Starting phenix.real_space_refine on Thu Mar 5 01:24:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f8o_31491/03_2026/7f8o_31491.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f8o_31491/03_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_31491/03_2026/7f8o_31491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f8o_31491/03_2026/7f8o_31491.map" model { file = "/net/cci-nas-00/data/ceres_data/7f8o_31491/03_2026/7f8o_31491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f8o_31491/03_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-5986/lib/python3.9/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: 78 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: 2.32, per 1000 atoms: 0.13 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: 1.52 Conformation dependent library (CDL) restraints added in 721.0 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: 0.41 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: 2.68 Time building geometry restraints manager: 2.04 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 - 35.91: 10906 35.91 - 71.81: 196 71.81 - 107.72: 7 107.72 - 143.62: 7 143.62 - 179.53: 21 Dihedral angle restraints: 11137 sinusoidal: 4613 harmonic: 6524 Sorted by residual: dihedral pdb=" O5 LBN D 501 " pdb=" C2 LBN D 501 " pdb=" C3 LBN D 501 " pdb=" O7 LBN D 501 " ideal model delta sinusoidal sigma weight residual 62.67 -116.86 179.53 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN F 501 " pdb=" C2 LBN F 501 " pdb=" C3 LBN F 501 " pdb=" O7 LBN F 501 " ideal model delta sinusoidal sigma weight residual 62.67 -116.80 179.47 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN G 501 " pdb=" C2 LBN G 501 " pdb=" C3 LBN G 501 " pdb=" O7 LBN G 501 " ideal model delta sinusoidal sigma weight residual 62.67 -116.78 179.45 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 11134 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: 0.05 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: 1.610 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: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.130 Find NCS groups from input model: 0.160 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 15.885 179.528 6839 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 covalent geometry : bond 0.00810 (18410) covalent geometry : angle 0.87537 (24934) SS BOND : bond 0.00124 ( 14) SS BOND : angle 0.63284 ( 28) hydrogen bonds : bond 0.24168 ( 1079) hydrogen bonds : angle 6.33214 ( 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 : 0.660 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: 0.1278 time to fit residues: 107.0308 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 : 0.604 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3817 r_free = 0.3817 target = 0.173274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.134082 restraints weight = 20931.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.133550 restraints weight = 19370.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.135434 restraints weight = 17279.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.136338 restraints weight = 11807.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.136533 restraints weight = 11751.676| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18424 Z= 0.169 Angle : 0.635 7.562 24962 Z= 0.314 Chirality : 0.040 0.124 2933 Planarity : 0.004 0.046 2982 Dihedral : 18.292 175.443 2737 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.78 % Allowed : 10.83 % Favored : 87.39 % 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: 0.28 (0.19), residues: 2128 helix: 1.26 (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 0.027 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 covalent geometry : bond 0.00379 (18410) covalent geometry : angle 0.63407 (24934) SS BOND : bond 0.00212 ( 14) SS BOND : angle 1.01635 ( 28) hydrogen bonds : bond 0.05165 ( 1079) hydrogen bonds : angle 4.28451 ( 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 480 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 445 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: B 120 LEU cc_start: 0.9121 (mt) cc_final: 0.8896 (mt) REVERT: E 40 CYS cc_start: 0.9071 (t) cc_final: 0.8844 (t) REVERT: E 204 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8487 (ttpt) REVERT: F 204 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8326 (ttpt) REVERT: F 213 TYR cc_start: 0.8826 (t80) cc_final: 0.8586 (t80) REVERT: F 325 TYR cc_start: 0.7937 (m-10) cc_final: 0.7481 (m-80) REVERT: G 54 PHE cc_start: 0.6846 (m-80) cc_final: 0.6232 (m-80) REVERT: G 204 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8174 (ttpt) REVERT: G 331 TYR cc_start: 0.8819 (m-80) cc_final: 0.8243 (m-80) outliers start: 35 outliers final: 24 residues processed: 463 average time/residue: 0.1248 time to fit residues: 90.8663 Evaluate side-chains 449 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 425 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 171 optimal weight: 9.9990 chunk 9 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3782 r_free = 0.3782 target = 0.170197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.131573 restraints weight = 21073.