Starting phenix.real_space_refine on Sun May 18 02:18:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bei_16004/05_2025/8bei_16004_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bei_16004/05_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_16004/05_2025/8bei_16004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bei_16004/05_2025/8bei_16004.map" model { file = "/net/cci-nas-00/data/ceres_data/8bei_16004/05_2025/8bei_16004_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bei_16004/05_2025/8bei_16004_neut.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, F Time building chain proxies: 6.07, per 1000 atoms: 0.37 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: 3.73 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.49 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: 5.10 Time building geometry restraints manager: 4.41 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.120 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.800 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP F 56 HIS 0.002 0.000 HIS D 369 PHE 0.008 0.001 PHE B 139 TYR 0.018 0.001 TYR B 292 ARG 0.002 0.000 ARG D 81 Details of bonding type rmsd hydrogen bonds : bond 0.15179 ( 954) hydrogen bonds : angle 6.26472 ( 2772) covalent geometry : bond 0.00273 (16974) covalent geometry : angle 0.54584 (23064) *********************** 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 : 1.619 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: 0.3051 time to fit residues: 113.0050 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 : 1.634 ------------------------------------------------------------------------------- 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 177 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 D 223 HIS E 223 HIS E 369 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 = 0.3915 r_free = 0.3915 target = 0.183108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.156610 restraints weight = 15631.264| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 0.93 r_work: 0.3275 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16974 Z= 0.207 Angle : 0.603 7.367 23064 Z= 0.313 Chirality : 0.044 0.144 2574 Planarity : 0.006 0.077 2988 Dihedral : 4.633 41.346 2315 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.22 % Allowed : 16.21 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2052 helix: 1.08 (0.14), residues: 1284 sheet: 1.11 (0.73), residues: 60 loop : -0.55 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP C 345 HIS 0.004 0.001 HIS E 185 PHE 0.018 0.002 PHE D 80 TYR 0.016 0.002 TYR B 292 ARG 0.003 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.05671 ( 954) hydrogen bonds : angle 4.83963 ( 2772) covalent geometry : bond 0.00521 (16974) covalent geometry : angle 0.60258 (23064) *********************** 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 262 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 1.662 Fit side-chains REVERT: A 27 GLN cc_start: 0.7744 (mp10) cc_final: 0.7515 (mp10) REVERT: A 127 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8333 (mtt90) REVERT: B 62 GLN cc_start: 0.7620 (tp40) cc_final: 0.7385 (tp-100) REVERT: B 74 TYR cc_start: 0.8480 (t80) cc_final: 0.8279 (t80) REVERT: B 86 MET cc_start: 0.8988 (mtp) cc_final: 0.8660 (mtt) REVERT: B 147 ASP cc_start: 0.8150 (m-30) cc_final: 0.7892 (m-30) REVERT: B 233 MET cc_start: 0.5018 (mtt) cc_final: 0.4796 (mtt) REVERT: B 332 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7638 (mp) REVERT: C 27 GLN cc_start: 0.7805 (mp10) cc_final: 0.7254 (mp10) REVERT: C 86 MET cc_start: 0.8844 (mtp) cc_final: 0.8601 (mtt) REVERT: C 135 MET cc_start: 0.9029 (mtm) cc_final: 0.8788 (mtm) REVERT: C 168 ARG cc_start: 0.7530 (mtm110) cc_final: 0.7168 (mtt-85) REVERT: C 332 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7479 (mp) REVERT: E 150 GLN cc_start: 0.8152 (mt0) cc_final: 0.7913 (tt0) REVERT: F 85 MET cc_start: 0.8481 (mtm) cc_final: 0.8231 (mtp) outliers start: 56 outliers final: 35 residues processed: 250 average time/residue: 0.3262 time to fit residues: 117.4436 Evaluate side-chains 236 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 ASN 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 356 ASN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 267 VAL 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 234 LEU 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 356 ASN Chi-restraints excluded: chain D residue 374 THR 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 91 ASP Chi-restraints excluded: chain F residue 334 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 108 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 197 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS E 354 ASN F 352 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.188091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.139580 restraints weight = 15543.924| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.97 r_work: 0.3044 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1548 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= 0.110 Angle : 0.493 8.501 23064 Z= 0.252 Chirality : 0.039 0.148 2574 Planarity : 0.005 0.066 2988 Dihedral : 4.235 37.489 2315 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.33 % Allowed : 15.