Starting phenix.real_space_refine on Sun Aug 24 02:44:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bei_16004/08_2025/8bei_16004_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bei_16004/08_2025/8bei_16004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bei_16004/08_2025/8bei_16004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bei_16004/08_2025/8bei_16004.map" model { file = "/net/cci-nas-00/data/ceres_data/8bei_16004/08_2025/8bei_16004_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bei_16004/08_2025/8bei_16004_neut.cif" } resolution = 3.06 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 10650 2.51 5 N 2820 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16578 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2763 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 20, 'TRANS': 329} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.47, per 1000 atoms: 0.15 Number of scatterers: 16578 At special positions: 0 Unit cell: (123.17, 127.53, 94.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 3048 8.00 N 2820 7.00 C 10650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 669.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 68.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 94 through 111 removed outlier: 3.856A pdb=" N GLY A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 144 Proline residue: A 133 - end of helix removed outlier: 3.941A pdb=" N LYS A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 191 through 202 Processing helix chain 'A' and resid 206 through 220 removed outlier: 4.218A pdb=" N GLY A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 269 through 287 removed outlier: 3.626A pdb=" N VAL A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.733A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 326 removed outlier: 3.985A pdb=" N TYR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 332 through 355 removed outlier: 4.818A pdb=" N ALA A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 94 through 111 removed outlier: 3.855A pdb=" N GLY B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 144 Proline residue: B 133 - end of helix removed outlier: 3.941A pdb=" N LYS B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 171 through 185 Processing helix chain 'B' and resid 191 through 202 Processing helix chain 'B' and resid 206 through 220 removed outlier: 4.218A pdb=" N GLY B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 269 through 287 removed outlier: 3.626A pdb=" N VAL B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 306 removed outlier: 3.733A pdb=" N GLU B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.984A pdb=" N TYR B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 332 through 355 removed outlier: 4.818A pdb=" N ALA B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B 354 " --> pdb=" O LYS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 46 through 57 Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 94 through 111 removed outlier: 3.855A pdb=" N GLY C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 144 Proline residue: C 133 - end of helix removed outlier: 3.941A pdb=" N LYS C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 202 Processing helix chain 'C' and resid 206 through 220 removed outlier: 4.218A pdb=" N GLY C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 224 Processing helix chain 'C' and resid 228 through 238 Processing helix chain 'C' and resid 269 through 287 removed outlier: 3.627A pdb=" N VAL C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 306 removed outlier: 3.734A pdb=" N GLU C 304 " --> pdb=" O LYS C 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 326 removed outlier: 3.985A pdb=" N TYR C 318 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 332 through 355 removed outlier: 4.818A pdb=" N ALA C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C 354 " --> pdb=" O LYS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 46 through 57 Processing helix chain 'D' and resid 61 through 75 Processing helix chain 'D' and resid 79 through 88 Processing helix chain 'D' and resid 94 through 111 removed outlier: 3.856A pdb=" N GLY D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 144 Proline residue: D 133 - end of helix removed outlier: 3.941A pdb=" N LYS D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 167 Processing helix chain 'D' and resid 171 through 185 Processing helix chain 'D' and resid 191 through 202 Processing helix chain 'D' and resid 206 through 220 removed outlier: 4.219A pdb=" N GLY D 220 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 224 Processing helix chain 'D' and resid 228 through 238 Processing helix chain 'D' and resid 269 through 287 removed outlier: 3.626A pdb=" N VAL D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 306 removed outlier: 3.733A pdb=" N GLU D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 326 removed outlier: 3.984A pdb=" N TYR D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU D 321 " --> pdb=" O