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.132865 restraints weight = 18701.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.134223 restraints weight = 15632.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.135177 restraints weight = 11745.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135559 restraints weight = 10909.532| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2294 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= 0.147 Angle : 0.612 7.737 24962 Z= 0.295 Chirality : 0.038 0.149 2933 Planarity : 0.004 0.041 2982 Dihedral : 17.642 179.319 2737 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.24 % Allowed : 13.37 % Favored : 84.39 % 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: 0.07 (0.19), residues: 2128 helix: 1.04 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.37 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 217 TYR 0.021 0.001 TYR E 230 PHE 0.027 0.002 PHE D 235 TRP 0.017 0.002 TRP G 104 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00336 (18410) covalent geometry : angle 0.61109 (24934) SS BOND : bond 0.00250 ( 14) SS BOND : angle 1.02238 ( 28) hydrogen bonds : bond 0.04343 ( 1079) hydrogen bonds : angle 4.12061 ( 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 470 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 426 time to evaluate : 0.628 Fit side-chains REVERT: A 352 GLU cc_start: 0.6341 (tm-30) cc_final: 0.5794 (tm-30) REVERT: B 120 LEU cc_start: 0.9140 (mt) cc_final: 0.8925 (mt) REVERT: E 204 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8459 (ttpt) REVERT: F 213 TYR cc_start: 0.8779 (t80) cc_final: 0.8452 (t80) REVERT: F 325 TYR cc_start: 0.7994 (m-10) cc_final: 0.7568 (m-80) REVERT: G 54 PHE cc_start: 0.6998 (m-80) cc_final: 0.6419 (m-80) REVERT: G 331 TYR cc_start: 0.8792 (m-80) cc_final: 0.8260 (m-80) outliers start: 44 outliers final: 34 residues processed: 451 average time/residue: 0.1216 time to fit residues: 87.4587 Evaluate side-chains 445 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 411 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 174 optimal weight: 0.0040 chunk 155 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 100 ASN 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 = 0.3751 r_free = 0.3751 target = 0.167446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.128616 restraints weight = 21022.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.130309 restraints weight = 18566.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.132099 restraints weight = 14499.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.132289 restraints weight = 10750.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.132585 restraints weight = 10033.567| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18424 Z= 0.169 Angle : 0.629 7.796 24962 Z= 0.302 Chirality : 0.039 0.127 2933 Planarity : 0.004 0.039 2982 Dihedral : 17.311 178.911 2737 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.59 % Allowed : 15.15 % Favored : 82.26 % 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: 0.02 (0.19), residues: 2128 helix: 1.00 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.37 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 217 TYR 0.023 0.001 TYR E 345 PHE 0.025 0.001 PHE C 235 TRP 0.017 0.002 TRP E 104 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00405 (18410) covalent geometry : angle 0.62847 (24934) SS BOND : bond 0.00349 ( 14) SS BOND : angle 1.22517 ( 28) hydrogen bonds : bond 0.04041 ( 1079) hydrogen bonds : angle 4.04126 ( 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 499 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 448 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: B 120 LEU cc_start: 0.9144 (mt) cc_final: 0.8921 (mt) REVERT: B 338 ASN cc_start: 0.8234 (p0) cc_final: 0.7799 (p0) REVERT: B 349 LYS cc_start: 0.8429 (mtpp) cc_final: 0.8169 (mtpt) REVERT: E 204 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8437 (ttpt) REVERT: F 54 PHE cc_start: 0.7463 (m-80) cc_final: 0.6999 (m-80) REVERT: F 325 TYR cc_start: 0.8066 (m-10) cc_final: 0.7522 (m-80) REVERT: G 54 PHE cc_start: 0.7186 (m-80) cc_final: 