Starting phenix.real_space_refine on Fri Sep 27 15:48:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bei_16004/09_2024/8bei_16004_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bei_16004/09_2024/8bei_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bei_16004/09_2024/8bei_16004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bei_16004/09_2024/8bei_16004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bei_16004/09_2024/8bei_16004_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bei_16004/09_2024/8bei_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-5461/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: 6.09, 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: 3.83 Conformation dependent library (CDL) restraints added in 2.1 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: 1.61 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: 4.57 Time building geometry restraints manager: 4.45 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 31.610 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- 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= 0.171 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 *********************** 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 fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 1.916 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: 0.3141 time to fit residues: 116.2418 Evaluate side-chains 220 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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= 0.341 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 *********************** 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 fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 1.708 Fit side-chains REVERT: A 127 ARG cc_start: 0.8496 (mtt90) cc_final: 0.8285 (mtt90) REVERT: B 86 MET cc_start: 0.8970 (mtp) cc_final: 0.8636 (mtt) REVERT: B 147 ASP cc_start: 0.8210 (m-30) cc_final: 0.7980 (m-30) REVERT: B 332 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7922 (mp) REVERT: C 27 GLN cc_start: 0.7738 (mp10) cc_final: 0.7293 (mp10) REVERT: C 86 MET cc_start: 0.8827 (mtp) cc_final: 0.8585 (mtt) REVERT: C 135 MET cc_start: 0.8880 (mtm) cc_final: 0.8667 (mtm) REVERT: C 332 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7781 (mp) REVERT: F 85 MET cc_start: 0.8291 (mtm) cc_final: 0.7976 (mtp) outliers start: 56 outliers final: 35 residues processed: 250 average time/residue: 0.3185 time to fit residues: 115.0308 Evaluate side-chains 236 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 105 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 191 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16974 Z= 0.147 Angle : 0.486 8.322 23064 Z= 0.249 Chirality : 0.039 0.144 2574 Planarity : 0.005 0.065 2988 Dihedral : 4.229 38.308 2315 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.22 % Allowed : 15.80 % Favored : 80.98 % 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: 1.29 (0.18), residues: 2052 helix: 1.53 (0.14), residues: 1278 sheet: 1.12 (0.74), residues: 60 loop : -0.35 (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 E 139 TYR 0.013 0.001 TYR F 292 ARG 0.002 0.000 ARG B 122 *********************** 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 262 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 1.831 Fit side-chains revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8300 (mtt90) cc_final: 0.8098 (mtt90) REVERT: B 86 MET cc_start: 0.8866 (mtp) cc_final: 0.8524 (mtt) REVERT: B 147 ASP cc_start: 0.8184 (m-30) cc_final: 0.7937 (m-30) REVERT: B 233 MET cc_start: 0.5951 (mtt) cc_final: 0.5747 (mtt) REVERT: B 332 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7822 (mp) REVERT: C 27 GLN cc_start: 0.7694 (mp10) cc_final: 0.7214 (mp10) REVERT: C 86 MET cc_start: 0.8756 (mtp) cc_final: 0.8458 (mtt) REVERT: C 135 MET cc_start: 0.8836 (mtm) cc_final: 0.8436 (mtm) REVERT: F 85 MET cc_start: 0.8222 (mtm) cc_final: 0.7850 (mtp) REVERT: F 372 ASP cc_start: 0.7835 (p0) cc_final: 0.7033 (m-30) outliers start: 56 outliers final: 23 residues processed: 246 average time/residue: 0.3464 time to fit residues: 121.1273 Evaluate side-chains 226 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 374 THR 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 234 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 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 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 188 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16974 Z= 0.217 Angle : 0.512 8.487 23064 Z= 0.262 Chirality : 0.040 0.156 2574 Planarity : 0.005 0.061 2988 Dihedral : 3.955 