PHE D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 355 removed outlier: 4.817A pdb=" N ALA D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 354 " --> pdb=" O LYS D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 379 Processing helix chain 'E' and resid 38 through 45 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 79 through 88 Processing helix chain 'E' and resid 94 through 111 removed outlier: 3.856A pdb=" N GLY E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 144 Proline residue: E 133 - end of helix removed outlier: 3.940A pdb=" N LYS E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 171 through 185 Processing helix chain 'E' and resid 191 through 202 Processing helix chain 'E' and resid 206 through 220 removed outlier: 4.218A pdb=" N GLY E 220 " --> pdb=" O GLY E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 224 Processing helix chain 'E' and resid 228 through 238 Processing helix chain 'E' and resid 269 through 287 removed outlier: 3.627A pdb=" N VAL E 273 " --> pdb=" O ASP E 269 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE E 274 " --> pdb=" O PRO E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 306 removed outlier: 3.733A pdb=" N GLU E 304 " --> pdb=" O LYS E 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG E 305 " --> pdb=" O ALA E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 removed outlier: 3.984A pdb=" N TYR E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY E 320 " --> pdb=" O ASP E 316 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU E 321 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 332 through 355 removed outlier: 4.818A pdb=" N ALA E 343 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN E 354 " --> pdb=" O LYS E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 379 Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 46 through 57 Processing helix chain 'F' and resid 61 through 75 Processing helix chain 'F' and resid 79 through 88 Processing helix chain 'F' and resid 94 through 111 removed outlier: 3.856A pdb=" N GLY F 107 " --> pdb=" O ALA F 103 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 144 Proline residue: F 133 - end of helix removed outlier: 3.942A pdb=" N LYS F 144 " --> pdb=" O GLN F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 167 Processing helix chain 'F' and resid 171 through 185 Processing helix chain 'F' and resid 191 through 202 Processing helix chain 'F' and resid 206 through 220 removed outlier: 4.219A pdb=" N GLY F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 224 Processing helix chain 'F' and resid 228 through 238 Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.626A pdb=" N VAL F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE F 274 " --> pdb=" O PRO F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 306 removed outlier: 3.733A pdb=" N GLU F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG F 305 " --> pdb=" O ALA F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.985A pdb=" N TYR F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY F 320 " --> pdb=" O ASP F 316 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU F 321 " --> pdb=" O PHE F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 332 through 355 removed outlier: 4.817A pdb=" N ALA F 343 " --> pdb=" O ILE F 339 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN F 354 " --> pdb=" O LYS F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 379 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.186A pdb=" N ILE B 364 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR A 17 " --> pdb=" O ILE B 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 25 Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 365 removed outlier: 6.914A pdb=" N THR A 362 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR B 17 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 364 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 19 " --> pdb=" O ILE A 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 25 Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 19 removed outlier: 6.257A pdb=" N ILE E 364 " --> pdb=" O PRO C 15 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR C 17 " --> pdb=" O ILE E 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 25 Processing sheet with id=AA7, first strand: chain 'C' and resid 362 through 365 removed outlier: 7.041A pdb=" N THR C 362 " --> pdb=" O PRO E 15 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR E 17 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 364 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 19 " --> pdb=" O ILE C 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.237A pdb=" N ILE F 364 " --> pdb=" O PRO D 15 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR D 17 " --> pdb=" O ILE F 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AB1, first strand: chain 'D' and resid 362 through 365 removed outlier: 6.907A pdb=" N THR D 362 " --> pdb=" O PRO F 15 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR F 17 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 364 " --> pdb=" O THR F 17 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER F 19 " --> pdb=" O ILE D 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 22 through 25 Processing sheet with id=AB3, first strand: chain 'F' and resid 22 through 25 954 hydrogen bonds defined for protein. 