0.6634 (m-80) REVERT: G 90 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: G 331 TYR cc_start: 0.8796 (m-80) cc_final: 0.8241 (m-80) outliers start: 51 outliers final: 42 residues processed: 481 average time/residue: 0.1196 time to fit residues: 91.5676 Evaluate side-chains 470 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 427 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 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 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 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 339 ILE 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: 3.9990 chunk 7 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** 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 C 262 GLN D 89 GLN D 100 ASN 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 = 0.3756 r_free = 0.3756 target = 0.167793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.129787 restraints weight = 20890.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.131027 restraints weight = 18945.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.132529 restraints weight = 15946.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.132972 restraints weight = 11370.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.133382 restraints weight = 10619.164| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18424 Z= 0.148 Angle : 0.618 7.777 24962 Z= 0.294 Chirality : 0.039 0.137 2933 Planarity : 0.004 0.039 2982 Dihedral : 16.824 175.793 2737 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.90 % Allowed : 16.37 % Favored : 80.73 % 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: 0.04 (0.19), residues: 2128 helix: 1.00 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.31 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 217 TYR 0.022 0.001 TYR E 230 PHE 0.018 0.001 PHE C 141 TRP 0.017 0.002 TRP G 104 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00351 (18410) covalent geometry : angle 0.61700 (24934) SS BOND : bond 0.00309 ( 14) SS BOND : angle 1.04517 ( 28) hydrogen bonds : bond 0.03834 ( 1079) hydrogen bonds : angle 3.97713 ( 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 489 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 432 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: B 213 TYR cc_start: 0.8942 (t80) cc_final: 0.8686 (t80) REVERT: B 239 SER cc_start: 0.8561 (m) cc_final: 0.8325 (p) REVERT: C 331 TYR cc_start: 0.8730 (m-80) cc_final: 0.8383 (m-80) REVERT: C 338 ASN cc_start: 0.8052 (p0) cc_final: 0.7583 (p0) REVERT: F 54 PHE cc_start: 0.7456 (m-80) cc_final: 0.7047 (m-80) REVERT: F 325 TYR cc_start: 0.8071 (m-10) cc_final: 0.7486 (m-80) REVERT: G 54 PHE cc_start: 0.7282 (m-80) cc_final: 0.6803 (m-80) REVERT: G 331 TYR cc_start: 0.8808 (m-80) cc_final: 0.8315 (m-80) outliers start: 57 outliers final: 44 residues processed: 468 average time/residue: 0.1191 time to fit residues: 88.8998 Evaluate side-chains 464 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 420 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 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 144 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU 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 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 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 339 ILE 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: 0.7980 chunk 133 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 51 optimal weight: 0.0060 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 158 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 100 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 100 ASN D 90 GLN D 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 = 0.3780 r_free = 0.3780 target = 0.170021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.131511 restraints weight = 20718.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.133240 restraints weight = 18150.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.135016 restraints weight = 14110.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.135224 restraints weight = 10576.