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2052 helix: 1.50 (0.14), residues: 1278 sheet: 1.09 (0.73), residues: 60 loop : -0.37 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 56 HIS 0.002 0.001 HIS D 369 PHE 0.012 0.001 PHE A 139 TYR 0.014 0.001 TYR F 292 ARG 0.002 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 954) hydrogen bonds : angle 4.55933 ( 2772) covalent geometry : bond 0.00254 (16974) covalent geometry : angle 0.49257 (23064) *********************** 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 267 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 1.675 Fit side-chains REVERT: A 27 GLN cc_start: 0.7731 (mp10) cc_final: 0.7489 (mp10) REVERT: A 127 ARG cc_start: 0.8444 (mtt90) cc_final: 0.8228 (mtt90) REVERT: A 187 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: A 198 MET cc_start: 0.8740 (mtm) cc_final: 0.8526 (mtp) REVERT: B 74 TYR cc_start: 0.8385 (t80) cc_final: 0.8164 (t80) REVERT: B 86 MET cc_start: 0.8911 (mtp) cc_final: 0.8583 (mtt) REVERT: B 147 ASP cc_start: 0.8219 (m-30) cc_final: 0.7933 (m-30) REVERT: B 187 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: B 332 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7424 (mp) REVERT: C 27 GLN cc_start: 0.7764 (mp10) cc_final: 0.7175 (mp10) REVERT: C 86 MET cc_start: 0.8806 (mtp) cc_final: 0.8508 (mtt) REVERT: C 135 MET cc_start: 0.9063 (mtm) cc_final: 0.8645 (mtm) REVERT: C 168 ARG cc_start: 0.7380 (mtm110) cc_final: 0.6974 (mtt-85) REVERT: D 187 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: E 198 MET cc_start: 0.8654 (mtm) cc_final: 0.8359 (mtp) REVERT: F 85 MET cc_start: 0.8445 (mtm) cc_final: 0.8115 (mtp) REVERT: F 267 VAL cc_start: 0.6883 (OUTLIER) cc_final: 0.6637 (m) REVERT: F 372 ASP cc_start: 0.7777 (p0) cc_final: 0.6743 (m-30) outliers start: 58 outliers final: 26 residues processed: 251 average time/residue: 0.3406 time to fit residues: 121.9438 Evaluate side-chains 234 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 234 LEU 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 187 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 258 MET 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 B residue 376 ILE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 334 THR 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 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 356 ASN Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 334 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 129 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 192 optimal weight: 0.0870 chunk 109 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4001 r_free = 0.4001 target = 0.189329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.140498 restraints weight = 15512.201| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.95 r_work: 0.3054 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16974 Z= 0.105 Angle : 0.476 8.153 23064 Z= 0.242 Chirality : 0.039 0.154 2574 Planarity : 0.005 0.061 2988 Dihedral : 3.808 24.806 2309 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.59 % Allowed : 16.67 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.18), residues: 2052 helix: 1.69 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.25 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 56 HIS 0.002 0.001 HIS F 94 PHE 0.012 0.001 PHE E 139 TYR 0.013 0.001 TYR F 373 ARG 0.003 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 954) hydrogen bonds : angle 4.42203 ( 2772) covalent geometry : bond 0.00239 (16974) covalent geometry : angle 0.47611 (23064) *********************** 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 256 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 1.655 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.7574 (mp10) cc_final: 0.7295 (mp10) REVERT: A 121 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7812 (mm) REVERT: A 127 ARG cc_start: 0.8421 (mtt90) cc_final: 0.8210 (mtt90) REVERT: A 135 MET cc_start: 0.9086 (mtm) cc_final: 0.8622 (mtm) REVERT: B 86 MET cc_start: 0.8869 (mtp) cc_final: 0.8537 (mtt) REVERT: B 147 ASP cc_start: 0.8211 (m-30) cc_final: 0.7924 (m-30) REVERT: B 187 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: B 233 MET cc_start: 0.4966 (mtt) cc_final: 