001 PHE A 296 TRP 0.022 0.002 TRP D 199 HIS 0.011 0.001 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00372 (18480) covalent geometry : angle 0.56965 (25041) hydrogen bonds : bond 0.05332 ( 794) hydrogen bonds : angle 4.47553 ( 2139) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 245 time to evaluate : 0.711 Fit side-chains REVERT: A 25 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8300 (tp) REVERT: A 59 TYR cc_start: 0.8201 (m-80) cc_final: 0.7679 (m-80) REVERT: A 63 LYS cc_start: 0.8195 (mttm) cc_final: 0.7752 (mtpt) REVERT: A 110 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7020 (ttt180) REVERT: A 133 LYS cc_start: 0.7904 (ttpp) cc_final: 0.6312 (mmtt) REVERT: A 134 ARG cc_start: 0.7635 (mmm-85) cc_final: 0.7280 (mtm-85) REVERT: A 231 MET cc_start: 0.8580 (mtm) cc_final: 0.7960 (mtp) REVERT: A 248 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8267 (tt0) REVERT: A 250 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8278 (p) REVERT: A 267 MET cc_start: 0.9271 (mtp) cc_final: 0.8889 (mtm) REVERT: B 110 ARG cc_start: 0.7732 (ttm110) cc_final: 0.6989 (ttt180) REVERT: B 129 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 133 LYS cc_start: 0.7648 (ttmm) cc_final: 0.6512 (mmtt) REVERT: B 236 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7386 (mt0) REVERT: B 312 LYS cc_start: 0.8378 (mttp) cc_final: 0.8158 (mttt) REVERT: B 324 MET cc_start: 0.8061 (mtm) cc_final: 0.7506 (mmm) REVERT: B 336 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7983 (tp40) REVERT: C 5 LYS cc_start: 0.7180 (tttp) cc_final: 0.6591 (tttm) REVERT: C 16 GLN cc_start: 0.7933 (tt0) cc_final: 0.7415 (tm-30) REVERT: C 77 ARG cc_start: 0.7837 (mtt-85) cc_final: 0.6507 (mtm-85) REVERT: C 110 ARG cc_start: 0.7747 (mtt-85) cc_final: 0.6848 (mtp85) REVERT: C 112 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6663 (mp0) REVERT: C 145 GLU cc_start: 0.6580 (pm20) cc_final: 0.5656 (mm-30) REVERT: C 190 THR cc_start: 0.6937 (m) cc_final: 0.6611 (p) REVERT: C 336 GLN cc_start: 0.6382 (mm110) cc_final: 0.6102 (mm110) REVERT: D 4 ASP cc_start: 0.7420 (m-30) cc_final: 0.6979 (m-30) REVERT: D 85 MET cc_start: 0.6902 (mmm) cc_final: 0.6627 (tpt) REVERT: D 106 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.6160 (tpp) REVERT: D 120 MET cc_start: 0.5541 (tpp) cc_final: 0.5130 (mtt) REVERT: D 195 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6607 (mt0) REVERT: D 247 GLN cc_start: 0.7081 (tt0) cc_final: 0.6779 (tt0) REVERT: D 262 ASN cc_start: 0.8062 (t0) cc_final: 0.7767 (t0) REVERT: D 267 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8454 (tpp) REVERT: D 271 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6665 (mt0) REVERT: D 355 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6344 (mt0) REVERT: E 77 ARG cc_start: 0.7834 (mtp180) cc_final: 0.6540 (mtm-85) REVERT: E 84 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7394 (mm-30) REVERT: E 106 MET cc_start: 0.8145 (ttm) cc_final: 0.7331 (tmm) REVERT: E 110 ARG cc_start: 0.7546 (ttm110) cc_final: 0.6733 (mtp85) REVERT: E 112 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6766 (mp0) REVERT: E 324 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7356 (ttm) REVERT: E 363 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7240 (mp0) REVERT: E 377 LYS cc_start: 0.7253 (mttp) cc_final: 0.6148 (mtmt) REVERT: F 4 ASP cc_start: 0.7610 (m-30) cc_final: 0.7287 (m-30) REVERT: F 5 LYS cc_start: 0.7631 (pttp) cc_final: 0.6955 (ptpp) REVERT: F 6 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7391 (tm) REVERT: F 68 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6255 (mtp85) REVERT: F 106 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.6215 (tpp) REVERT: F 120 MET cc_start: 0.5492 (tpp) cc_final: 0.4999 (mtt) REVERT: F 195 GLN cc_start: 0.7042 (mp10) cc_final: 