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.135489 restraints weight = 10040.246| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2899 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= 0.123 Angle : 0.607 8.653 24962 Z= 0.287 Chirality : 0.038 0.127 2933 Planarity : 0.004 0.039 2982 Dihedral : 16.215 168.994 2737 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.54 % Allowed : 17.59 % Favored : 79.87 % 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: 0.19 (0.19), residues: 2128 helix: 1.15 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -2.26 (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 covalent geometry : bond 0.00283 (18410) covalent geometry : angle 0.60624 (24934) SS BOND : bond 0.00226 ( 14) SS BOND : angle 0.81323 ( 28) hydrogen bonds : bond 0.03597 ( 1079) hydrogen bonds : angle 3.89062 ( 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 482 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 432 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: B 213 TYR cc_start: 0.8970 (t80) cc_final: 0.8700 (t80) REVERT: C 338 ASN cc_start: 0.8138 (p0) cc_final: 0.7612 (p0) REVERT: E 338 ASN cc_start: 0.8196 (p0) cc_final: 0.7541 (p0) REVERT: F 54 PHE cc_start: 0.7373 (m-80) cc_final: 0.7057 (m-80) REVERT: F 325 TYR cc_start: 0.8070 (m-10) cc_final: 0.7427 (m-80) REVERT: G 54 PHE cc_start: 0.7230 (m-80) cc_final: 0.6829 (m-80) REVERT: G 90 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: G 331 TYR cc_start: 0.8821 (m-80) cc_final: 0.8396 (m-80) outliers start: 50 outliers final: 40 residues processed: 464 average time/residue: 0.1201 time to fit residues: 88.5040 Evaluate side-chains 454 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 413 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 259 VAL Chi-restraints excluded: chain B residue 145 GLU 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 D residue 100 ASN 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 144 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 128 optimal weight: 0.4980 chunk 33 optimal weight: 0.0050 chunk 56 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 108 optimal weight: 0.0370 chunk 192 optimal weight: 0.0970 chunk 140 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.3070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 100 ASN C 262 GLN D 100 ASN E 100 ASN F 89 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 = 0.3809 r_free = 0.3809 target = 0.172761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.134701 restraints weight = 20891.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.137026 restraints weight = 17927.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.138043 restraints weight = 14632.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.138551 restraints weight = 10592.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.138744 restraints weight = 10202.178| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18424 Z= 0.111 Angle : 0.594 11.309 24962 Z= 0.281 Chirality : 0.038 0.133 2933 Planarity : 0.004 0.039 2982 Dihedral : 15.523 159.794 2737 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.19 % Allowed : 18.20 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 0.004 0.000 ARG D 217 TYR 0.023 0.001 TYR E 345 PHE 0.022 0.001 PHE A 141 TRP 0.015 0.002 TRP C 104 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00242 (18410) covalent geometry : angle 0.59427 (24934) SS BOND : bond 0.00149 ( 14) SS BOND : angle 0.58373 ( 28) hydrogen bonds : bond 0.03405 ( 1079) hydrogen bonds : angle 3.83026 ( 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 461 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 418 time to evaluate : 0.567 Fit side-chains REVERT: A 120 LEU cc_start: 0.8571 (mt) cc_final: 0.8249 (mt) REVERT: B 213 TYR cc_start: 0.8977 (t80) cc_final: 0.8732 (t80) REVERT: C 252 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7431 (mp) REVERT: C 333 LEU cc_start: 0.8368 (mt) cc_final: 0.8111 (mt) REVERT: C 338 ASN cc_start: 0.8171 (p0) cc_final: 0.7613 (p0) REVERT: C 349 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7729 (mttm) REVERT: E 338 ASN cc_start: 0.8175 (p0) cc_final: 0.7674 (p0) REVERT: F 325 TYR cc_start: 0.7962 (m-10) cc_final: 0.7169 (m-80) REVERT: G 252 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7153 (mp) REVERT: G 331 TYR cc_start: 0.8794 (m-80) cc_final: 0.8348 (m-80) outliers start: 43 outliers final: 32 residues processed: 449 average time/residue: 0.1238 time to fit residues: 88.2728 Evaluate side-chains 434 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 400 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 73 optimal weight: 0.7980 chunk 159 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 95 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3772 r_free = 0.3772 target = 0.169283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.131148 restraints weight = 20866.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.133267 restraints weight = 18297.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.134545 restraints weight = 14754.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.134846 restraints weight = 10926.