0.4654 (mtt) REVERT: C 27 GLN cc_start: 0.7734 (mp10) cc_final: 0.7121 (mp10) REVERT: C 86 MET cc_start: 0.8795 (mtp) cc_final: 0.8503 (mtt) REVERT: C 135 MET cc_start: 0.9102 (mtm) cc_final: 0.8653 (mtm) REVERT: C 168 ARG cc_start: 0.7266 (mtm110) cc_final: 0.6869 (mtt-85) REVERT: E 292 TYR cc_start: 0.7358 (t80) cc_final: 0.7153 (t80) REVERT: E 372 ASP cc_start: 0.7876 (p0) cc_final: 0.6953 (m-30) REVERT: F 267 VAL cc_start: 0.6859 (OUTLIER) cc_final: 0.6597 (m) REVERT: F 325 LYS cc_start: 0.7919 (tptt) cc_final: 0.7694 (tppt) REVERT: F 372 ASP cc_start: 0.7747 (p0) cc_final: 0.6853 (m-30) outliers start: 45 outliers final: 31 residues processed: 239 average time/residue: 0.3290 time to fit residues: 111.8959 Evaluate side-chains 242 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 267 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 187 GLU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 258 MET 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 121 ILE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 164 MET 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 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 267 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 187 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 182 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.189939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.141100 restraints weight = 15688.610| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.00 r_work: 0.3059 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16974 Z= 0.099 Angle : 0.468 8.188 23064 Z= 0.237 Chirality : 0.039 0.164 2574 Planarity : 0.005 0.057 2988 Dihedral : 3.662 20.400 2303 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.64 % Allowed : 17.01 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2052 helix: 1.81 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.18 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 56 HIS 0.002 0.000 HIS F 94 PHE 0.011 0.001 PHE A 139 TYR 0.011 0.001 TYR D 292 ARG 0.003 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 954) hydrogen bonds : angle 4.33669 ( 2772) covalent geometry : bond 0.00224 (16974) covalent geometry : angle 0.46798 (23064) *********************** 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 253 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.7556 (mp10) cc_final: 0.7273 (mp10) REVERT: A 135 MET cc_start: 0.9090 (mtm) cc_final: 0.8650 (mtm) REVERT: B 86 MET cc_start: 0.8887 (mtp) cc_final: 0.8552 (mtt) REVERT: B 187 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: B 233 MET cc_start: 0.4998 (mtt) cc_final: 0.4664 (mtt) REVERT: C 27 GLN cc_start: 0.7747 (mp10) cc_final: 0.7124 (mp10) REVERT: C 86 MET cc_start: 0.8763 (mtp) cc_final: 0.8471 (mtt) REVERT: C 135 MET cc_start: 0.9108 (mtm) cc_final: 0.8685 (mtm) REVERT: C 168 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6853 (mtt-85) REVERT: E 372 ASP cc_start: 0.7856 (p0) cc_final: 0.6909 (m-30) REVERT: F 267 VAL cc_start: 0.6897 (OUTLIER) cc_final: 0.6638 (m) REVERT: F 372 ASP cc_start: 0.7599 (p0) cc_final: 0.6884 (m-30) outliers start: 46 outliers final: 33 residues processed: 239 average time/residue: 0.3356 time to fit residues: 114.6313 Evaluate side-chains 235 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 267 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 187 GLU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 258 MET 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 121 ILE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 267 VAL 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 353 LEU 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 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 150 GLN Chi-restraints excluded: chain F residue 267 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 112 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 F 369 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.180545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.130618 restraints weight = 15849.492| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.10 r_work: 0.2931 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 16974 Z= 0.275 Angle : 0.654 10.048 23064 Z= 0.337 Chirality : 0.046 0.187 2574 Planarity : 0.006 0.058 2988 Dihedral : 4.388 33.625 2303 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.85 % Allowed : 16.44 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2052 helix: 0.96 (0.13), residues: 1284 sheet: 0.65 (0.68), residues: 60 loop : -0.44 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 345 HIS 0.005 0.001 HIS F 188 PHE 0.025 0.002 PHE A 80 TYR 0.016 0.002 TYR D 292 ARG 0.005 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.06317 ( 954) hydrogen bonds : angle 4.70595 ( 2772) covalent geometry : bond 0.00711 (16974) covalent geometry : angle 0.65426 (23064) *********************** 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 277 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 210 time to evaluate : 1.909 Fit side-chains REVERT: A 27 GLN cc_start: 0.7668 (mp10) cc_final: 0.7453 (mp10) REVERT: B 147 ASP cc_start: 0.8470 (m-30) cc_final: 0.8058 (m-30) REVERT: B 233 MET cc_start: 0.5144 (mtt) cc_final: 0.4851 (mtt) REVERT: B 319 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7120 (p) REVERT: B 332 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7743 (mp) REVERT: B 372 ASP cc_start: 0.7811 (p0) cc_final: 0.6498 (m-30) REVERT: C 27 GLN cc_start: 0.7832 (mp10) cc_final: 0.7236 (mp10) REVERT: C 59 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7550 (mm) REVERT: C 362 THR cc_start: 0.8367 (t) cc_final: 0.8140 (t) REVERT: D 82 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8710 (mm) REVERT: E 319 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7324 (p) REVERT: E 372 ASP cc_start: 0.8207 (p0) cc_final: 0.7073 (m-30) REVERT: F 62 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7682 (tp-100) REVERT: F 85 MET cc_start: 0.8495 (mtm) cc_final: 0.8169 (mtp) REVERT: F 319 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7075 (p) REVERT: F 372 ASP cc_start: 0.7817 (p0) cc_final: 0.6908 (m-30) outliers start: 67 outliers final: 45 residues processed: 265 average time/residue: 0.3174 time to fit residues: 121.7277 Evaluate side-chains 256 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 267 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 187 GLU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 332 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 267 VAL 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 147 ASP 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 187 GLU Chi-restraints excluded: chain E residue 193 SER 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 353 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 166 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 153 optimal weight: 0.0770 chunk 154 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.187054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.138576 restraints weight = 15616.446| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.04 r_work: 0.3048 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2102 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= 0.101 Angle : 0.483 8.501 23064 Z= 0.247 Chirality : 0.039 0.184 2574 Planarity : 0.005 0.054 2988 Dihedral : 3.938 27.047 2303 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.53 % Allowed : 17.59 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2052 helix: 1.55 (0.14), residues: 1278 sheet: 0.83 (0.71), residues: 60 loop : -0.24 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 56 HIS 0.002 0.001 HIS D 94 PHE 0.012 0.001 PHE A 139 TYR 0.017 0.001 TYR D 292 ARG 0.005 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 954) hydrogen bonds : angle 4.45502 ( 2772) covalent geometry : bond 0.00226 (16974) covalent geometry : angle 0.48322 (23064) *********************** 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 252 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 1.648 Fit side-chains REVERT: A 27 GLN cc_start: 0.7665 (mp10) cc_final: 0.7460 (mp10) REVERT: A 135 MET cc_start: 0.9054 (mtm) cc_final: 0.8719 (mtm) REVERT: B 85 MET cc_start: 0.8418 (mtp) cc_final: 0.8149 (mtp) REVERT: B 86 MET cc_start: 0.8904 (mtp) cc_final: 0.8639 (mtt) REVERT: B 319 SER cc_start: 0.7763 (OUTLIER) cc_final: 0.7007 (p) REVERT: B 373 TYR cc_start: 0.8057 (t80) cc_final: 0.7706 (t80) REVERT: C 27 GLN cc_start: 0.7781 (mp10) cc_final: 0.7170 (mp10) REVERT: C 59 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7598 (mm) REVERT: C 86 MET cc_start: 0.8766 (mtp) cc_final: 0.8499 (mtt) REVERT: D 82 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8638 (mm) REVERT: E 372 ASP cc_start: 0.8102 (p0) cc_final: 0.7128 (m-30) REVERT: F 372 ASP cc_start: 0.7805 (p0) cc_final: 0.7038 (m-30) outliers start: 44 outliers final: 34 residues processed: 243 average time/residue: 0.3250 time to fit residues: 112.8324 Evaluate side-chains 242 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 267 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 258 MET Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 358 ILE 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 267 VAL Chi-restraints excluded: chain C residue 319 SER 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 353 LEU 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 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 147 ASP Chi-restraints excluded: chain F residue 150 