0.6525 (mt0) REVERT: F 203 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7525 (tp) REVERT: F 214 GLN cc_start: 0.6849 (tm-30) cc_final: 0.6370 (tt0) REVERT: F 256 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: F 262 ASN cc_start: 0.7845 (t0) cc_final: 0.7616 (t0) REVERT: F 271 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6538 (mp10) REVERT: F 278 SER cc_start: 0.8448 (t) cc_final: 0.8109 (p) REVERT: F 336 GLN cc_start: 0.6991 (tp40) cc_final: 0.6062 (pt0) REVERT: F 355 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7033 (mt0) outliers start: 64 outliers final: 26 residues processed: 288 average time/residue: 0.5831 time to fit residues: 186.3571 Evaluate side-chains 269 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 191 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 48 optimal weight: 0.0170 chunk 25 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 130 GLN D 192 ASN D 253 HIS D 370 GLN D 375 ASN E 113 GLN F 306 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.204970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130736 restraints weight = 17021.815| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.88 r_work: 0.3175 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18480 Z= 0.206 Angle : 0.640 8.945 25041 Z= 0.332 Chirality : 0.045 0.157 2769 Planarity : 0.005 0.060 3195 Dihedral : 8.193 85.983 2547 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.00 % Allowed : 16.07 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.17), residues: 2201 helix: 0.76 (0.19), residues: 789 sheet: -0.63 (0.22), residues: 505 loop : -1.26 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 362 TYR 0.016 0.002 TYR B 159 PHE 0.033 0.002 PHE A 296 TRP 0.022 0.002 TRP F 158 HIS 0.011 0.002 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00505 (18480) covalent geometry : angle 0.63959 (25041) hydrogen bonds : bond 0.06056 ( 794) hydrogen bonds : angle 4.57197 ( 2139) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 226 time to evaluate : 0.698 Fit side-chains REVERT: A 25 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 59 TYR cc_start: 0.8373 (m-80) cc_final: 0.7874 (m-80) REVERT: A 63 LYS cc_start: 0.8299 (mttm) cc_final: 0.7943 (mtpt) REVERT: A 110 ARG cc_start: 0.7816 (ttm110) cc_final: 0.7224 (ttt180) REVERT: A 134 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7679 (mtp180) REVERT: A 231 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8153 (mtp) REVERT: A 248 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8415 (tt0) REVERT: A 312 LYS cc_start: 0.8566 (mttt) cc_final: 0.8360 (mttp) REVERT: A 334 ILE cc_start: 0.8631 (tt) cc_final: 0.8310 (pt) REVERT: A 336 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8256 (tp40) REVERT: B 84 GLU cc_start: 0.8279 (pt0) cc_final: 0.8006 (pt0) REVERT: B 110 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7221 (ttt180) REVERT: B 129 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 133 LYS cc_start: 0.8010 (ttmm) cc_final: 0.6889 (mmtt) REVERT: B 236 GLN cc_start: 0.8550 (tm-30) cc_final: 0.7749 (mt0) REVERT: B 324 MET cc_start: 0.8217 (mtm) cc_final: 0.7733 (mmm) REVERT: B 336 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8203 (tp40) REVERT: C 5 LYS cc_start: 0.7474 (tttp) cc_final: 0.7009 (tttm) REVERT: C 16 GLN cc_start: 0.8090 (tt0) cc_final: 0.7618 (tm-30) REVERT: C 77 ARG cc_start: 0.7982 (mtt-85) cc_final: 0.6764 (mtm-85) REVERT: C 110 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7075 (mtp85) REVERT: C 145 GLU cc_start: 0.6678 (pm20) cc_final: 0.5768 (mm-30) REVERT: C 190 THR cc_start: 0.7143 (m) cc_final: 0.6775 (p) REVERT: D 106 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.6166 (tpp) REVERT: D 120 MET cc_start: 0.5651 (tpp) cc_final: 0.5080 (mtt) REVERT: D 192 ASN cc_start: 0.8465 (p0) cc_final: 0.8255 (p0) REVERT: D 195 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6991 (mt0) REVERT: D 247 GLN cc_start: 0.7380 (tt0) cc_final: 0.7144 (tt0) REVERT: D 267 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8552 (tpp) REVERT: D 271 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6748 (mt0) REVERT: D 355 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6527 (mp10) REVERT: E 77 ARG cc_start: 0.8063 (mtp180) cc_final: 0.6798 (mtm-85) REVERT: E 84 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: E 106 MET cc_start: 0.8349 (ttm) cc_final: 0.7592 (tmm) REVERT: E 110 ARG cc_start: 0.7715 (ttm110) cc_final: 0.6979 (mtp85) REVERT: E 112 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7029 (mp0) REVERT: E 324 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7672 (ttm) REVERT: E 363 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7402 (mp0) REVERT: E 377 LYS cc_start: 0.7422 (mttp) cc_final: 0.6395 (mtmt) REVERT: F 4 ASP cc_start: 0.7702 (m-30) cc_final: 0.7415 (m-30) REVERT: F 5 LYS cc_start: 0.7698 (pttp) cc_final: 0.7035 (ptpp) REVERT: F 6 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7056 (tm) REVERT: F 106 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.6302 (tpp) REVERT: F 195 GLN cc_start: 0.7483 (mp10) cc_final: 0.6897 (mt0) REVERT: F 203 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7893 (tp) REVERT: F 214 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6678 (tt0) REVERT: F 256 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: F 262 ASN cc_start: 0.8021 (t0) cc_final: 0.7687 (t0) REVERT: F 267 MET cc_start: 0.8954 (mmt) cc_final: 0.8513 (tpp) REVERT: F 271 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6514 (mp10) REVERT: F 278 SER cc_start: 0.8628 (t) cc_final: 0.8349 (p) REVERT: F 312 LYS cc_start: 0.7495 (mtpp) cc_final: 0.7270 (mtpp) REVERT: F 336 GLN cc_start: 0.7359 (tp40) cc_final: 0.6412 (pt0) REVERT: F 355 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7134 (mt0) outliers start: 78 outliers final: 41 residues processed: 284 average time/residue: 0.5814 time to fit residues: 183.4099 Evaluate side-chains 277 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 31 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 130 GLN D 370 GLN D 375 ASN F 302 ASN F 307 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.209123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142062 restraints weight = 17134.504| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.68 r_work: 0.3309 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18480 Z= 0.106 Angle : 0.508 7.506 25041 Z= 0.272 Chirality : 0.040 0.145 2769 Planarity : 0.005 0.054 3195 Dihedral : 7.824 88.286 2547 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.23 % Allowed : 17.15 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.17), residues: 2201 helix: 1.17 (0.19), residues: 790 sheet: -0.47 (0.22), residues: 494 loop : -1.15 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 362 TYR 0.012 0.001 TYR B 159 PHE 0.022 0.001 PHE A 296 TRP 0.025 0.001 TRP D 199 HIS 0.010 0.001 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00228 (18480) covalent geometry : angle 0.50819 (25041) hydrogen bonds : bond 0.04257 ( 794) hydrogen bonds : angle 4.29142 ( 2139) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 243 time to evaluate : 0.519 Fit side-chains REVERT: A 59 TYR cc_start: 0.8378 (m-80) cc_final: 0.7991 (m-80) REVERT: A 63 LYS cc_start: 0.8178 (mttm) cc_final: 0.7908 (mtpt) REVERT: A 110 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7271 (ttt180) REVERT: A 134 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7529 (mtm-85) REVERT: A 231 MET cc_start: 0.8520 (mtm) cc_final: 0.7970 (mtp) REVERT: A 248 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8269 (tt0) REVERT: B 110 