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.135044 restraints weight = 11409.587| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18424 Z= 0.146 Angle : 0.630 9.730 24962 Z= 0.298 Chirality : 0.039 0.172 2933 Planarity : 0.004 0.039 2982 Dihedral : 15.289 159.988 2737 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.34 % Allowed : 18.61 % Favored : 79.05 % 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: 0.29 (0.19), residues: 2128 helix: 1.22 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.17 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 217 TYR 0.058 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 covalent geometry : bond 0.00349 (18410) covalent geometry : angle 0.62970 (24934) SS BOND : bond 0.00303 ( 14) SS BOND : angle 1.07560 ( 28) hydrogen bonds : bond 0.03610 ( 1079) hydrogen bonds : angle 3.86863 ( 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 466 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 420 time to evaluate : 0.627 Fit side-chains REVERT: B 213 TYR cc_start: 0.8984 (t80) cc_final: 0.8709 (t80) REVERT: B 349 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8139 (mtpt) REVERT: C 338 ASN cc_start: 0.8215 (p0) cc_final: 0.7663 (p0) REVERT: D 120 LEU cc_start: 0.8663 (mt) cc_final: 0.8257 (mt) REVERT: D 235 PHE cc_start: 0.7825 (t80) cc_final: 0.7567 (t80) REVERT: D 352 GLU cc_start: 0.6773 (tm-30) cc_final: 0.6126 (tm-30) REVERT: E 120 LEU cc_start: 0.8676 (mt) cc_final: 0.8350 (mt) REVERT: E 338 ASN cc_start: 0.8204 (p0) cc_final: 0.7730 (p0) REVERT: F 54 PHE cc_start: 0.7375 (m-80) cc_final: 0.6977 (m-80) REVERT: F 296 PHE cc_start: 0.7601 (m-10) cc_final: 0.7299 (m-80) REVERT: F 325 TYR cc_start: 0.8034 (m-10) cc_final: 0.7246 (m-80) REVERT: G 54 PHE cc_start: 0.7320 (m-80) cc_final: 0.6883 (m-80) REVERT: G 90 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: G 331 TYR cc_start: 0.8876 (m-80) cc_final: 0.8336 (m-80) REVERT: G 345 TYR cc_start: 0.8808 (t80) cc_final: 0.8580 (t80) outliers start: 46 outliers final: 36 residues processed: 452 average time/residue: 0.1171 time to fit residues: 85.2134 Evaluate side-chains 454 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 417 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 5 optimal weight: 0.0020 chunk 164 optimal weight: 0.0040 chunk 206 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** 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 = 0.3814 r_free = 0.3814 target = 0.173136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.135270 restraints weight = 20673.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.136976 restraints weight = 17920.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.138282 restraints weight = 13999.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.138763 restraints weight = 11052.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.139109 restraints weight = 10502.629| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3243 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= 0.117 Angle : 0.621 11.237 24962 Z= 0.292 Chirality : 0.038 0.169 2933 Planarity : 0.004 0.040 2982 Dihedral : 14.705 160.633 2737 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.08 % Allowed : 19.06 % Favored : 78.85 % 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: 1.21 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.08 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 217 TYR 0.033 0.001 TYR D 345 PHE 0.024 0.001 PHE A 141 TRP 0.015 0.002 TRP G 104 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00260 (18410) covalent geometry : angle 0.62110 (24934) SS BOND : bond 0.00139 ( 14) SS BOND : angle 0.60343 ( 28) hydrogen bonds : bond 0.03400 ( 1079) hydrogen bonds : angle 3.84862 ( 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 436 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 395 time to evaluate : 0.635 Fit side-chains REVERT: B 213 TYR cc_start: 0.8956 (t80) cc_final: 0.8693 (t80) REVERT: C 252 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7367 (mp) REVERT: C 338 ASN cc_start: 0.8219 (p0) cc_final: 0.7690 (p0) REVERT: D 352 GLU cc_start: 0.6679 (tm-30) cc_final: 0.6087 (tm-30) REVERT: E 338 ASN cc_start: 0.8324 (p0) cc_final: 0.7906 (p0) REVERT: F 325 TYR cc_start: 0.7983 (m-10) cc_final: 0.7204 (m-80) REVERT: G 90 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7125 (mp10) REVERT: G 331 TYR cc_start: 0.8835 (m-80) cc_final: 0.8302 (m-80) REVERT: G 345 TYR cc_start: 0.8743 (t80) cc_final: 0.8540 (t80) outliers start: 41 outliers final: 33 residues processed: 429 average time/residue: 0.1213 time to fit residues: 82.7997 Evaluate side-chains 420 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 385 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 100 ASN 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 335 LEU 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 76 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.0010 chunk 169 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 180 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.172356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.134167 restraints weight = 20621.