Starting phenix.real_space_refine on Sat Jul 4 03:23:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f8o_31491/07_2026/7f8o_31491.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f8o_31491/07_2026/7f8o_31491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f8o_31491/07_2026/7f8o_31491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f8o_31491/07_2026/7f8o_31491.map" model { file = "/net/cci-nas-00/data/ceres_data/7f8o_31491/07_2026/7f8o_31491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f8o_31491/07_2026/7f8o_31491.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7f8o_31491/07_2026/7f8o_31491.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f8o_31491/07_2026/7f8o_31491.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 77 5.16 5 C 12012 2.51 5 N 2681 2.21 5 O 3241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18032 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2498 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 297} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'LBN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'LBN:plan-2': 1, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 12 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.64, per 1000 atoms: 0.15 Number of scatterers: 18032 At special positions: 0 Unit cell: (109.35, 108.54, 116.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 21 15.00 O 3241 8.00 N 2681 7.00 C 12012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.71 Conformation dependent library (CDL) restraints added in 789.4 milliseconds 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4256 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 7 sheets defined 73.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.007A pdb=" N TYR A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.565A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 131 through 155 Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 237 Processing helix chain 'A' and resid 238 through 242 removed outlier: 4.083A pdb=" N ASP A 242 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 270 through 296 Proline residue: A 289 - end of helix removed outlier: 3.560A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 302 through 312 removed outlier: 4.150A pdb=" N LEU A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 308 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.640A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 4.007A pdb=" N TYR B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.564A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 131 through 155 Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 237 Processing helix chain 'B' and resid 238 through 242 removed outlier: 4.084A pdb=" N ASP B 242 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 270 through 296 Proline residue: B 289 - end of helix removed outlier: 3.560A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 302 through 312 removed outlier: 4.150A pdb=" N LEU B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 308 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.641A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 removed outlier: 4.007A pdb=" N TYR C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.565A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'C' and resid 131 through 155 Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 237 Processing helix chain 'C' and resid 238 through 242 removed outlier: 4.083A pdb=" N ASP C 242 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 270 through 296 Proline residue: C 289 - end of helix removed outlier: 3.560A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 302 through 312 removed outlier: 4.151A pdb=" N LEU C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 308 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.640A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 351 " --> pdb=" O CYS C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 removed outlier: 4.007A pdb=" N TYR D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.564A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 121 through 131 Processing helix chain 'D' and resid 131 through 155 Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 237 Processing helix chain 'D' and resid 238 through 242 removed outlier: 4.083A pdb=" N ASP D 242 " --> pdb=" O SER D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 270 through 296 Proline residue: D 289 - end of helix removed outlier: 3.559A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 302 through 312 removed outlier: 4.150A pdb=" N LEU D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL D 308 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.640A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 351 " --> pdb=" O CYS D 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 removed outlier: 4.007A