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7245 (ttt180) REVERT: B 129 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 133 LYS cc_start: 0.7839 (ttmm) cc_final: 0.6709 (mmtt) REVERT: B 236 GLN cc_start: 0.8458 (tm-30) cc_final: 0.7753 (mt0) REVERT: B 324 MET cc_start: 0.7879 (mtm) cc_final: 0.7526 (mmm) REVERT: B 336 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8137 (tp40) REVERT: C 5 LYS cc_start: 0.7301 (tttp) cc_final: 0.6772 (tttm) REVERT: C 16 GLN cc_start: 0.8143 (tt0) cc_final: 0.7586 (tm-30) REVERT: C 77 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.6711 (mtm-85) REVERT: C 110 ARG cc_start: 0.7811 (mtt-85) cc_final: 0.7043 (mtp85) REVERT: C 112 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7021 (mp0) REVERT: C 145 GLU cc_start: 0.6605 (pm20) cc_final: 0.5750 (mm-30) REVERT: C 190 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6831 (p) REVERT: D 74 LEU cc_start: 0.6392 (mp) cc_final: 0.6190 (mm) REVERT: D 106 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.6104 (tpp) REVERT: D 120 MET cc_start: 0.5703 (tpp) cc_final: 0.5083 (mtt) REVERT: D 195 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6686 (mt0) REVERT: D 247 GLN cc_start: 0.7176 (tt0) cc_final: 0.6916 (tt0) REVERT: D 262 ASN cc_start: 0.7926 (t0) cc_final: 0.7586 (t0) REVERT: D 267 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8617 (tpp) REVERT: D 271 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6748 (mt0) REVERT: E 77 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7079 (mtp-110) REVERT: E 84 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: E 106 MET cc_start: 0.8231 (ttm) cc_final: 0.7519 (tmm) REVERT: E 110 ARG cc_start: 0.7657 (ttm110) cc_final: 0.6976 (mtp85) REVERT: E 324 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7446 (ttm) REVERT: E 363 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7410 (mp0) REVERT: E 377 LYS cc_start: 0.7566 (mttp) cc_final: 0.6262 (mmmt) REVERT: F 4 ASP cc_start: 0.7666 (m-30) cc_final: 0.7377 (m-30) REVERT: F 6 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7325 (tm) REVERT: F 106 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6329 (tpp) REVERT: F 120 MET cc_start: 0.5452 (tpp) cc_final: 0.5021 (mtt) REVERT: F 195 GLN cc_start: 0.7068 (mp10) cc_final: 0.6576 (mt0) REVERT: F 203 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7854 (tp) REVERT: F 214 GLN cc_start: 0.7092 (tm-30) cc_final: 0.6610 (tt0) REVERT: F 256 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: F 262 ASN cc_start: 0.7782 (t0) cc_final: 0.7521 (t0) REVERT: F 267 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8473 (tpp) REVERT: F 271 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6391 (mp10) REVERT: F 323 ASP cc_start: 0.7083 (p0) cc_final: 0.6839 (p0) REVERT: F 336 GLN cc_start: 0.7349 (tp40) cc_final: 0.6422 (pt0) outliers start: 63 outliers final: 20 residues processed: 287 average time/residue: 0.6258 time to fit residues: 199.7884 Evaluate side-chains 263 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 271 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 176 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 107 optimal weight: 0.0060 chunk 205 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 240 GLN D 375 ASN F 302 ASN F 307 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.206431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.133612 restraints weight = 17220.985| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.26 r_work: 0.3183 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18480 Z= 0.169 Angle : 0.589 7.303 25041 Z= 0.308 Chirality : 0.043 0.150 2769 Planarity : 0.005 0.051 3195 Dihedral : 8.017 88.160 2547 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.87 % Allowed : 18.17 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.17), residues: 