2772 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: 2.65 Time building geometry restraints manager: 1.85 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: 5446 1.34 - 1.46: 2930 1.46 - 1.58: 8490 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 16974 Sorted by residual: bond pdb=" CB PRO F 375 " pdb=" CG PRO F 375 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.32e+00 bond pdb=" CB PRO E 375 " pdb=" CG PRO E 375 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.30e+00 bond pdb=" CB PRO A 375 " pdb=" CG PRO A 375 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.28e+00 bond pdb=" CB PRO D 375 " pdb=" CG PRO D 375 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.27e+00 bond pdb=" CB PRO B 375 " pdb=" CG PRO B 375 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.27e+00 ... (remaining 16969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 22364 1.30 - 2.60: 535 2.60 - 3.90: 131 3.90 - 5.20: 20 5.20 - 6.50: 14 Bond angle restraints: 23064 Sorted by residual: angle pdb=" N VAL D 240 " pdb=" CA VAL D 240 " pdb=" C VAL D 240 " ideal model delta sigma weight residual 112.80 109.23 3.57 1.15e+00 7.56e-01 9.64e+00 angle pdb=" N VAL C 240 " pdb=" CA VAL C 240 " pdb=" C VAL C 240 " ideal model delta sigma weight residual 112.80 109.26 3.54 1.15e+00 7.56e-01 9.48e+00 angle pdb=" N VAL B 240 " pdb=" CA VAL B 240 " pdb=" C VAL B 240 " ideal model delta sigma weight residual 112.80 109.27 3.53 1.15e+00 7.56e-01 9.42e+00 angle pdb=" N VAL A 240 " pdb=" CA VAL A 240 " pdb=" C VAL A 240 " ideal model delta sigma weight residual 112.80 109.27 3.53 1.15e+00 7.56e-01 9.40e+00 angle pdb=" N VAL F 240 " pdb=" CA VAL F 240 " pdb=" C VAL F 240 " ideal model delta sigma weight residual 112.80 109.29 3.51 1.15e+00 7.56e-01 9.32e+00 ... (remaining 23059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 8788 17.70 - 35.40: 1016 35.40 - 53.10: 246 53.10 - 70.80: 54 70.80 - 88.50: 12 Dihedral angle restraints: 10116 sinusoidal: 3996 harmonic: 6120 Sorted by residual: dihedral pdb=" CB GLU C 167 " pdb=" CG GLU C 167 " pdb=" CD GLU C 167 " pdb=" OE1 GLU C 167 " ideal model delta sinusoidal sigma weight residual 0.00 88.50 -88.50 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 167 " pdb=" CG GLU B 167 " pdb=" CD GLU B 167 " pdb=" OE1 GLU B 167 " ideal model delta sinusoidal sigma weight residual 0.00 88.46 -88.46 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU F 167 " pdb=" CG GLU F 167 " pdb=" CD GLU F 167 " pdb=" OE1 GLU F 167 " ideal model delta sinusoidal sigma weight residual 0.00 88.43 -88.43 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 10113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1377 0.024 - 0.047: 687 0.047 - 0.071: 309 0.071 - 0.095: 133 0.095 - 0.118: 68 Chirality restraints: 2574 Sorted by residual: chirality pdb=" CB ILE E 190 " pdb=" CA ILE E 190 " pdb=" CG1 ILE E 190 " pdb=" CG2 ILE E 190 " both_signs ideal model delta sigma weight residual False 2.64 2.53 0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA PRO D 270 " pdb=" N PRO D 270 " pdb=" C PRO D 270 " pdb=" CB PRO D 270 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA PRO C 270 " pdb=" N PRO C 270 " pdb=" C PRO C 270 " pdb=" CB PRO C 270 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 2571 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 374 " 0.066 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO E 375 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO E 375 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 375 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 374 " -0.066 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO C 375 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 375 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 375 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 374 " -0.066 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO F 375 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO F 375 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 375 " -0.053 5.00e-02 4.00e+02 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3184 2.77 - 3.30: 15653 3.30 - 3.84: 27550 3.84 - 4.37: 32508 4.37 - 4.90: 57026 Nonbonded interactions: 135921 Sorted by model distance: nonbonded pdb=" OG SER C 45 " pdb=" OE1 GLU C 49 " model vdw 2.240 3.040 nonbonded pdb=" OG SER F 45 " pdb=" OE1 GLU F 49 " model vdw 2.240 3.040 nonbonded pdb=" OG SER D 45 " pdb=" OE1 GLU D 49 " model vdw 2.240 3.040 nonbonded pdb=" OG SER B 45 " pdb=" OE1 GLU B 49 " model vdw 2.240 3.040 nonbonded pdb=" OG SER A 45 " pdb=" OE1 GLU A 49 " model vdw 2.241 3.040 ... (remaining 135916 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.650 