pdb=" N TYR E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.564A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 131 through 155 Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 237 Processing helix chain 'E' and resid 238 through 242 removed outlier: 4.084A pdb=" N ASP E 242 " --> pdb=" O SER E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 270 through 296 Proline residue: E 289 - end of helix removed outlier: 3.560A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 302 through 312 removed outlier: 4.150A pdb=" N LEU E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL E 308 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.641A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 351 " --> pdb=" O CYS E 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 removed outlier: 4.007A pdb=" N TYR F 10 " --> pdb=" O LEU F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.564A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 100 through 108 removed outlier: 3.548A pdb=" N TRP F 104 " --> pdb=" O ASN F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 120 Processing helix chain 'F' and resid 121 through 131 Processing helix chain 'F' and resid 131 through 155 Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 237 Processing helix chain 'F' and resid 238 through 242 removed outlier: 4.083A pdb=" N ASP F 242 " --> pdb=" O SER F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 270 through 296 Proline residue: F 289 - end of helix removed outlier: 3.559A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 302 through 312 removed outlier: 4.149A pdb=" N LEU F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL F 308 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.640A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 351 " --> pdb=" O CYS F 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 removed outlier: 4.006A pdb=" N TYR G 10 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.564A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP G 104 " --> pdb=" O ASN G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 120 Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'G' and resid 131 through 155 Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.705A pdb=" N SER G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 237 Processing helix chain 'G' and resid 238 through 242 removed outlier: 4.084A pdb=" N ASP G 242 " --> pdb=" O SER G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 256 Processing helix chain 'G' and resid 270 through 296 Proline residue: G 289 - end of helix removed outlier: 3.560A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 302 through 312 removed outlier: 4.150A pdb=" N LEU G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL G 308 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.641A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 353 removed outlier: 3.800A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 351 " --> pdb=" O CYS G 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN A 264 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN B 264 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN C 264 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN D 264 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.513A pdb=" N GLN E 264 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN F 264 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN G 264 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 1079 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5213 1.34 - 1.46: 3162 1.46 - 1.57: 9881 1.57 - 1.69: 21 1.69 - 1.81: 133 Bond restraints: 18410 Sorted by residual: bond pdb=" O2 LBN C 501 " pdb=" P1 LBN C 501 " ideal model delta sigma weight residual 1.650 1.785 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" O2 LBN G 502 " pdb=" P1 LBN G 502 " ideal model delta sigma weight residual 1.650 1.785 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" O2 LBN E 501 " pdb=" P1 LBN E 501 " ideal model delta sigma weight residual 1.650 1.785 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" O2 LBN G 501 " pdb=" P1 LBN G 501 " ideal model delta sigma weight residual 1.650 1.785 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" O2 LBN F 502 " pdb=" P1 LBN F 502 " ideal model delta sigma weight residual 1.650 1.785 -0.135 2.00e-02 2.50e+03 4.55e+01 ... (remaining 18405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 24170 1.82 - 3.64: 398 3.64 - 5.46: 195 5.46 - 7.27: 94 7.27 - 9.09: 77 Bond angle restraints: 24934 Sorted by residual: angle pdb=" N ILE C 58 " pdb=" CA ILE C 58 " pdb=" C ILE C 58 " ideal model delta sigma weight residual 113.71 108.73 4.98 9.50e-01 1.11e+00 2.75e+01 angle pdb=" N ILE B 58 " pdb=" CA ILE B 58 " pdb=" C ILE B 58 " ideal model delta sigma weight residual 113.71 108.75 4.96 9.50e-01 1.11e+00 2.72e+01 angle