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135997 restraints weight = 18004.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.136741 restraints weight = 16311.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.137641 restraints weight = 11473.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.137944 restraints weight = 10516.995| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18424 Z= 0.127 Angle : 0.641 11.983 24962 Z= 0.301 Chirality : 0.039 0.153 2933 Planarity : 0.004 0.040 2982 Dihedral : 14.487 161.310 2737 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.19 % Allowed : 19.57 % Favored : 78.24 % 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: 0.26 (0.19), residues: 2128 helix: 1.14 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -2.07 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 217 TYR 0.042 0.001 TYR D 345 PHE 0.025 0.001 PHE B 299 TRP 0.021 0.002 TRP A 104 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00291 (18410) covalent geometry : angle 0.64070 (24934) SS BOND : bond 0.00214 ( 14) SS BOND : angle 0.81213 ( 28) hydrogen bonds : bond 0.03466 ( 1079) hydrogen bonds : angle 3.86918 ( 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 443 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 400 time to evaluate : 0.712 Fit side-chains REVERT: B 213 TYR cc_start: 0.8967 (t80) cc_final: 0.8694 (t80) REVERT: C 338 ASN cc_start: 0.8293 (p0) cc_final: 0.7752 (p0) REVERT: D 252 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7087 (mp) REVERT: D 352 GLU cc_start: 0.6622 (tm-30) cc_final: 0.6060 (tm-30) REVERT: E 338 ASN cc_start: 0.8369 (p0) cc_final: 0.7877 (p0) REVERT: F 325 TYR cc_start: 0.8005 (m-10) cc_final: 0.7227 (m-80) REVERT: F 338 ASN cc_start: 0.8146 (p0) cc_final: 0.7494 (p0) REVERT: G 90 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: G 240 LEU cc_start: 0.7898 (mm) cc_final: 0.7648 (pp) REVERT: G 331 TYR cc_start: 0.8867 (m-80) cc_final: 0.8307 (m-80) REVERT: G 338 ASN cc_start: 0.8111 (p0) cc_final: 0.7627 (p0) outliers start: 43 outliers final: 35 residues processed: 436 average time/residue: 0.1186 time to fit residues: 83.4490 Evaluate side-chains 436 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 399 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 237 LEU 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 252 ILE 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 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 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 344 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 91 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 131 optimal weight: 0.0980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 89 GLN D 100 ASN D 264 GLN 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 = 0.3813 r_free = 0.3813 target = 0.173006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.134940 restraints weight = 20721.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.136894 restraints weight = 18049.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.138502 restraints weight = 13875.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.138838 restraints weight = 10449.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.139035 restraints weight = 9889.503| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18424 Z= 0.123 Angle : 0.645 16.334 24962 Z= 0.301 Chirality : 0.039 0.149 2933 Planarity : 0.004 0.041 2982 Dihedral : 14.285 161.686 2737 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.19 % Allowed : 19.42 % 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: 0.22 (0.19), residues: 2128 helix: 1.10 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -2.08 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 217 TYR 0.041 0.001 TYR C 345 PHE 0.028 0.001 PHE A 141 TRP 0.017 0.002 TRP A 104 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00281 (18410) covalent geometry : angle 0.64465 (24934) SS BOND : bond 0.00202 ( 14) SS BOND : angle 0.76094 ( 28) hydrogen bonds : bond 0.03421 ( 1079) hydrogen bonds : angle 3.85816 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2795.82 seconds wall clock time: 49 minutes 36.25 seconds (2976.25 seconds total)