2201 helix: 1.11 (0.19), residues: 778 sheet: -0.54 (0.22), residues: 495 loop : -1.18 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 362 TYR 0.017 0.001 TYR B 159 PHE 0.026 0.002 PHE A 296 TRP 0.020 0.002 TRP D 199 HIS 0.012 0.002 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00408 (18480) covalent geometry : angle 0.58916 (25041) hydrogen bonds : bond 0.05344 ( 794) hydrogen bonds : angle 4.38973 ( 2139) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 0.784 Fit side-chains REVERT: A 25 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8594 (tp) REVERT: A 59 TYR cc_start: 0.8430 (m-80) cc_final: 0.7914 (m-80) REVERT: A 63 LYS cc_start: 0.8241 (mttm) cc_final: 0.7862 (mtpt) REVERT: A 110 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7187 (ttt180) REVERT: A 134 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7547 (mtp180) REVERT: A 231 MET cc_start: 0.8676 (mtm) cc_final: 0.8119 (mtp) REVERT: A 248 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8415 (tt0) REVERT: A 334 ILE cc_start: 0.8629 (tt) cc_final: 0.8297 (pt) REVERT: B 110 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7143 (ttt180) REVERT: B 129 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7963 (mt-10) REVERT: B 133 LYS cc_start: 0.7970 (ttmm) cc_final: 0.6764 (mmtt) REVERT: B 236 GLN cc_start: 0.8521 (tm-30) cc_final: 0.7669 (mt0) REVERT: B 324 MET cc_start: 0.8134 (mtm) cc_final: 0.7596 (mmm) REVERT: B 336 GLN cc_start: 0.8434 (tp-100) cc_final: 0.8197 (tp40) REVERT: C 5 LYS cc_start: 0.7306 (tttp) cc_final: 0.6740 (tttm) REVERT: C 16 GLN cc_start: 0.8051 (tt0) cc_final: 0.7581 (tm-30) REVERT: C 77 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.6845 (mtp-110) REVERT: C 110 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7055 (mtp85) REVERT: C 145 GLU cc_start: 0.6577 (pm20) cc_final: 0.5670 (mm-30) REVERT: C 190 THR cc_start: 0.7096 (OUTLIER) cc_final: 0.6714 (p) REVERT: D 4 ASP cc_start: 0.7383 (m-30) cc_final: 0.6914 (m-30) REVERT: D 74 LEU cc_start: 0.6233 (mp) cc_final: 0.5998 (mm) REVERT: D 106 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.6091 (tpp) REVERT: D 120 MET cc_start: 0.5687 (tpp) cc_final: 0.5101 (mtt) REVERT: D 195 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6866 (mt0) REVERT: D 247 GLN cc_start: 0.7236 (tt0) cc_final: 0.6954 (tt0) REVERT: D 267 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8581 (tpp) REVERT: D 271 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6677 (mt0) REVERT: D 355 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6439 (mt0) REVERT: E 77 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7009 (mtp-110) REVERT: E 84 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: E 106 MET cc_start: 0.8295 (ttm) cc_final: 0.7508 (tmm) REVERT: E 110 ARG cc_start: 0.7724 (ttm110) cc_final: 0.6950 (mtp85) REVERT: E 324 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7534 (ttm) REVERT: E 363 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7436 (mp0) REVERT: E 377 LYS cc_start: 0.7265 (mttp) cc_final: 0.5997 (mmmt) REVERT: F 4 ASP cc_start: 0.7658 (m-30) cc_final: 0.7362 (m-30) REVERT: F 6 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7066 (tm) REVERT: F 106 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6341 (tpp) REVERT: F 120 MET cc_start: 0.5371 (tpp) cc_final: 0.5092 (ttt) REVERT: F 203 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7816 (tp) REVERT: F 214 GLN cc_start: 0.6961 (tm-30) cc_final: 0.6480 (tt0) REVERT: F 262 ASN cc_start: 0.7976 (t0) cc_final: 0.7718 (t0) REVERT: F 267 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8485 (tpp) REVERT: F 271 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6243 (mp10) REVERT: F 323 ASP cc_start: 0.7053 (p0) cc_final: 0.6820 (p0) REVERT: F 336 GLN cc_start: 