pdb=" N ILE E 58 " pdb=" CA ILE E 58 " pdb=" C ILE E 58 " ideal model delta sigma weight residual 113.71 108.76 4.95 9.50e-01 1.11e+00 2.72e+01 angle pdb=" N ILE A 58 " pdb=" CA ILE A 58 " pdb=" C ILE A 58 " ideal model delta sigma weight residual 113.71 108.76 4.95 9.50e-01 1.11e+00 2.71e+01 angle pdb=" N ILE F 58 " pdb=" CA ILE F 58 " pdb=" C ILE F 58 " ideal model delta sigma weight residual 113.71 108.77 4.94 9.50e-01 1.11e+00 2.70e+01 ... (remaining 24929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.48: 10773 31.48 - 62.96: 238 62.96 - 94.44: 0 94.44 - 125.93: 7 125.93 - 157.41: 7 Dihedral angle restraints: 11025 sinusoidal: 4501 harmonic: 6524 Sorted by residual: dihedral pdb=" C1 LBN C 502 " pdb=" O1 LBN C 502 " pdb=" P1 LBN C 502 " pdb=" O3 LBN C 502 " ideal model delta sinusoidal sigma weight residual -84.60 72.81 -157.41 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C1 LBN A 502 " pdb=" O1 LBN A 502 " pdb=" P1 LBN A 502 " pdb=" O3 LBN A 502 " ideal model delta sinusoidal sigma weight residual -84.60 72.80 -157.40 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C1 LBN G 502 " pdb=" O1 LBN G 502 " pdb=" P1 LBN G 502 " pdb=" O3 LBN G 502 " ideal model delta sinusoidal sigma weight residual -84.60 72.80 -157.40 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 11022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2204 0.043 - 0.087: 617 0.087 - 0.130: 91 0.130 - 0.174: 0 0.174 - 0.217: 21 Chirality restraints: 2933 Sorted by residual: chirality pdb=" C2 LBN D 501 " pdb=" C1 LBN D 501 " pdb=" C3 LBN D 501 " pdb=" O7 LBN D 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C2 LBN F 501 " pdb=" C1 LBN F 501 " pdb=" C3 LBN F 501 " pdb=" O7 LBN F 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C2 LBN E 501 " pdb=" C1 LBN E 501 " pdb=" C3 LBN E 501 " pdb=" O7 LBN E 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2930 not shown) Planarity restraints: 2982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 123 " 0.026 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO D 124 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 123 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO G 124 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 124 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 124 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO C 124 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " 0.022 5.00e-02 4.00e+02 ... (remaining 2979 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 168 2.66 - 3.22: 18003 3.22 - 3.78: 27862 3.78 - 4.34: 37999 4.34 - 4.90: 64176 Nonbonded interactions: 148208 Sorted by model distance: nonbonded pdb=" OH TYR A 111 " pdb=" O LEU B 52 " model vdw 2.106 3.040 nonbonded pdb=" OH TYR B 111 " pdb=" O LEU C 52 " model vdw 2.200 3.040 nonbonded pdb=" NE2 GLN F 76 " pdb=" O SER G 68 " model vdw 2.251 3.120 nonbonded pdb=" O GLY A 27 " pdb=" NZ LYS G 24 " model vdw 2.264 3.120 nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.266 3.040 ... (remaining 148203 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.240 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.008 0.135 18424 Z= 0.402 Angle : 0.875 9.093 24962 Z= 0.363 Chirality : 0.040 0.217 2933 Planarity : 0.003 0.038 2982 Dihedral : 12.856 157.407 6727 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.71 % Allowed : 5.69 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2128 helix: 1.48 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -2.50 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 300 TYR 0.005 0.001 TYR C 10 PHE 0.008 0.001 PHE A 244 TRP 0.008 0.001 TRP F 104 HIS 0.001 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00810 / 0.40 (18410) covalent geometry : angle 0.87537 / 0.36 (24934) SS BOND : bond 0.00124 / 0.09 ( 14) SS BOND : angle 0.63284 / 0.45 ( 28) hydrogen bonds : bond 0.24168 / 15.68 ( 1079) hydrogen bonds : angle 6.33214 / 4.43 ( 3048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 528 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 120 LEU cc_start: 0.8943 (mt) cc_final: 0.8691 (mt) REVERT: B 237 LEU cc_start: 0.8457 (mt) cc_final: 0.8176 (mt) REVERT: D 82 SER cc_start: 0.8984 (p) cc_final: 0.8718 (m) REVERT: E 204 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8257 (ttpt) REVERT: E 352 GLU cc_start: 0.6317 (tm-30) cc_final: 0.5822 (tm-30) REVERT: F 325 TYR cc_start: 0.7708 (m-10) cc_final: 0.7371 (m-80) outliers start: 14 outliers final: 0 residues processed: 537 average time/residue: 0.1304 time to fit residues: 109.3891 Evaluate side-chains 441 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 100 ASN A 134 HIS B 89 GLN B 100 ASN C 89 GLN C 100 ASN C 262 GLN D 89 GLN D 100 ASN E 100 ASN F 89 GLN F 100 ASN G 100 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.174219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.135178 restraints weight = 20868.