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16974 Z= 0.134 Angle : 0.546 6.504 23064 Z= 0.323 Chirality : 0.038 0.118 2574 Planarity : 0.006 0.098 2988 Dihedral : 16.061 88.496 6168 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.38 % Allowed : 15.92 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.19), residues: 2052 helix: 1.31 (0.15), residues: 1260 sheet: 1.50 (0.80), residues: 60 loop : -0.40 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 81 TYR 0.018 0.001 TYR B 292 PHE 0.008 0.001 PHE B 139 TRP 0.007 0.001 TRP F 56 HIS 0.002 0.000 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00273 (16974) covalent geometry : angle 0.54584 (23064) hydrogen bonds : bond 0.15179 ( 954) hydrogen bonds : angle 6.26472 ( 2772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.483 Fit side-chains REVERT: A 27 GLN cc_start: 0.7581 (mp10) cc_final: 0.6981 (mp10) REVERT: A 292 TYR cc_start: 0.7125 (t80) cc_final: 0.6742 (t80) REVERT: B 74 TYR cc_start: 0.8263 (t80) cc_final: 0.8057 (t80) REVERT: B 147 ASP cc_start: 0.8056 (m-30) cc_final: 0.7801 (m-30) REVERT: C 27 GLN cc_start: 0.7679 (mp10) cc_final: 0.7189 (mp10) REVERT: C 135 MET cc_start: 0.8739 (mtm) cc_final: 0.8310 (mtm) REVERT: C 168 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7413 (mtt-85) REVERT: D 85 MET cc_start: 0.7729 (mtm) cc_final: 0.7437 (mtm) REVERT: D 317 PHE cc_start: 0.8430 (t80) cc_final: 0.8214 (t80) REVERT: E 85 MET cc_start: 0.8372 (mtm) cc_final: 0.8064 (mtp) REVERT: F 85 MET cc_start: 0.8172 (mtm) cc_final: 0.7906 (mtp) outliers start: 24 outliers final: 11 residues processed: 254 average time/residue: 0.1258 time to fit residues: 46.9712 Evaluate side-chains 220 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain F residue 356 ASN Chi-restraints excluded: chain F residue 374 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 223 HIS C 223 HIS D 223 HIS E 223 HIS F 43 GLN F 223 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.191332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.164573 restraints weight = 15504.470| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 0.88 r_work: 0.3407 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16974 Z= 0.118 Angle : 0.496 6.350 23064 Z= 0.257 Chirality : 0.040 0.135 2574 Planarity : 0.006 0.076 2988 Dihedral : 4.349 42.773 2315 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.16 % Allowed : 14.43 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.18), residues: 2052 helix: 1.62 (0.14), residues: 1278 sheet: 1.44 (0.77), residues: 60 loop : -0.38 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 379 TYR 0.016 0.001 TYR F 373 PHE 0.012 0.001 PHE E 139 TRP 0.009 0.002 TRP B 345 HIS 0.002 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00260 (16974) covalent geometry : angle 0.49638 (23064) hydrogen bonds : bond 0.04252 ( 954) hydrogen bonds : angle 4.71189 ( 2772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 203 time to evaluate : 0.632 Fit side-chains REVERT: A 27 GLN cc_start: 0.7708 (mp10) cc_final: 0.6877 (mp10) REVERT: A 135 MET cc_start: 0.8949 (mtm) cc_final: 0.8569 (mtp) REVERT: B 147 ASP cc_start: 0.8086 (m-30) cc_final: 0.7782 (m-30) REVERT: B 233 MET cc_start: 0.5172 (mtt) cc_final: 0.4971 (mtt) REVERT: B 332 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7494 (mp) REVERT: C 27 GLN cc_start: 0.7781 (mp10) cc_final: 0.7149 (mp10) REVERT: C 86 MET cc_start: 0.8805 (mtp) cc_final: 0.8503 (mtt) REVERT: C 135 MET cc_start: 0.9019 (mtm) cc_final: 0.8552 (mtm) REVERT: C 168 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7211 (mtt-85) REVERT: C 258 MET cc_start: 0.6594 (mpp) cc_final: 0.6308 (ptp) REVERT: C 276 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7430 (tt0) REVERT: C 332 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7415 (mp) REVERT: E 233 MET cc_start: 0.4702 (mtt) cc_final: 0.4474 (mtt) REVERT: E 292 TYR cc_start: 0.7466 (t80) cc_final: 0.7080 (t80) REVERT: F 187 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8112 (tt0) outliers start: 55 outliers final: 28 residues processed: 244 average time/residue: 0.1356 time to fit residues: 47.3418 Evaluate side-chains 228 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 356 ASN Chi-restraints excluded: chain F residue 374 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 159 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 172 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN F 352 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.189434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140115 restraints weight = 15691.543| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.03 r_work: 0.3093 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16974 Z= 0.113 Angle : 0.487 8.049 23064 Z= 0.249 Chirality : 0.039 0.143 2574 Planarity : 0.005 0.066 2988 Dihedral : 4.040 34.656 2315 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.64 % Allowed : 15.98 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.18), residues: 2052 helix: 1.69 