0.7289 (tp40) cc_final: 0.6290 (pt0) outliers start: 56 outliers final: 31 residues processed: 270 average time/residue: 0.6870 time to fit residues: 206.0239 Evaluate side-chains 264 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 353 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 217 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 11 optimal weight: 0.2980 chunk 74 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 240 GLN C 130 GLN D 375 ASN F 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.204730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.131371 restraints weight = 17105.671| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.95 r_work: 0.3148 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18480 Z= 0.209 Angle : 0.647 8.417 25041 Z= 0.336 Chirality : 0.045 0.155 2769 Planarity : 0.005 0.066 3195 Dihedral : 8.232 85.896 2547 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.08 % Allowed : 18.12 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.17), residues: 2201 helix: 0.95 (0.19), residues: 771 sheet: -0.61 (0.22), residues: 499 loop : -1.17 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 44 TYR 0.016 0.002 TYR B 159 PHE 0.030 0.002 PHE A 296 TRP 0.023 0.002 TRP F 158 HIS 0.013 0.002 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00515 (18480) covalent geometry : angle 0.64696 (25041) hydrogen bonds : bond 0.06062 ( 794) hydrogen bonds : angle 4.52464 ( 2139) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 0.745 Fit side-chains REVERT: A 25 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8692 (tp) REVERT: A 59 TYR cc_start: 0.8472 (m-80) cc_final: 0.7915 (m-80) REVERT: A 63 LYS cc_start: 0.8272 (mttm) cc_final: 0.7912 (mtpt) REVERT: A 110 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7252 (ttt180) REVERT: A 134 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7673 (mtp180) REVERT: A 231 MET cc_start: 0.8682 (mtm) cc_final: 0.8067 (mtp) REVERT: A 248 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8471 (tt0) REVERT: A 334 ILE cc_start: 0.8641 (tt) cc_final: 0.8303 (pt) REVERT: A 336 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8284 (tp40) REVERT: B 110 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7218 (ttt180) REVERT: B 129 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 133 LYS cc_start: 0.8042 (ttmm) cc_final: 0.6846 (mmtt) REVERT: B 236 GLN cc_start: 0.8602 (tm-30) cc_final: 0.7753 (mt0) REVERT: B 324 MET cc_start: 0.8193 (mtm) cc_final: 0.7717 (mmm) REVERT: B 336 GLN cc_start: 0.8503 (tp-100) cc_final: 0.8235 (tp40) REVERT: C 5 LYS cc_start: 0.7418 (tttp) cc_final: 0.6957 (tttm) REVERT: C 16 GLN cc_start: 0.7961 (tt0) cc_final: 0.7456 (tm-30) REVERT: C 77 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.6800 (mtm-85) REVERT: C 110 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.7042 (mtp85) REVERT: C 145 GLU cc_start: 0.6599 (pm20) cc_final: 0.5715 (mm-30) REVERT: C 190 THR cc_start: 0.7250 (OUTLIER) cc_final: 0.6869 (p) REVERT: C 336 GLN cc_start: 0.6730 (mm110) cc_final: 0.6467 (mm110) REVERT: C 377 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.5936 (tppt) REVERT: D 74 LEU cc_start: 0.6256 (mp) cc_final: 0.5990 (mm) REVERT: D 106 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6051 (tpp) REVERT: D 120 MET cc_start: 0.5770 (tpp) cc_final: 0.5062 (mtt) REVERT: D 195 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7049 (mt0) REVERT: D 267 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8608 (tpp) REVERT: D 271 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6644 (mp10) REVERT: D 355 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6490 (mt0) REVERT: E 77 ARG cc_start: 0.8144 (mtp180) cc_final: 0.7125 (mtp-110) REVERT: E 84 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: E 106 MET cc_start: 