GLN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 107 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.187653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.138629 restraints weight = 15527.589| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.98 r_work: 0.3010 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16974 Z= 0.115 Angle : 0.493 8.550 23064 Z= 0.252 Chirality : 0.040 0.189 2574 Planarity : 0.005 0.054 2988 Dihedral : 3.836 24.217 2303 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.76 % Allowed : 17.47 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.18), residues: 2052 helix: 1.68 (0.14), residues: 1278 sheet: 0.89 (0.72), residues: 60 loop : -0.19 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 56 HIS 0.002 0.001 HIS F 94 PHE 0.013 0.001 PHE D 80 TYR 0.022 0.001 TYR C 292 ARG 0.005 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 954) hydrogen bonds : angle 4.38924 ( 2772) covalent geometry : bond 0.00273 (16974) covalent geometry : angle 0.49340 (23064) *********************** 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 260 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 1.643 Fit side-chains REVERT: A 27 GLN cc_start: 0.7641 (mp10) cc_final: 0.7415 (mp10) REVERT: A 135 MET cc_start: 0.9093 (mtm) cc_final: 0.8751 (mtm) REVERT: B 85 MET cc_start: 0.8433 (mtp) cc_final: 0.8223 (mtp) REVERT: B 86 MET cc_start: 0.8904 (mtp) cc_final: 0.8609 (mtt) REVERT: B 258 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.4994 (pmm) REVERT: B 319 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7030 (p) REVERT: B 372 ASP cc_start: 0.7782 (p0) cc_final: 0.6615 (m-30) REVERT: B 373 TYR cc_start: 0.8072 (t80) cc_final: 0.7744 (t80) REVERT: C 27 GLN cc_start: 0.7772 (mp10) cc_final: 0.7158 (mp10) REVERT: C 59 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7600 (mm) REVERT: C 86 MET cc_start: 0.8789 (mtp) cc_final: 0.8518 (mtt) REVERT: D 82 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8655 (mm) REVERT: E 198 MET cc_start: 0.8825 (mtm) cc_final: 0.8545 (mtp) REVERT: E 319 SER cc_start: 0.7922 (OUTLIER) cc_final: 0.7181 (p) REVERT: E 372 ASP cc_start: 0.8146 (p0) cc_final: 0.7052 (m-30) REVERT: F 372 ASP cc_start: 0.7777 (p0) cc_final: 0.7099 (m-30) outliers start: 48 outliers final: 40 residues processed: 249 average time/residue: 0.3217 time to fit residues: 115.9660 Evaluate side-chains 250 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 319 SER 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 258 MET Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 358 ILE 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 187 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 319 SER 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 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 353 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 243 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 194 optimal weight: 0.5980 chunk 175 optimal weight: 0.0980 chunk 205 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 133 optimal weight: 0.2980 chunk 114 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.189544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.141200 restraints weight = 15567.358| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.90 r_work: 0.3107 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16974 Z= 0.090 Angle : 0.462 8.162 23064 Z= 0.234 Chirality : 0.038 0.182 2574 Planarity : 0.005 0.053 2988 Dihedral : 3.656 20.056 2303 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.47 % Allowed : 17.59 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.18), residues: 2052 helix: 1.88 (0.14), residues: 1278 sheet: 0.99 (0.73), residues: 60 loop : -0.10 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 56 HIS 0.002 0.000 HIS D 94 PHE 0.013 0.001 PHE A 139 TYR 0.019 0.001 TYR D 292 ARG 0.006 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 954) hydrogen bonds : angle 4.32306 ( 2772) covalent geometry : bond 0.00195 (16974) covalent geometry : angle 0.46169 (23064) *********************** 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 245 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 1.674 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.9056 (mtm) cc_final: 0.8612 (mtm) REVERT: B 86 MET cc_start: 0.8840 (mtp) cc_final: 0.8554 (mtt) REVERT: B 319 SER cc_start: 0.7781 (OUTLIER) cc_final: 0.7047 (p) REVERT: B 372 ASP cc_start: 0.7688 (p0) cc_final: 0.6670 (m-30) REVERT: B 373 TYR cc_start: 0.8015 (t80) cc_final: 0.7694 (t80) REVERT: C 27 GLN cc_start: 0.7737 (mp10) cc_final: 0.7126 (mp10) REVERT: C 59 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7564 (mm) REVERT: C 86 MET cc_start: 0.8688 (mtp) cc_final: 0.8429 (mtt) REVERT: C 187 