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.135038 restraints weight = 18504.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.136598 restraints weight = 17950.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.137777 restraints weight = 11726.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.137925 restraints weight = 11329.124| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18424 Z= 0.169 Angle : 0.633 7.594 24962 Z= 0.313 Chirality : 0.040 0.123 2933 Planarity : 0.004 0.046 2982 Dihedral : 11.379 152.161 2625 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.78 % Allowed : 10.88 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 2128 helix: 1.28 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -2.32 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 254 TYR 0.026 0.001 TYR E 345 PHE 0.029 0.002 PHE C 235 TRP 0.016 0.002 TRP A 104 HIS 0.004 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (18410) covalent geometry : angle 0.63290 / 0.31 (24934) SS BOND : bond 0.00184 / 0.12 ( 14) SS BOND : angle 0.97977 / 0.69 ( 28) hydrogen bonds : bond 0.05327 / 3.46 ( 1079) hydrogen bonds : angle 4.29059 / 3.05 ( 3048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 447 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: B 120 LEU cc_start: 0.9119 (mt) cc_final: 0.8893 (mt) REVERT: E 40 CYS cc_start: 0.9062 (t) cc_final: 0.8834 (t) REVERT: E 204 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8480 (ttpt) REVERT: F 204 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8311 (ttpt) REVERT: F 213 TYR cc_start: 0.8790 (t80) cc_final: 0.8540 (t80) REVERT: F 325 TYR cc_start: 0.7928 (m-10) cc_final: 0.7471 (m-80) REVERT: G 54 PHE cc_start: 0.6870 (m-80) cc_final: 0.6234 (m-80) REVERT: G 204 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8171 (ttpt) REVERT: G 331 TYR cc_start: 0.8810 (m-80) cc_final: 0.8231 (m-80) outliers start: 35 outliers final: 24 residues processed: 465 average time/residue: 0.1191 time to fit residues: 87.1338 Evaluate side-chains 452 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 428 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 208 optimal weight: 0.1980 chunk 171 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN C 100 ASN C 262 GLN D 89 GLN E 90 GLN E 100 ASN F 90 GLN F 100 ASN G 100 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.168962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.130343 restraints weight = 21087.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.132451 restraints weight = 18444.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.133460 restraints weight = 15135.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.133913 restraints weight = 11205.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.134144 restraints weight = 10866.116| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18424 Z= 0.153 Angle : 0.617 8.151 24962 Z= 0.298 Chirality : 0.039 0.160 2933 Planarity : 0.004 0.041 2982 Dihedral : 10.491 146.047 2625 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.29 % Allowed : 13.47 % Favored : 84.24 % 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 are not related in a simple way. whole: 0.05 (0.19), residues: 2128 helix: 1.03 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 254 TYR 0.021 0.001 TYR E 230 PHE 0.028 0.002 PHE D 235 TRP 0.018 0.002 TRP G 104 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (18410) covalent geometry : angle 0.61590 / 0.30 (24934) SS BOND : bond 0.00293 / 0.20 ( 14) SS BOND : angle 1.08416 / 0.77 ( 28) hydrogen bonds : bond 0.04368 / 2.84 ( 1079) hydrogen bonds : angle 4.12848 / 2.94 ( 3048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 435 time to evaluate : 0.601 Fit side-chains REVERT: A 352 GLU cc_start: 0.6330 (tm-30) cc_final: 0.5777 (tm-30) REVERT: B 120 LEU cc_start: 0.9144 (mt) cc_final: 0.8921 (mt) REVERT: E 204 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8470 (ttpt) REVERT: F 213 TYR cc_start: 0.8787 (t80) cc_final: 0.8448 (t80) REVERT: F 325 TYR cc_start: 0.7982 (m-10) cc_final: 0.7556 (m-80) REVERT: G 54 PHE cc_start: 0.7024 (m-80) cc_final: 0.6451 (m-80) REVERT: G 331 TYR cc_start: 0.8788 (m-80) cc_final: 0.8256 (m-80) outliers start: 45 outliers final: 35 residues processed: 461 average time/residue: 0.1177 time to fit residues: 86.6267 Evaluate side-chains 458 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 423 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 177 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 174 optimal weight: 0.0010 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 90 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 100 ASN C 89 GLN C 100 ASN D 89 GLN D 100 ASN F 90 GLN F 100 ASN G 100 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.164529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.126388 restraints weight = 21152.