0.8363 (ttm) cc_final: 0.7577 (tmm) REVERT: E 110 ARG cc_start: 0.7782 (ttm110) cc_final: 0.7010 (mtp85) REVERT: E 324 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7637 (ttm) REVERT: E 363 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7444 (mp0) REVERT: E 377 LYS cc_start: 0.7340 (mttp) cc_final: 0.6016 (mmmt) REVERT: F 4 ASP cc_start: 0.7708 (m-30) cc_final: 0.7444 (m-30) REVERT: F 68 ARG cc_start: 0.6543 (mtp85) cc_final: 0.4815 (mtm110) REVERT: F 106 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6356 (tpp) REVERT: F 120 MET cc_start: 0.5395 (tpp) cc_final: 0.5148 (ttt) REVERT: F 195 GLN cc_start: 0.7405 (mp10) cc_final: 0.6906 (mt0) REVERT: F 203 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7900 (tp) REVERT: F 214 GLN cc_start: 0.7124 (tm-30) cc_final: 0.6646 (tt0) REVERT: F 262 ASN cc_start: 0.8016 (t0) cc_final: 0.7744 (t0) REVERT: F 267 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8554 (tpp) REVERT: F 271 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6304 (mp10) REVERT: F 336 GLN cc_start: 0.7368 (tp40) cc_final: 0.6368 (pt0) REVERT: F 355 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7294 (mt0) outliers start: 60 outliers final: 31 residues processed: 270 average time/residue: 0.6794 time to fit residues: 203.8124 Evaluate side-chains 268 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 96 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 130 GLN D 375 ASN F 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.206585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132452 restraints weight = 17134.665| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.88 r_work: 0.3212 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18480 Z= 0.144 Angle : 0.570 7.891 25041 Z= 0.300 Chirality : 0.042 0.149 2769 Planarity : 0.005 0.055 3195 Dihedral : 8.059 87.138 2547 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.67 % Allowed : 18.74 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.17), residues: 2201 helix: 1.16 (0.19), residues: 766 sheet: -0.59 (0.22), residues: 493 loop : -1.11 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 362 TYR 0.016 0.001 TYR B 159 PHE 0.032 0.001 PHE A 296 TRP 0.023 0.002 TRP D 199 HIS 0.014 0.001 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00336 (18480) covalent geometry : angle 0.56987 (25041) hydrogen bonds : bond 0.05126 ( 794) hydrogen bonds : angle 4.39231 ( 2139) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.756 Fit side-chains REVERT: A 25 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8648 (tp) REVERT: A 59 TYR cc_start: 0.8456 (m-80) cc_final: 0.7915 (m-80) REVERT: A 63 LYS cc_start: 0.8218 (mttm) cc_final: 0.7881 (mtpt) REVERT: A 110 ARG cc_start: 0.7812 (ttm110) cc_final: 0.7250 (ttt180) REVERT: A 134 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7579 (mtp180) REVERT: A 231 MET cc_start: 0.8620 (mtm) cc_final: 0.8068 (mtp) REVERT: A 248 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8429 (tt0) REVERT: B 110 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7171 (ttt180) REVERT: B 129 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7938 (mt-10) REVERT: B 133 LYS cc_start: 0.7931 (ttmm) cc_final: 0.6662 (mmtt) REVERT: B 236 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7715 (mt0) REVERT: B 324 MET cc_start: 0.8028 (mtm) cc_final: 0.7581 (mmm) REVERT: B 336 GLN cc_start: 0.8433 (tp-100) cc_final: 0.8171 (tp40) REVERT: C 5 LYS cc_start: 0.7375 (tttp) cc_final: 0.6926 (tttm) REVERT: C 16 GLN cc_start: 0.8035 (tt0) cc_final: 0.7566 (tm-30) REVERT: C 77 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.6783 (mtm-85) REVERT: C 110 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7020 (mtp85) REVERT: C 112 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6989 (mp0) REVERT: C 145 GLU