Starting phenix.real_space_refine on Thu Sep 18 01:31:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cjq_7482/09_2025/6cjq_7482.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cjq_7482/09_2025/6cjq_7482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cjq_7482/09_2025/6cjq_7482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cjq_7482/09_2025/6cjq_7482.map" model { file = "/net/cci-nas-00/data/ceres_data/6cjq_7482/09_2025/6cjq_7482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cjq_7482/09_2025/6cjq_7482.cif" } resolution = 3.42 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 8472 2.51 5 N 2068 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12768 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "D" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 58 Restraints were copied for chains: B, C Time building chain proxies: 3.40, per 1000 atoms: 0.27 Number of scatterers: 12768 At special positions: 0 Unit cell: (106.322, 106.322, 120.571, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 2200 8.00 N 2068 7.00 C 8472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 153 " distance=0.00 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 387 " distance=0.00 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 599.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 67.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 10 through 35 removed outlier: 4.537A pdb=" N VAL A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.712A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 65 removed outlier: 6.464A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.101A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 4.831A pdb=" N PHE A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 91 through 98 removed outlier: 4.690A pdb=" N VAL A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 104 No H-bonds generated for 'chain 'A' and resid 103 through 104' Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.766A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 removed outlier: 4.152A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.865A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 removed outlier: 4.172A pdb=" N TYR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 224 removed outlier: 3.822A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.580A pdb=" N HIS A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.638A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.612A pdb=" N LEU A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 278' Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.939A pdb=" N GLU A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 298' Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.857A pdb=" N ASP A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 5.129A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 394 through 403 removed outlier: 4.824A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.106A pdb=" N GLN A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 4.537A pdb=" N VAL B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 3.712A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 65 removed outlier: 6.464A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Proline residue: B 45 - end of helix removed outlier: 4.101A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 4.831A pdb=" N PHE B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 91 through 98 removed outlier: 4.690A pdb=" N VAL B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 104 No H-bonds generated for 'chain 'B' and resid 103 through 104' Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.766A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 removed outlier: 4.152A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.865A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 removed outlier: 4.172A pdb=" N TYR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 224 removed outlier: 3.822A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.580A pdb=" N HIS B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.638A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.612A pdb=" N LEU B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 278' Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.939A pdb=" N GLU B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 298' Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.857A pdb=" N ASP B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 5.129A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 394 through 403 removed outlier: 4.824A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 415 removed outlier: 4.106A pdb=" N GLN B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 35 removed outlier: 4.537A pdb=" N VAL C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Proline residue: C 31 - end of helix removed outlier: 3.712A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 65 removed outlier: 6.464A pdb=" N LEU C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Proline residue: C 45 - end of helix removed outlier: 4.101A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 4.831A pdb=" N PHE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 91 through 98 removed outlier: 4.690A pdb=" N VAL C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 104 No H-bonds generated for 'chain 'C' and resid 103 through 104' Processing helix chain 'C' and resid 105 through 114 removed outlier: 3.766A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 removed outlier: 4.152A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 158 removed outlier: 3.865A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 181 removed outlier: 4.172A pdb=" N TYR C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 224 removed outlier: 3.822A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.580A pdb=" N HIS C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.638A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 278 removed outlier: 3.612A pdb=" N LEU C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 278' Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 293 through 298 removed outlier: 3.939A pdb=" N GLU C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 293 through 298' Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.857A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 5.129A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 394 through 403 removed outlier: 4.824A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 415 removed outlier: 4.106A pdb=" N GLN C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 35 removed outlier: 4.537A pdb=" N VAL D 14 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP D 15 " --> pdb=" O TYR D 11 " (cutoff:3.500A) Proline residue: D 31 - end of helix removed outlier: 3.712A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 65 removed outlier: 6.464A pdb=" N LEU D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Proline residue: D 45 - end of helix removed outlier: 4.101A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 4.831A pdb=" N PHE D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 91 through 98 removed outlier: 4.690A pdb=" N VAL D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE D 96 " --> pdb=" O ASP D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 104 No H-bonds generated for 'chain 'D' and resid 103 through 104' Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.766A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 removed outlier: 4.152A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 158 removed outlier: 3.865A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 removed outlier: 4.172A pdb=" N TYR D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 224 removed outlier: 3.822A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.580A pdb=" N HIS D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.638A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 278 removed outlier: 3.612A pdb=" N LEU D 276 " --> pdb=" O GLU D 272 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 278' Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.939A pdb=" N GLU D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 293 through 298' Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.857A pdb=" N ASP D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 5.129A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 394 through 403 removed outlier: 4.824A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 415 removed outlier: 4.106A pdb=" N GLN D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1680 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: 1.83 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3100 1.33 - 1.45: 2308 1.45 - 1.57: 7572 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 13028 Sorted by residual: bond pdb=" CG LEU B 43 " pdb=" CD2 LEU B 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CG LEU A 43 " pdb=" CD2 LEU A 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CG LEU C 43 " pdb=" CD2 LEU C 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CG LEU D 43 " pdb=" CD2 LEU D 43 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" C PRO C 300 " pdb=" N LEU C 301 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.40e-02 5.10e+03 3.30e+00 ... (remaining 13023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 16276 2.14 - 4.28: 972 4.28 - 6.42: 212 6.42 - 8.56: 144 8.56 - 10.70: 28 Bond angle restraints: 17632 Sorted by residual: angle pdb=" C ASP D 92 " pdb=" N LEU D 93 " pdb=" CA LEU D 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP A 92 " pdb=" N LEU A 93 " pdb=" CA LEU A 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP B 92 " pdb=" N LEU B 93 " pdb=" CA LEU B 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP C 92 " pdb=" N LEU C 93 " pdb=" CA LEU C 93 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C LEU C 39 " pdb=" N PHE C 40 " pdb=" CA PHE C 40 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 ... (remaining 17627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.81: 7516 19.81 - 39.63: 320 39.63 - 59.44: 48 59.44 - 79.26: 16 79.26 - 99.07: 4 Dihedral angle restraints: 7904 sinusoidal: 3292 harmonic: 4612 Sorted by residual: dihedral pdb=" CB CYS B 153 " pdb=" SG CYS B 153 " pdb=" SG CYS B 153 " pdb=" CB CYS B 153 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 387 " pdb=" SG CYS B 387 " pdb=" SG CYS B 387 " pdb=" CB CYS B 387 " ideal model delta sinusoidal sigma weight residual 125.12 92.50 32.62 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CA ILE A 189 " pdb=" C ILE A 189 " pdb=" N THR A 190 " pdb=" CA THR A 190 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 7901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1724 0.083 - 0.165: 316 0.165 - 0.248: 24 0.248 - 0.330: 4 0.330 - 0.413: 4 Chirality restraints: 2072 Sorted by residual: chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB ILE D 58 " pdb=" CA ILE D 58 " pdb=" CG1 ILE D 58 " pdb=" CG2 ILE D 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 2069 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 93 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU C 93 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU C 93 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 94 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 93 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU B 93 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU B 93 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 94 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 93 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU A 93 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU A 93 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 94 " -0.019 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3712 2.82 - 3.34: 11504 3.34 - 3.86: 20656 3.86 - 4.38: 21964 4.38 - 4.90: 39418 Nonbonded interactions: 97254 Sorted by model distance: nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU A 65 " pdb=" NH2 ARG A 124 " model vdw 2.309 3.120 ... (remaining 97249 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 503 or (resid 506 and (name C15 or name