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.126611 restraints weight = 19225.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.127939 restraints weight = 18545.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.128524 restraints weight = 13745.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.128723 restraints weight = 13318.632| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 18424 Z= 0.213 Angle : 0.665 7.673 24962 Z= 0.320 Chirality : 0.040 0.130 2933 Planarity : 0.004 0.040 2982 Dihedral : 10.607 143.510 2625 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.85 % Allowed : 15.10 % Favored : 82.05 % 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 are not related in a simple way. whole: -0.10 (0.19), residues: 2128 helix: 0.90 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.43 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 254 TYR 0.023 0.002 TYR E 230 PHE 0.022 0.002 PHE B 141 TRP 0.018 0.002 TRP E 104 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 (18410) covalent geometry : angle 0.66344 / 0.32 (24934) SS BOND : bond 0.00431 / 0.29 ( 14) SS BOND : angle 1.45785 / 1.05 ( 28) hydrogen bonds : bond 0.04237 / 2.75 ( 1079) hydrogen bonds : angle 4.11790 / 2.92 ( 3048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 453 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.7806 (pt0) cc_final: 0.7558 (pt0) REVERT: B 120 LEU cc_start: 0.9118 (mt) cc_final: 0.8886 (mt) REVERT: B 349 LYS cc_start: 0.8441 (mtpp) cc_final: 0.8132 (mtpt) REVERT: C 333 LEU cc_start: 0.8433 (mt) cc_final: 0.8124 (mt) REVERT: E 204 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8430 (ttpt) REVERT: F 254 ARG cc_start: 0.8121 (mtt-85) cc_final: 0.7879 (mtt90) REVERT: F 325 TYR cc_start: 0.8125 (m-10) cc_final: 0.7581 (m-80) REVERT: G 90 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: G 331 TYR cc_start: 0.8784 (m-80) cc_final: 0.8238 (m-80) outliers start: 56 outliers final: 43 residues processed: 490 average time/residue: 0.1171 time to fit residues: 91.4921 Evaluate side-chains 480 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 436 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 212 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 154 optimal weight: 0.0170 chunk 178 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 100 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 90 GLN D 100 ASN E 90 GLN F 100 ASN G 100 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.169730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.131596 restraints weight = 20668.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.133666 restraints weight = 17397.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.134846 restraints weight = 14622.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.135281 restraints weight = 10584.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.135351 restraints weight = 10895.095| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18424 Z= 0.126 Angle : 0.607 7.812 24962 Z= 0.290 Chirality : 0.038 0.125 2933 Planarity : 0.004 0.040 2982 Dihedral : 9.958 136.255 2625 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.54 % Allowed : 16.62 % Favored : 80.83 % 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 are not related in a simple way. whole: 0.05 (0.19), residues: 2128 helix: 1.05 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -2.33 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 254 TYR 0.034 0.001 TYR E 345 PHE 0.021 0.001 PHE F 141 TRP 0.017 0.002 TRP G 104 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (18410) covalent geometry : angle 0.60688 / 0.29 (24934) SS BOND : bond 0.00242 / 0.16 ( 14) SS BOND : angle 0.79985 / 0.58 ( 28) hydrogen bonds : bond 0.03755 / 2.45 ( 1079) hydrogen bonds : angle 3.96102 / 2.82 ( 3048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 438 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: B 213 TYR cc_start: 0.8976 (t80) cc_final: 0.8774 (t80) REVERT: B 239 SER cc_start: 0.8554 (m) cc_final: 0.8317 (p) REVERT: B 349 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8116 (mtpt) REVERT: C 252 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7628 (mp) REVERT: C 338 ASN cc_start: 0.8040 (p0) cc_final: 0.7589 (p0) REVERT: E 338 ASN cc_start: 0.8142 (p0) cc_final: 0.7584 (p0) REVERT: F 54 PHE cc_start: 0.7430 (m-80) cc_final: 0.7117 (m-80) REVERT: F 325 TYR cc_start: 0.8031 (m-10) cc_final: 0.7450 (m-80) REVERT: G 54 PHE cc_start: 0.7292 (m-80) cc_final: 0.6848 (m-80) REVERT: G 331 TYR cc_start: 0.8729 (m-80) cc_final: 0.8311 (m-80) outliers start: 50 outliers final: 39 residues processed: 468 average time/residue: 0.1144 time to fit residues: 85.6492 Evaluate side-chains 463 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 423 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 41 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 51 optimal weight: 0.0970 chunk 46 optimal weight: 0.0050 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 158 optimal weight: 0.0670 overall best weight: 0.