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: D 82 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8641 (mm) REVERT: E 187 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: E 198 MET cc_start: 0.8747 (mtm) cc_final: 0.8543 (mtp) REVERT: E 372 ASP cc_start: 0.8081 (p0) cc_final: 0.7075 (m-30) REVERT: F 372 ASP cc_start: 0.7702 (p0) cc_final: 0.7164 (m-30) outliers start: 43 outliers final: 32 residues processed: 235 average time/residue: 0.3277 time to fit residues: 110.6206 Evaluate side-chains 233 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 258 MET 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 187 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 319 SER 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 267 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 374 THR 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 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 150 GLN 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 130 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.186421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.137633 restraints weight = 15603.664| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.98 r_work: 0.3040 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16974 Z= 0.129 Angle : 0.505 8.779 23064 Z= 0.258 Chirality : 0.040 0.198 2574 Planarity : 0.005 0.054 2988 Dihedral : 3.781 23.064 2303 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.41 % Allowed : 17.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2052 helix: 1.73 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.17 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 345 HIS 0.002 0.001 HIS D 369 PHE 0.013 0.001 PHE D 80 TYR 0.020 0.001 TYR D 292 ARG 0.005 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 954) hydrogen bonds : angle 4.36931 ( 2772) covalent geometry : bond 0.00314 (16974) covalent geometry : angle 0.50521 (23064) ********************** 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 249 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 1.699 Fit side-chains REVERT: A 135 MET cc_start: 0.9095 (mtm) cc_final: 0.8753 (mtm) REVERT: B 85 MET cc_start: 0.8375 (mtp) cc_final: 0.8142 (mtp) REVERT: B 86 MET cc_start: 0.8928 (mtp) cc_final: 0.8641 (mtt) REVERT: B 147 ASP cc_start: 0.8364 (m-30) cc_final: 0.7907 (m-30) REVERT: B 319 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7080 (p) REVERT: B 372 ASP cc_start: 0.7795 (p0) cc_final: 0.6772 (m-30) REVERT: B 373 TYR cc_start: 0.8031 (t80) cc_final: 0.7722 (t80) REVERT: C 59 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7560 (mm) REVERT: C 86 MET cc_start: 0.8771 (mtp) cc_final: 0.8500 (mtt) REVERT: D 82 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8689 (mm) REVERT: E 372 ASP cc_start: 0.8047 (p0) cc_final: 0.7041 (m-30) REVERT: F 372 ASP cc_start: 0.7711 (p0) cc_final: 0.7159 (m-30) outliers start: 42 outliers final: 36 residues processed: 241 average time/residue: 0.3184 time to fit residues: 111.3019 Evaluate side-chains 241 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 358 ILE 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 187 GLU Chi-restraints excluded: chain C residue 267 VAL 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 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 374 THR 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 368 SER Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 243 VAL 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 187 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 193 optimal weight: 0.0470 chunk 133 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 204 optimal weight: 0.7980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.188095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.139400 restraints weight = 15598.085| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.98 r_work: 0.3165 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16974 Z= 0.102 Angle : 0.480 8.597 23064 Z= 0.243 Chirality : 0.039 0.193 2574 Planarity : 0.005 0.053 2988 Dihedral : 3.717 21.665 2303 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.36 % Allowed : 17.87 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.18), residues: 2052 helix: 1.83 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.12 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 56 HIS 0.002 0.000 HIS D 94 PHE 0.012 0.001 PHE A 139 TYR 0.019 0.001 TYR D 292 ARG 0.006 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 954) hydrogen bonds : angle 4.34634 ( 2772) covalent geometry : bond 0.00235 (16974) covalent geometry : angle 0.48009 (23064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7186.21 seconds wall clock time: 125 minutes 13.19 seconds (7513.19 seconds total)