C16 or \ name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)) or resid 501)) selection = (chain 'B' and (resid 10 through 503 or (resid 506 and (name C15 or name C16 or \ name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)) or resid 501)) selection = (chain 'C' and (resid 10 through 503 or (resid 506 and (name C15 or name C16 or \ name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)) or resid 501)) selection = (chain 'D' and (resid 10 through 501 or (resid 502 and (name C15 or name C16 or \ name C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)) or resid 505 or (resid 506 and (name C15 or name C16 \ or name C17 or name C19 or name C20 or name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.000 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.009 0.070 13028 Z= 0.387 Angle : 1.365 10.700 17634 Z= 0.671 Chirality : 0.064 0.413 2072 Planarity : 0.009 0.051 2156 Dihedral : 12.070 99.069 4924 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.60 % Allowed : 6.85 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.36 (0.18), residues: 1552 helix: -2.04 (0.14), residues: 916 sheet: -1.86 (0.47), residues: 88 loop : -2.32 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 124 TYR 0.026 0.003 TYR C 211 PHE 0.011 0.002 PHE B 366 TRP 0.021 0.004 TRP A 264 HIS 0.005 0.002 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00908 (13028) covalent geometry : angle 1.36477 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.09937 ( 584) hydrogen bonds : angle 5.08537 ( 1680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 268 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8855 (tp) REVERT: B 171 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8851 (tp) REVERT: C 171 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8853 (tp) REVERT: D 171 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8858 (tp) outliers start: 8 outliers final: 0 residues processed: 272 average time/residue: 0.1437 time to fit residues: 53.2314 Evaluate side-chains 131 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 4.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 364 GLN B 217 ASN B 364 GLN C 217 ASN C 364 GLN D 217 ASN D 364 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089240 restraints weight = 23552.339| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.58 r_work: 0.2922 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 13028 Z= 0.254 Angle : 0.774 8.724 17634 Z= 0.373 Chirality : 0.046 0.205 2072 Planarity : 0.007 0.055 2156 Dihedral : 9.949 80.196 1972 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.32 % Allowed : 9.67 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.21), residues: 1552 helix: -0.41 (0.17), residues: 928 sheet: -1.07 (0.42), residues: 132 loop : -1.85 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 124 TYR 0.014 0.002 TYR D 128 PHE 0.011 0.002 PHE A 302 TRP 0.010 0.002 TRP C 176 HIS 0.005 0.001 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00635 (13028) covalent geometry : angle 0.77383 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04633 ( 584) hydrogen bonds : angle 4.11613 ( 1680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 114 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 17 residues processed: 168 average time/residue: 0.0999 time to fit residues: 25.7628 Evaluate side-chains 115 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.091648 restraints weight = 23581.380| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.51 r_work: 0.2980 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13028 Z= 0.119 Angle : 0.686 9.082 17634 Z= 0.310 Chirality : 0.042 0.196 2072 Planarity : 0.005 0.054 2156 Dihedral : 8.039 57.423 1964 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.53 % Allowed : 12.43 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.22), residues: 1552 helix: 0.31 (0.18), residues: 924 sheet: -1.17 (0.42), residues: 112 loop : -1.19 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 124 TYR 0.008 0.001 TYR A 128 PHE 0.006 0.001 PHE A 242 TRP 0.012 0.001 TRP D 264 HIS 0.001 0.000 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00280 (13028) covalent geometry : angle 0.68615 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03464 ( 584) hydrogen bonds : angle 3.75653 ( 1680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 154 average time/residue: 0.0934 time to fit residues: 22.0717 Evaluate side-chains 125 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.091055 restraints weight = 23487.730| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.48 r_work: 0.2951 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13028 Z= 0.160 Angle : 0.690 9.955 17634 Z= 0.314 Chirality : 0.043 0.209 2072 Planarity : 0.005 0.056 2156 Dihedral : 7.658 46.580 1964 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.60 % Allowed : 13.91 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.22), residues: 1552 helix: 0.62 (0.18), residues: 920 sheet: -0.19 (0.49), residues: 88 loop : -1.21 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 343 TYR 0.009 0.001 TYR A 175 PHE 0.010 0.001 PHE D 40 TRP 0.008 0.001 TRP D 264 HIS 0.002 0.000 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00399 (13028) covalent geometry : angle 0.68987 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03612 ( 584) hydrogen bonds : angle 3.68835 ( 1680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8553 (m-10) REVERT: A 221 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8990 (tp) REVERT: B 26 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8550 (m-10) REVERT: B 221 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8997 (tp) REVERT: C 26 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8535 (m-10) REVERT: C 47 ASP cc_start: 0.6572 (m-30) cc_final: 0.6346 (m-30) REVERT: C 221 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8997 (tp) REVERT: D 26 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8489 (m-10) REVERT: D 221 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9013 (tp) outliers start: 35 outliers final: 20 residues processed: 