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 90 GLN D 100 ASN F 89 GLN F 100 ASN G 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.171025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.132736 restraints weight = 20695.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.134294 restraints weight = 18202.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.135452 restraints weight = 15210.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.136408 restraints weight = 11334.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.136640 restraints weight = 10681.671| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18424 Z= 0.115 Angle : 0.595 8.598 24962 Z= 0.282 Chirality : 0.038 0.134 2933 Planarity : 0.004 0.038 2982 Dihedral : 9.333 128.033 2625 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.34 % Allowed : 18.20 % Favored : 79.46 % 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 are not related in a simple way. whole: 0.21 (0.19), residues: 2128 helix: 1.17 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -2.27 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 217 TYR 0.021 0.001 TYR E 230 PHE 0.027 0.001 PHE A 141 TRP 0.016 0.002 TRP D 104 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (18410) covalent geometry : angle 0.59523 / 0.28 (24934) SS BOND : bond 0.00178 / 0.12 ( 14) SS BOND : angle 0.61484 / 0.44 ( 28) hydrogen bonds : bond 0.03541 / 2.32 ( 1079) hydrogen bonds : angle 3.87441 / 2.77 ( 3048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 427 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 346 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7989 (mmmt) REVERT: C 252 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7505 (mp) REVERT: C 338 ASN cc_start: 0.8113 (p0) cc_final: 0.7639 (p0) REVERT: E 338 ASN cc_start: 0.8202 (p0) cc_final: 0.7653 (p0) REVERT: F 325 TYR cc_start: 0.8041 (m-10) cc_final: 0.7312 (m-80) REVERT: G 54 PHE cc_start: 0.7198 (m-80) cc_final: 0.6805 (m-80) REVERT: G 331 TYR cc_start: 0.8819 (m-80) cc_final: 0.8398 (m-80) outliers start: 46 outliers final: 35 residues processed: 456 average time/residue: 0.1152 time to fit residues: 83.0364 Evaluate side-chains 443 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 407 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 128 optimal weight: 0.0870 chunk 33 optimal weight: 9.9990 chunk 56 optimal weight: 0.1980 chunk 165 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 108 optimal weight: 0.0980 chunk 192 optimal weight: 0.1980 chunk 140 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 100 ASN D 100 ASN E 100 ASN F 100 ASN G 100 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.173573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135755 restraints weight = 20872.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.137593 restraints weight = 17873.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.139350 restraints weight = 13816.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.139461 restraints weight = 10709.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.139790 restraints weight = 9894.785| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18424 Z= 0.110 Angle : 0.596 8.764 24962 Z= 0.281 Chirality : 0.037 0.135 2933 Planarity : 0.004 0.038 2982 Dihedral : 8.747 118.668 2625 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.34 % Allowed : 18.25 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 2128 helix: 1.21 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -2.17 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 217 TYR 0.036 0.001 TYR B 213 PHE 0.023 0.001 PHE B 299 TRP 0.015 0.002 TRP D 104 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (18410) covalent geometry : angle 0.59607 / 0.28 (24934) SS BOND : bond 0.00143 / 0.09 ( 14) SS BOND : angle 0.52719 / 0.37 ( 28) hydrogen bonds : bond 0.03391 / 2.23 ( 1079) hydrogen bonds : angle 3.82589 / 2.73 ( 3048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 396 time to evaluate : 0.541 Fit side-chains REVERT: C 252 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7340 (mp) REVERT: C 338 ASN cc_start: 0.8202 (p0) cc_final: 0.7647 (p0) REVERT: C 349 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7824 (mttm) REVERT: E 120 LEU cc_start: 0.8664 (mt) cc_final: 0.8306 (mt) REVERT: E 338 ASN cc_start: 0.8353 (p0) cc_final: 0.7751 (p0) REVERT: F 325 TYR cc_start: 0.7969 (m-10) cc_final: 0.7181 (m-80) REVERT: G 252 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7105 (mp) REVERT: G 331 TYR cc_start: 0.8820 (m-80) cc_final: 0.8333 (m-80) REVERT: G 345 TYR cc_start: 0.8763 (t80) cc_final: 0.8549 (t80) outliers start: 46 outliers final: 36 residues processed: 430 average time/residue: 0.1187 time to fit residues: 80.8833 Evaluate side-chains 419 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 381 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 73 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 195 optimal weight: 0.0010 chunk 196 optimal weight: 0.6980 chunk 208 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 100 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 100 ASN E 100 ASN F 100 ASN G 100 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.172320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.134194 restraints weight = 20783.