cc_start: 0.6572 (pm20) cc_final: 0.5710 (mm-30) REVERT: C 190 THR cc_start: 0.7253 (OUTLIER) cc_final: 0.6867 (p) REVERT: C 272 TYR cc_start: 0.7024 (m-80) cc_final: 0.6823 (m-80) REVERT: C 377 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.5955 (tppt) REVERT: D 85 MET cc_start: 0.6865 (mmm) cc_final: 0.6645 (tpt) REVERT: D 106 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.6098 (tpp) REVERT: D 120 MET cc_start: 0.5912 (tpp) cc_final: 0.5165 (mtt) REVERT: D 195 GLN cc_start: 0.7434 (mp10) cc_final: 0.6923 (mt0) REVERT: D 267 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8618 (tpp) REVERT: D 271 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6683 (mp10) REVERT: D 355 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6432 (mt0) REVERT: E 77 ARG cc_start: 0.8048 (mtp180) cc_final: 0.7042 (mtp-110) REVERT: E 84 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7492 (mm-30) REVERT: E 106 MET cc_start: 0.8322 (ttm) cc_final: 0.7539 (tmm) REVERT: E 110 ARG cc_start: 0.7749 (ttm110) cc_final: 0.6997 (mtp85) REVERT: E 324 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7539 (ttm) REVERT: E 362 ARG cc_start: 0.7305 (ttp-110) cc_final: 0.7024 (ttp-110) REVERT: E 363 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7431 (mp0) REVERT: E 377 LYS cc_start: 0.7364 (mttp) cc_final: 0.6033 (mmmt) REVERT: F 2 ARG cc_start: 0.5660 (ttp-110) cc_final: 0.5370 (ttp-110) REVERT: F 68 ARG cc_start: 0.6595 (mtp85) cc_final: 0.4852 (mtm110) REVERT: F 106 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.6340 (tpp) REVERT: F 120 MET cc_start: 0.5383 (tpp) cc_final: 0.5140 (ttt) REVERT: F 195 GLN cc_start: 0.7226 (mp10) cc_final: 0.6731 (mt0) REVERT: F 203 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7897 (tp) REVERT: F 214 GLN cc_start: 0.7035 (tm-30) cc_final: 0.6519 (tt0) REVERT: F 262 ASN cc_start: 0.7980 (t0) cc_final: 0.7718 (t0) REVERT: F 267 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8542 (tpp) REVERT: F 271 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6291 (mp10) REVERT: F 323 ASP cc_start: 0.6994 (p0) cc_final: 0.6772 (p0) REVERT: F 336 GLN cc_start: 0.7340 (tp40) cc_final: 0.6352 (pt0) REVERT: F 355 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7266 (mt0) outliers start: 52 outliers final: 28 residues processed: 263 average time/residue: 0.6149 time to fit residues: 179.6224 Evaluate side-chains 263 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 147 optimal weight: 10.0000 chunk 60 optimal weight: 0.0170 chunk 121 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 124 optimal weight: 0.0020 overall best weight: 0.7628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 130 GLN D 304 HIS F 16 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.209341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142756 restraints weight = 17297.122| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.71 r_work: 0.3302 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18480 Z= 0.108 Angle : 0.510 7.725 25041 Z= 0.272 Chirality : 0.041 0.145 2769 Planarity : 0.005 0.053 3195 Dihedral : 7.758 86.660 2547 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.26 % Allowed : 19.40 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.17), residues: 2201 helix: 1.41 (0.19), residues: 771 sheet: -0.49 (0.22), residues: 497 loop : -1.02 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 362 TYR 0.012 0.001 TYR B 159 PHE 0.023 0.001 PHE B 296 TRP 0.024 0.001 TRP D 199 HIS 0.011 0.001 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00240 (18480) covalent geometry : angle 0.51018 (25041) hydrogen bonds : bond 0.04128 ( 794) hydrogen bonds : angle 4.20278 ( 2139) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7163.66 seconds wall clock time: 122 minutes 17.27 seconds (7337.27 seconds total)