150 average time/residue: 0.1054 time to fit residues: 23.9603 Evaluate side-chains 135 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 0.0040 chunk 70 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.091844 restraints weight = 23335.948| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.34 r_work: 0.2998 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13028 Z= 0.114 Angle : 0.664 10.479 17634 Z= 0.296 Chirality : 0.042 0.211 2072 Planarity : 0.005 0.055 2156 Dihedral : 6.968 45.769 1964 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.12 % Allowed : 14.36 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.23), residues: 1552 helix: 0.92 (0.18), residues: 916 sheet: 0.21 (0.51), residues: 88 loop : -1.01 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 124 TYR 0.007 0.001 TYR A 175 PHE 0.015 0.001 PHE A 397 TRP 0.008 0.001 TRP D 264 HIS 0.001 0.000 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00268 (13028) covalent geometry : angle 0.66366 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03192 ( 584) hydrogen bonds : angle 3.57867 ( 1680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8482 (m-10) REVERT: A 221 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8985 (tp) REVERT: B 26 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: B 221 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8997 (tp) REVERT: C 26 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8475 (m-10) REVERT: C 221 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8992 (tp) REVERT: D 26 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8521 (m-10) REVERT: D 221 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9002 (tp) outliers start: 42 outliers final: 24 residues processed: 157 average time/residue: 0.1032 time to fit residues: 24.8767 Evaluate side-chains 135 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.090294 restraints weight = 23239.447| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.30 r_work: 0.3008 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13028 Z= 0.115 Angle : 0.663 11.611 17634 Z= 0.293 Chirality : 0.042 0.224 2072 Planarity : 0.005 0.057 2156 Dihedral : 6.622 45.695 1964 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.53 % Allowed : 15.40 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.57 (0.23), residues: 1552 helix: 1.15 (0.18), residues: 916 sheet: 0.50 (0.52), residues: 88 loop : -0.90 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 124 TYR 0.009 0.001 TYR D 26 PHE 0.008 0.001 PHE A 397 TRP 0.006 0.001 TRP D 264 HIS 0.001 0.000 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00274 (13028) covalent geometry : angle 0.66326 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03131 ( 584) hydrogen bonds : angle 3.50686 ( 1680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8461 (m-10) REVERT: A 221 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8983 (tp) REVERT: B 26 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8501 (m-10) REVERT: B 221 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8999 (tp) REVERT: C 26 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8546 (m-10) REVERT: C 221 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8996 (tp) REVERT: D 26 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8529 (m-10) REVERT: D 221 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9006 (tp) outliers start: 34 outliers final: 22 residues processed: 159 average time/residue: 0.1038 time to fit residues: 24.7432 Evaluate side-chains 125 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 chunk 35 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.090042 restraints weight = 23451.368| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.29 r_work: 0.3000 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13028 Z= 0.119 Angle : 0.698 15.325 17634 Z= 0.302 Chirality : 0.042 0.226 2072 Planarity : 0.005 0.060 2156 Dihedral : 6.441 46.902 1964 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.79 % Allowed : 15.18 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.23), residues: 1552 helix: 1.27 (0.19), residues: 916 sheet: 0.53 (0.52), residues: 88 loop : -0.81 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 29 TYR 0.009 0.001 TYR C 26 PHE 0.007 0.001 PHE A 397 TRP 0.005 0.001 TRP D 264 HIS 0.001 0.000 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00282 (13028) covalent geometry : angle 0.69826 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03109 ( 584) hydrogen bonds : angle 3.49095 ( 1680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 117 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8487 (m-10) REVERT: A 221 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8984 (tp) REVERT: B 26 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8490 (m-10) REVERT: B 221 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8987 (tp) REVERT: C 26 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8532 (m-10) REVERT: C 221 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8989 (tp) REVERT: D 26 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8531 (m-10) REVERT: D 221 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8994 (tp) outliers start: 51 outliers final: 29 residues processed: 163 average time/residue: 0.1078 time to fit residues: 26.8257 Evaluate side-chains 135 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.093491 restraints weight = 23086.417| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.54 r_work: 0.2992 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13028 Z= 0.143 Angle : 0.747 17.445 17634 Z= 0.317 Chirality : 0.043 0.237 2072 Planarity : 0.005 0.061 2156 Dihedral : 6.528 49.144 1964 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.79 % Allowed : 15.18 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.23), residues: 1552 helix: 1.26 (0.18), residues: 920 sheet: 0.52 (0.52), residues: 88 loop : -0.73 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.010 0.001 TYR D 26 PHE 0.005 0.001 PHE D 40 TRP 0.006 0.001 TRP A 176 HIS 0.002 0.000 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00350 (13028) covalent geometry : angle 0.74660 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03328 ( 584) hydrogen bonds : angle 3.49343 ( 1680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 115 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.8500 (m-10) REVERT: A 221 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8976 (tp) REVERT: B 26 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8513 (m-10) REVERT: B 221 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8991 (tp) REVERT: B 334 MET cc_start: 0.7906 (tpp) cc_final: 0.7656 (tpt) REVERT: C 26 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8498 (m-10) REVERT: C 221 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8989 (tp) REVERT: C 334 MET cc_start: 0.7862 (tpp) cc_final: 0.7601 (tpt) REVERT: D 26 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8551 (m-10) REVERT: D 221 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8992 (tp) outliers start: 51 outliers final: 26 residues processed: 160 average time/residue: 0.1228 time to fit residues: 28.3779 Evaluate side-chains 133 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 0.0770 chunk 139 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092774 restraints weight = 23208.580| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.50 r_work: 0.2990 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13028 Z= 0.125 Angle : 0.740 17.098 17634 Z= 0.314 Chirality : 0.043 0.240 2072 Planarity : 0.005 0.062 2156 Dihedral : 6.329 49.816 1964 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.27 % Allowed : 15.70 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.23), residues: 1552 helix: 1.29 (0.18), residues: 924 sheet: 0.53 (0.52), residues: 88 loop : -0.57 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.009 0.001 TYR C 26 PHE 0.005 0.001 PHE A 397 TRP 0.006 0.001 TRP D 176 HIS 0.001 0.000 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00297 (13028) covalent geometry : angle 0.74043 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03184 ( 584) hydrogen bonds : angle 3.46203 ( 1680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: A 221 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8973 (tp) REVERT: B 26 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8511 (m-10) REVERT: B 221 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8988 (tp) REVERT: C 26 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8526 (m-10) REVERT: C 221 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8986 (tp) REVERT: D 26 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8530 (m-10) REVERT: D 221 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8990 (tp) outliers start: 44 outliers final: 26 residues processed: 144 average time/residue: 0.1033 time to fit residues: 22.8122 Evaluate side-chains 137 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 46 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 64 optimal weight: 0.0270 chunk 148 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.093216 restraints weight = 23430.914| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.52 r_work: 0.2991 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13028 Z= 0.127 Angle : 0.741 16.790 17634 Z= 0.315 Chirality : 0.043 0.251 2072 Planarity : 0.005 0.063 2156 Dihedral : 6.209 51.219 1964 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.90 % Allowed : 15.92 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.23), residues: 1552 helix: 1.38 (0.19), residues: 924 sheet: 0.51 (0.52), residues: 88 loop : -0.54 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 29 TYR 0.011 0.001 TYR A 327 PHE 0.005 0.001 PHE C 40 TRP 0.006 0.001 TRP C 264 HIS 0.001 0.000 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00302 (13028) covalent geometry : angle 0.74136 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03175 ( 584) hydrogen bonds : angle 3.44680 ( 1680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8466 (m-10) REVERT: A 221 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8983 (tp) REVERT: B 26 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8563 (m-10) REVERT: B 221 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8995 (tp) REVERT: C 26 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8529 (m-10) REVERT: C 40 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6578 (t80) REVERT: C 57 ASP cc_start: 0.8848 (t70) cc_final: 0.8595 (t0) REVERT: C 221 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8998 (tp) REVERT: D 26 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8466 (m-10) REVERT: D 221 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9002 (tp) outliers start: 39 outliers final: 25 residues processed: 143 average time/residue: 0.1044 time to fit residues: 22.8338 Evaluate side-chains 139 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 94 optimal weight: 0.2980 chunk 143 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 116 optimal weight: 0.0270 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.121052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.094702 restraints weight = 23196.239| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.50 r_work: 0.3021 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13028 Z= 0.104 Angle : 0.730 16.503 17634 Z= 0.308 Chirality : 0.042 0.255 2072 Planarity : 0.005 0.064 2156 Dihedral : 5.841 52.089 1964 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.31 % Allowed : 16.74 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.23), residues: 1552 helix: 1.65 (0.19), residues: 900 sheet: 0.52 (0.52), residues: 88 loop : -0.60 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.010 0.001 TYR B 327 PHE 0.005 0.001 PHE A 40 TRP 0.006 0.001 TRP D 264 HIS 0.001 0.000 HIS D 149 Details of bonding type rmsd covalent geometry : bond 0.00224 (13028) covalent geometry : angle 0.73054 (17632) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.02921 ( 584) hydrogen bonds : angle 3.39333 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.95 seconds wall clock time: 43 minutes 27.39 seconds (2607.39 seconds total)