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.136355 restraints weight = 17919.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.138146 restraints weight = 13539.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.138268 restraints weight = 10313.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.138656 restraints weight = 9810.108| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18424 Z= 0.118 Angle : 0.604 8.487 24962 Z= 0.284 Chirality : 0.038 0.157 2933 Planarity : 0.004 0.039 2982 Dihedral : 8.391 110.904 2625 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.49 % Allowed : 18.71 % Favored : 78.80 % 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 are not related in a simple way. whole: 0.34 (0.19), residues: 2128 helix: 1.26 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.15 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 217 TYR 0.060 0.001 TYR C 345 PHE 0.027 0.001 PHE A 141 TRP 0.016 0.002 TRP D 104 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (18410) covalent geometry : angle 0.60431 / 0.28 (24934) SS BOND : bond 0.00186 / 0.12 ( 14) SS BOND : angle 0.68868 / 0.49 ( 28) hydrogen bonds : bond 0.03425 / 2.24 ( 1079) hydrogen bonds : angle 3.81261 / 2.72 ( 3048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 400 time to evaluate : 0.641 Fit side-chains REVERT: A 346 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7980 (mmmt) REVERT: B 213 TYR cc_start: 0.8921 (t80) cc_final: 0.8686 (t80) REVERT: B 349 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8014 (mtpt) REVERT: C 252 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7412 (mp) REVERT: C 338 ASN cc_start: 0.8300 (p0) cc_final: 0.7756 (p0) REVERT: D 120 LEU cc_start: 0.8659 (mt) cc_final: 0.8254 (mt) REVERT: D 352 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6142 (tm-30) REVERT: E 204 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8342 (ttpt) REVERT: E 338 ASN cc_start: 0.8333 (p0) cc_final: 0.7812 (p0) REVERT: F 325 TYR cc_start: 0.8001 (m-10) cc_final: 0.7189 (m-80) REVERT: G 252 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7195 (mp) REVERT: G 331 TYR cc_start: 0.8833 (m-80) cc_final: 0.8358 (m-80) outliers start: 49 outliers final: 39 residues processed: 440 average time/residue: 0.1155 time to fit residues: 80.1065 Evaluate side-chains 431 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 390 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 5 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 100 ASN F 100 ASN G 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.171832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.134288 restraints weight = 20755.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.135849 restraints weight = 18340.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.137336 restraints weight = 15413.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.137630 restraints weight = 11088.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.137829 restraints weight = 11608.529| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18424 Z= 0.129 Angle : 0.626 11.381 24962 Z= 0.295 Chirality : 0.039 0.158 2933 Planarity : 0.004 0.039 2982 Dihedral : 8.210 105.961 2625 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.34 % Allowed : 18.91 % Favored : 78.75 % 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 are not related in a simple way. whole: 0.29 (0.19), residues: 2128 helix: 1.20 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.10 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 217 TYR 0.051 0.001 TYR C 345 PHE 0.027 0.001 PHE A 141 TRP 0.016 0.002 TRP E 104 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (18410) covalent geometry : angle 0.62528 / 0.29 (24934) SS BOND : bond 0.00219 / 0.14 ( 14) SS BOND : angle 0.81034 / 0.58 ( 28) hydrogen bonds : bond 0.03479 / 2.27 ( 1079) hydrogen bonds : angle 3.84493 / 2.74 ( 3048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 402 time to evaluate : 0.566 Fit side-chains REVERT: A 268 ILE cc_start: 0.9197 (mm) cc_final: 0.8944 (mm) REVERT: B 213 TYR cc_start: 0.8937 (t80) cc_final: 0.8727 (t80) REVERT: B 349 LYS cc_start: 0.8418 (mtpp) cc_final: 0.8039 (mtpt) REVERT: C 201 LYS cc_start: 