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.28 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 122 TYR 0.014 0.001 TYR D 292 PHE 0.013 0.001 PHE D 80 TRP 0.006 0.002 TRP B 56 HIS 0.002 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00262 (16974) covalent geometry : angle 0.48748 (23064) hydrogen bonds : bond 0.04097 ( 954) hydrogen bonds : angle 4.47466 ( 2772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.578 Fit side-chains REVERT: A 27 GLN cc_start: 0.7613 (mp10) cc_final: 0.7324 (mp10) REVERT: A 73 ARG cc_start: 0.8347 (mtt90) cc_final: 0.8130 (mtt-85) REVERT: A 135 MET cc_start: 0.9069 (mtm) cc_final: 0.8679 (mtp) REVERT: B 86 MET cc_start: 0.8886 (mtp) cc_final: 0.8542 (mtt) REVERT: B 147 ASP cc_start: 0.8131 (m-30) cc_final: 0.7857 (m-30) REVERT: B 233 MET cc_start: 0.4868 (mtt) cc_final: 0.4555 (mtt) REVERT: B 332 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7362 (mp) REVERT: C 27 GLN cc_start: 0.7712 (mp10) cc_final: 0.7096 (mp10) REVERT: C 86 MET cc_start: 0.8792 (mtp) cc_final: 0.8495 (mtt) REVERT: C 135 MET cc_start: 0.9069 (mtm) cc_final: 0.8633 (mtm) REVERT: C 168 ARG cc_start: 0.7348 (mtm110) cc_final: 0.6958 (mtt-85) REVERT: C 332 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7124 (mp) REVERT: F 85 MET cc_start: 0.8387 (mtm) cc_final: 0.8089 (mtp) REVERT: F 325 LYS cc_start: 0.7925 (tptt) cc_final: 0.7709 (tppt) outliers start: 46 outliers final: 24 residues processed: 247 average time/residue: 0.1414 time to fit residues: 49.8112 Evaluate side-chains 230 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 356 ASN Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 HIS F 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.185185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.137728 restraints weight = 15624.607| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.03 r_work: 0.3016 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16974 Z= 0.153 Angle : 0.533 8.597 23064 Z= 0.272 Chirality : 0.041 0.154 2574 Planarity : 0.005 0.062 2988 Dihedral : 3.960 26.690 2309 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.70 % Allowed : 16.38 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.18), residues: 2052 helix: 1.46 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -0.30 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 127 TYR 0.016 0.001 TYR F 292 PHE 0.017 0.002 PHE D 80 TRP 0.007 0.002 TRP D 345 HIS 0.003 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00379 (16974) covalent geometry : angle 0.53309 (23064) hydrogen bonds : bond 0.04709 ( 954) hydrogen bonds : angle 4.50906 ( 2772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 0.629 Fit side-chains REVERT: A 27 GLN cc_start: 0.7678 (mp10) cc_final: 0.7451 (mp10) REVERT: A 135 MET cc_start: 0.9146 (mtm) cc_final: 0.8810 (mtm) REVERT: B 86 MET cc_start: 0.8960 (mtp) cc_final: 0.8642 (mtt) REVERT: B 147 ASP cc_start: 0.8270 (m-30) cc_final: 0.7993 (m-30) REVERT: B 332 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7484 (mp) REVERT: C 27 GLN cc_start: 0.7743 (mp10) cc_final: 0.7125 (mp10) REVERT: C 135 MET cc_start: 0.9117 (mtm) cc_final: 0.8844 (mtm) REVERT: C 168 ARG cc_start: 0.7296 (mtm110) cc_final: 0.6916 (mtt-85) REVERT: E 150 GLN cc_start: 0.8244 (mt0) cc_final: 0.7854 (tt0) REVERT: E 372 ASP cc_start: 0.7866 (p0) cc_final: 0.6919 (m-30) REVERT: F 187 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: F 372 ASP cc_start: 0.7726 (p0) cc_final: 0.6546 (m-30) outliers start: 47 outliers final: 28 residues processed: 246 average time/residue: 0.1356 time to fit residues: 48.2300 Evaluate side-chains 239 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 118 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 HIS F 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.184593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.135427 restraints weight = 15734.047| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.07 r_work: 0.2996 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16974 Z= 0.150 Angle : 0.527 8.948 23064 Z= 0.269 Chirality : 0.041 0.165 2574 Planarity : 0.005 0.059 2988 Dihedral : 3.967 26.704 2303 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.99 % Allowed : 16.15 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.18), residues: 2052 helix: 1.43 (0.14), residues: 1284 sheet: 0.87 (0.70), residues: 60 loop : -0.26 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.016 0.001 TYR F 292 PHE 0.017 0.001 PHE D 80 TRP 0.006 0.002 TRP A 345 HIS 0.003 0.001 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00372 (16974) covalent geometry : angle 0.52708 (23064) hydrogen bonds : bond 0.04578 ( 954) hydrogen bonds : angle 4.49521 ( 2772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.421 Fit side-chains REVERT: A 27 GLN cc_start: 0.7676 (mp10) cc_final: 0.7458 (mp10) REVERT: A 121 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7922 (mm) REVERT: A 135 MET cc_start: 0.9154 (mtm) cc_final: 0.8820 (mtm) REVERT: B 147 ASP cc_start: 0.8240 (m-30) cc_final: 0.7949 (m-30) REVERT: B 233 MET cc_start: 0.5073 (mtt) cc_final: 0.4751 (mtt) REVERT: B 332 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7566 (mp) REVERT: C 27 GLN cc_start: 0.7763 (mp10) cc_final: 0.7146 (mp10) REVERT: C 135 MET cc_start: 0.9114 (mtm) cc_final: 0.8853 (mtm) REVERT: C 168 ARG cc_start: 0.7269 (mtm110) cc_final: 0.6873 (mtt-85) REVERT: C 258 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6191 (ptp) REVERT: E 82 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8680 (mm) REVERT: E 86 MET cc_start: 0.9165 (mtt) cc_final: 0.8873 (mtp) REVERT: E 372 ASP cc_start: 0.8061 (p0) cc_final: 0.6944 (m-30) REVERT: F 85 MET cc_start: 0.8494 (mtm) cc_final: 0.8184 (mtp) REVERT: F 187 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: F 372 ASP cc_start: 0.7737 (p0) cc_final: 0.6904 (m-30) outliers start: 52 outliers final: 38 residues processed: 248 average time/residue: 0.1401 time to fit residues: 50.1288 Evaluate side-chains 250 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 85 optimal weight: 0.0070 chunk 203 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 52 optimal weight: 0.4980 chunk 191 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 352 GLN F 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.188316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.139853 restraints weight = 15668.878| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.00 r_work: 0.3056 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16974 Z= 0.097 Angle : 0.469 8.552 23064 Z= 0.238 Chirality : 0.039 0.175 2574 Planarity : 0.005 0.056 2988 Dihedral : 3.730 22.034 2303 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.70 % Allowed : 17.07 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.18), residues: 2052 helix: 1.78 (0.14), residues: 1278 sheet: 1.01 (0.72), residues: 60 loop : -0.13 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 122 TYR 0.016 0.001 TYR F 292 PHE 0.012 0.001 PHE E 139 TRP 0.007 0.001 TRP C 56 HIS 0.002 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00218 (16974) covalent geometry : angle 0.46876 (23064) hydrogen bonds : bond 0.03597 ( 954) hydrogen bonds : angle 4.36868 ( 2772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.431 Fit side-chains REVERT: A 135 MET cc_start: 0.9097 (mtm) cc_final: 0.8575 (mtm) REVERT: B 86 MET cc_start: 0.8853 (mtp) cc_final: 0.8531 (mtt) REVERT: B 233 MET cc_start: 0.5092 (mtt) cc_final: 0.4770 (mtt) REVERT: B 332 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7400 (mp) REVERT: B 373 TYR cc_start: 0.8036 (t80) cc_final: 0.7763 (t80) REVERT: C 27 GLN cc_start: 0.7757 (mp10) cc_final: 0.7136 (mp10) REVERT: C 59 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7601 (mm) REVERT: C 86 MET cc_start: 0.8748 (mtp) cc_final: 0.8464 (mtt) REVERT: C 135 MET cc_start: 0.9087 (mtm) cc_final: 0.8699 (mtm) REVERT: C 168 ARG cc_start: 0.7258 (mtm110) cc_final: 0.6868 (mtt-85) REVERT: C 258 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6242 (ptp) REVERT: D 82 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8691 (mm) REVERT: E 82 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8607 (mm) REVERT: E 190 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6606 (mt) REVERT: E 319 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7270 (p) REVERT: E 372 ASP cc_start: 0.8026 (p0) cc_final: 0.6996 (m-30) REVERT: F 372 ASP cc_start: 0.7562 (p0) cc_final: 0.6916 (m-30) outliers start: 47 outliers final: 30 residues processed: 240 average time/residue: 0.1334 time to fit residues: 45.7000 Evaluate side-chains 243 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 129 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 354 ASN F 369 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.184939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135655 restraints weight = 15584.579| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.06 r_work: 0.3055 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16974 Z= 0.171 Angle : 0.549 9.445 23064 Z= 0.280 Chirality : 0.042 0.182 2574 Planarity : 0.005 0.055 2988 Dihedral : 3.988 27.029 2303 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.10 % Allowed : 16.84 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.18), residues: 2052 helix: 1.44 (0.14), residues: 1284 sheet: 0.79 (0.69), residues: 60 loop : -0.23 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.018 0.001 TYR D 292 PHE 0.020 0.002 PHE D 80 TRP 0.008 0.002 TRP C 345 HIS 0.003 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00431 (16974) covalent geometry : angle 0.54871 (23064) hydrogen bonds : bond 0.04919 ( 954) hydrogen bonds : angle 4.46889 ( 2772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.479 Fit side-chains REVERT: A 135 MET cc_start: 0.9127 (mtm) cc_final: 0.8844 (mtm) REVERT: A 198 MET cc_start: 0.8762 (mtm) cc_final: 0.8436 (mtp) REVERT: B 86 MET cc_start: 0.8957 (mtp) cc_final: 0.8669 (mtt) REVERT: B 147 ASP cc_start: 0.8374 (m-30) cc_final: 0.7950 (m-30) REVERT: B 319 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7119 (p) REVERT: B 373 TYR cc_start: 0.8080 (t80) cc_final: 0.7732 (t80) REVERT: C 27 GLN cc_start: 0.7770 (mp10) cc_final: 0.7144 (mp10) REVERT: C 59 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7584 (mm) REVERT: C 85 MET cc_start: 0.8035 (mtt) cc_final: 0.7827 (mtm) REVERT: C 135 MET cc_start: 0.9079 (mtm) cc_final: 0.8851 (mtm) REVERT: C 168 ARG cc_start: 0.7298 (mtm110) cc_final: 0.6902 (mtt-85) REVERT: C 258 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6492 (ptp) REVERT: C 362 THR cc_start: 0.7999 (t) cc_final: 0.7763 (t) REVERT: D 82 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8686 (mm) REVERT: E 82 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8719 (mm) REVERT: E 319 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7333 (p) REVERT: E 372 ASP cc_start: 0.8069 (p0) cc_final: 0.7056 (m-30) REVERT: F 319 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7118 (p) REVERT: F 372 ASP cc_start: 0.7771 (p0) cc_final: 0.7009 (m-30) outliers start: 54 outliers final: 36 residues processed: 248 average time/residue: 0.1404 time to fit residues: 49.5631 Evaluate side-chains 245 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 174 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN F 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.185798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.138504 restraints weight = 15620.947| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.98 r_work: 0.3030 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16974 Z= 0.117 Angle : 0.496 8.732 23064 Z= 0.251 Chirality : 0.040 0.189 2574 Planarity : 0.005 0.054 2988 Dihedral : 3.849 24.337 2303 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.76 % Allowed : 17.13 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.18), residues: 2052 helix: 1.65 (0.14), residues: 1278 sheet: 0.89 (0.71), residues: 60 loop : -0.15 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 122 TYR 0.018 0.001 TYR D 292 PHE 0.011 0.001 PHE D 80 TRP 0.006 0.001 TRP C 56 HIS 0.002 0.001 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00280 (16974) covalent geometry : angle 0.49554 (23064) hydrogen bonds : bond 0.03993 ( 954) hydrogen bonds : angle 4.40772 ( 2772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 0.516 Fit side-chains REVERT: A 135 MET cc_start: 0.9145 (mtm) cc_final: 0.8714 (mtm) REVERT: A 198 MET cc_start: 0.8731 (mtm) cc_final: 0.8354 (mtp) REVERT: B 86 MET cc_start: 0.8889 (mtp) cc_final: 0.8586 (mtt) REVERT: B 147 ASP cc_start: 0.8357 (m-30) cc_final: 0.7919 (m-30) REVERT: B 319 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7096 (p) REVERT: B 372 ASP cc_start: 0.7749 (p0) cc_final: 0.6607 (m-30) REVERT: B 373 TYR cc_start: 0.8082 (t80) cc_final: 0.7760 (t80) REVERT: C 27 GLN cc_start: 0.7762 (mp10) cc_final: 0.7132 (mp10) REVERT: C 59 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7591 (mm) REVERT: C 86 MET cc_start: 0.8788 (mtp) cc_final: 0.8507 (mtt) REVERT: C 135 MET cc_start: 0.9109 (mtm) cc_final: 0.8755 (mtm) REVERT: C 168 ARG cc_start: 0.7295 (mtm110) cc_final: 0.6903 (mtt-85) REVERT: C 258 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6462 (ptp) REVERT: C 362 THR cc_start: 0.8022 (t) cc_final: 0.7799 (t) REVERT: D 82 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8697 (mm) REVERT: D 233 MET cc_start: 0.3111 (mtp) cc_final: 0.2596 (mtp) REVERT: E 82 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8670 (mm) REVERT: E 319 SER cc_start: 0.7967 (OUTLIER) cc_final: 0.7222 (p) REVERT: E 372 ASP cc_start: 0.8078 (p0) cc_final: 0.7128 (m-30) REVERT: F 372 ASP cc_start: 0.7741 (p0) cc_final: 0.7060 (m-30) outliers start: 48 outliers final: 39 residues processed: 242 average time/residue: 0.1621 time to fit residues: 56.4479 Evaluate side-chains 252 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN F 43 GLN F 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.186776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.137823 restraints weight = 15543.330| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.01 r_work: 0.3147 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16974 Z= 0.114 Angle : 0.493 8.927 23064 Z= 0.250 Chirality : 0.039 0.197 2574 Planarity : 0.005 0.054 2988 Dihedral : 3.786 23.283 2303 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.87 % Allowed : 16.84 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.18), residues: 2052 helix: 1.70 (0.14), residues: 1278 sheet: 0.89 (0.71), residues: 60 loop : -0.12 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 122 TYR 0.025 0.001 TYR C 292 PHE 0.012 0.001 PHE D 80 TRP 0.006 0.001 TRP C 56 HIS 0.002 0.001 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00270 (16974) covalent geometry : angle 0.49323 (23064) hydrogen bonds : bond 0.03944 ( 954) hydrogen bonds : angle 4.38065 ( 2772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.611 Fit side-chains REVERT: A 135 MET cc_start: 0.9071 (mtm) cc_final: 0.8639 (mtm) REVERT: A 198 MET cc_start: 0.8660 (mtm) cc_final: 0.8409 (mtp) REVERT: B 86 MET cc_start: 0.8844 (mtp) cc_final: 0.8540 (mtt) REVERT: B 147 ASP cc_start: 0.8289 (m-30) cc_final: 0.7830 (m-30) REVERT: B 233 MET cc_start: 0.5038 (mtt) cc_final: 0.4811 (mtt) REVERT: B 319 SER cc_start: 0.7779 (OUTLIER) cc_final: 0.7040 (p) REVERT: B 372 ASP cc_start: 0.7688 (p0) cc_final: 0.6595 (m-30) REVERT: B 373 TYR cc_start: 0.8049 (t80) cc_final: 0.7733 (t80) REVERT: C 27 GLN cc_start: 0.7738 (mp10) cc_final: 0.7106 (mp10) REVERT: C 59 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7528 (mm) REVERT: C 86 MET cc_start: 0.8724 (mtp) cc_final: 0.8456 (mtt) REVERT: C 135 MET cc_start: 0.9027 (mtm) cc_final: 0.8648 (mtm) REVERT: C 168 ARG cc_start: 0.7228 (mtm110) cc_final: 0.6820 (mtt-85) REVERT: C 258 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6553 (ptp) REVERT: D 82 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8646 (mm) REVERT: D 233 MET cc_start: 0.3156 (mtp) cc_final: 0.2618 (mtp) REVERT: D 354 ASN cc_start: 0.6854 (OUTLIER) cc_final: 0.6574 (p0) REVERT: E 82 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8603 (mm) REVERT: E 198 MET cc_start: 0.8734 (mtm) cc_final: 0.8480 (mtp) REVERT: E 319 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7236 (p) REVERT: E 372 ASP cc_start: 0.8024 (p0) cc_final: 0.7022 (m-30) REVERT: F 372 ASP cc_start: 0.7598 (p0) cc_final: 0.7026 (m-30) outliers start: 50 outliers final: 39 residues processed: 242 average time/residue: 0.1531 time to fit residues: 53.8545 Evaluate side-chains 253 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.181435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.132296 restraints weight = 15681.350| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.10 r_work: 0.3042 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16974 Z= 0.203 Angle : 0.588 9.749 23064 Z= 0.300 Chirality : 0.043 0.209 2574 Planarity : 0.005 0.054 2988 Dihedral : 4.155 29.774 2303 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.93 % Allowed : 16.90 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.18), residues: 2052 helix: 1.26 (0.14), residues: 1284 sheet: 0.57 (0.68), residues: 60 loop : -0.34 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 81 TYR 0.022 0.002 TYR C 292 PHE 0.020 0.002 PHE D 80 TRP 0.011 0.003 TRP C 345 HIS 0.004 0.001 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00516 (16974) covalent geometry : angle 0.58822 (23064) hydrogen bonds : bond 0.05389 ( 954) hydrogen bonds : angle 4.55855 ( 2772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 0.543 Fit side-chains REVERT: A 198 MET cc_start: 0.8772 (mtm) cc_final: 0.8357 (mtp) REVERT: B 147 ASP cc_start: 0.8394 (m-30) cc_final: 0.7959 (m-30) REVERT: B 319 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7171 (p) REVERT: B 372 ASP cc_start: 0.7731 (p0) cc_final: 0.6556 (m-30) REVERT: B 373 TYR cc_start: 0.8144 (t80) cc_final: 0.7840 (t80) REVERT: C 27 GLN cc_start: 0.7784 (mp10) cc_final: 0.7166 (mp10) REVERT: C 59 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7593 (mm) REVERT: C 85 MET cc_start: 0.8096 (mtt) cc_final: 0.7876 (mtm) REVERT: C 168 ARG cc_start: 0.7326 (mtm110) cc_final: 0.6902 (mtt-85) REVERT: C 258 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6720 (ptp) REVERT: C 362 THR cc_start: 0.8242 (t) cc_final: 0.7990 (t) REVERT: D 82 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8700 (mm) REVERT: E 82 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8739 (mm) REVERT: E 319 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7320 (p) REVERT: E 372 ASP cc_start: 0.8182 (p0) cc_final: 0.7157 (m-30) REVERT: F 319 SER cc_start: 0.7884 (OUTLIER) cc_final: 0.7124 (p) REVERT: F 372 ASP cc_start: 0.7713 (p0) cc_final: 0.7134 (m-30) outliers start: 51 outliers final: 43 residues processed: 247 average time/residue: 0.1652 time to fit residues: 59.0143 Evaluate side-chains 260 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 150 GLN E 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.187357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.138762 restraints weight = 15503.056| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.97 r_work: 0.3055 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16974 Z= 0.108 Angle : 0.491 8.725 23064 Z= 0.250 Chirality : 0.039 0.200 2574 Planarity : 0.005 0.053 2988 Dihedral : 3.883 25.033 2303 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.64 % Allowed : 17.53 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.18), residues: 2052 helix: 1.62 (0.14), residues: 1278 sheet: 0.81 (0.70), residues: 60 loop : -0.21 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 122 TYR 0.021 0.001 TYR C 292 PHE 0.011 0.001 PHE A 139 TRP 0.007 0.001 TRP C 56 HIS 0.002 0.001 HIS D 348 Details of bonding type rmsd covalent geometry : bond 0.00249 (16974) covalent geometry : angle 0.49122 (23064) hydrogen bonds : bond 0.03838 ( 954) hydrogen bonds : angle 4.43124 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3334.13 seconds wall clock time: 58 minutes 0.06 seconds (3480.06 seconds total)