0.7904 (mptt) cc_final: 0.7702 (mptt) REVERT: C 338 ASN cc_start: 0.8262 (p0) cc_final: 0.7788 (p0) REVERT: D 352 GLU cc_start: 0.6665 (tm-30) cc_final: 0.6061 (tm-30) REVERT: E 120 LEU cc_start: 0.8644 (mt) cc_final: 0.8315 (mt) REVERT: E 338 ASN cc_start: 0.8303 (p0) cc_final: 0.7871 (p0) REVERT: F 54 PHE cc_start: 0.7247 (m-80) cc_final: 0.6876 (m-80) REVERT: F 325 TYR cc_start: 0.8005 (m-10) cc_final: 0.7185 (m-80) REVERT: G 331 TYR cc_start: 0.8847 (m-80) cc_final: 0.8306 (m-80) outliers start: 46 outliers final: 38 residues processed: 441 average time/residue: 0.1153 time to fit residues: 81.2907 Evaluate side-chains 437 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 399 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 76 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 100 ASN E 100 ASN F 100 ASN G 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.170587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.132796 restraints weight = 20729.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.133508 restraints weight = 19008.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.135043 restraints weight = 16852.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.135586 restraints weight = 12070.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.135799 restraints weight = 12171.620| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18424 Z= 0.142 Angle : 0.649 12.633 24962 Z= 0.305 Chirality : 0.040 0.165 2933 Planarity : 0.004 0.040 2982 Dihedral : 8.158 100.803 2625 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.49 % Allowed : 19.06 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 2128 helix: 1.12 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.07 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 217 TYR 0.055 0.002 TYR G 345 PHE 0.027 0.001 PHE A 141 TRP 0.016 0.002 TRP G 104 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (18410) covalent geometry : angle 0.64864 / 0.31 (24934) SS BOND : bond 0.00274 / 0.18 ( 14) SS BOND : angle 1.01547 / 0.72 ( 28) hydrogen bonds : bond 0.03582 / 2.34 ( 1079) hydrogen bonds : angle 3.90036 / 2.78 ( 3048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 406 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: B 213 TYR cc_start: 0.8942 (t80) cc_final: 0.8689 (t80) REVERT: B 349 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8052 (mtpt) REVERT: C 201 LYS cc_start: 0.7902 (mptt) cc_final: 0.7699 (mptt) REVERT: C 338 ASN cc_start: 0.8287 (p0) cc_final: 0.7839 (p0) REVERT: D 352 GLU cc_start: 0.6642 (tm-30) cc_final: 0.6045 (tm-30) REVERT: E 338 ASN cc_start: 0.8423 (p0) cc_final: 0.7955 (p0) REVERT: F 54 PHE cc_start: 0.7326 (m-80) cc_final: 0.6961 (m-80) REVERT: F 325 TYR cc_start: 0.8043 (m-10) cc_final: 0.7267 (m-80) REVERT: G 90 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: G 331 TYR cc_start: 0.8844 (m-80) cc_final: 0.8302 (m-80) outliers start: 49 outliers final: 40 residues processed: 447 average time/residue: 0.1191 time to fit residues: 85.1336 Evaluate side-chains 445 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 404 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 91 optimal weight: 3.9990 chunk 180 optimal weight: 0.0980 chunk 131 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 214 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN F 100 ASN G 100 ASN G 264 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.172113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.133919 restraints weight = 20729.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.135494 restraints weight = 18050.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.136728 restraints weight = 14061.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.137371 restraints weight = 11228.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.137813 restraints weight = 10630.294| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18424 Z= 0.122 Angle : 0.635 12.194 24962 Z= 0.297 Chirality : 0.039 0.153 2933 Planarity : 0.004 0.040 2982 Dihedral : 7.830 93.737 2625 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.34 % Allowed : 19.27 % Favored : 78.39 % 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 are not related in a simple way. whole: 0.23 (0.19), residues: 2128 helix: 1.12 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.05 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 217 TYR 0.048 0.001 TYR C 345 PHE 0.026 0.001 PHE B 299 TRP 0.014 0.002 TRP G 104 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (18410) covalent geometry : angle 0.63473 / 0.30 (24934) SS BOND : bond 0.00192 / 0.12 ( 14) SS BOND : angle 0.74323 / 0.52 ( 28) hydrogen bonds : bond 0.03428 / 2.24 ( 1079) hydrogen bonds : angle 3.84888 / 2.75 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.09 seconds wall clock time: 48 minutes 57.02 seconds (2937.02 seconds total)