24.245 2309 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.82 % Allowed : 16.55 % Favored : 80.63 % 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: 1.28 (0.18), residues: 2052 helix: 1.51 (0.14), residues: 1278 sheet: 0.96 (0.72), residues: 60 loop : -0.28 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 345 HIS 0.002 0.001 HIS D 369 PHE 0.016 0.001 PHE D 80 TYR 0.013 0.001 TYR F 373 ARG 0.003 0.000 ARG A 73 *********************** 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 251 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 202 time to evaluate : 1.897 Fit side-chains revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8183 (mm) REVERT: A 127 ARG cc_start: 0.8360 (mtt90) cc_final: 0.8158 (mtt90) REVERT: A 135 MET cc_start: 0.8886 (mtm) cc_final: 0.8570 (mtm) REVERT: B 86 MET cc_start: 0.8895 (mtp) cc_final: 0.8549 (mtt) REVERT: B 147 ASP cc_start: 0.8222 (m-30) cc_final: 0.8003 (m-30) REVERT: B 233 MET cc_start: 0.6087 (mtt) cc_final: 0.5784 (mtt) REVERT: B 332 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7915 (mp) REVERT: C 27 GLN cc_start: 0.7701 (mp10) cc_final: 0.7209 (mp10) REVERT: C 86 MET cc_start: 0.8783 (mtp) cc_final: 0.8496 (mtt) REVERT: C 135 MET cc_start: 0.8918 (mtm) cc_final: 0.8581 (mtm) REVERT: E 372 ASP cc_start: 0.7935 (p0) cc_final: 0.7237 (m-30) REVERT: F 372 ASP cc_start: 0.7738 (p0) cc_final: 0.7070 (m-30) outliers start: 49 outliers final: 34 residues processed: 238 average time/residue: 0.3412 time to fit residues: 115.1576 Evaluate side-chains 236 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 200 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 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 193 SER Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE 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 91 ASP Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 150 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 182 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16974 Z= 0.268 Angle : 0.544 8.919 23064 Z= 0.278 Chirality : 0.042 0.169 2574 Planarity : 0.005 0.058 2988 Dihedral : 4.047 27.677 2303 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.51 % Allowed : 16.90 % Favored : 79.60 % 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: 1.10 (0.18), residues: 2052 helix: 1.35 (0.14), residues: 1284 sheet: 0.77 (0.70), residues: 60 loop : -0.33 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 345 HIS 0.003 0.001 HIS D 369 PHE 0.018 0.001 PHE D 80 TYR 0.011 0.001 TYR D 292 ARG 0.003 0.000 ARG A 73 *********************** 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 268 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 207 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 135 MET cc_start: 0.8863 (mtm) cc_final: 0.8631 (mtm) REVERT: B 147 ASP cc_start: 0.8214 (m-30) cc_final: 0.7973 (m-30) REVERT: B 233 MET cc_start: 0.6192 (mtt) cc_final: 0.5862 (mtt) REVERT: B 319 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7773 (p) REVERT: B 332 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 27 GLN cc_start: 0.7742 (mp10) cc_final: 0.7248 (mp10) REVERT: E 82 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8754 (mm) REVERT: E 319 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7937 (p) REVERT: E 372 ASP cc_start: 0.8099 (p0) cc_final: 0.7137 (m-30) REVERT: F 372 ASP cc_start: 0.7792 (p0) cc_final: 0.7136 (m-30) outliers start: 61 outliers final: 44 residues processed: 252 average time/residue: 0.3447 time to fit residues: 125.4374 Evaluate side-chains 249 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 200 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 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 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 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 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 121 ILE 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 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 91 ASP 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 362 THR 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 334 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16974 Z= 0.224 Angle : 0.514 8.454 23064 Z= 0.263 Chirality : 0.040 0.179 2574 Planarity : 0.005 0.056 2988 Dihedral : 3.980 26.596 2303 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.33 % Allowed : 17.01 % Favored : 79.66 % 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: 1.48 (0.14), residues: 1278 sheet: 0.75 (0.70), residues: 60 loop : -0.29 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 56 HIS 0.002 0.001 HIS E 185 PHE 0.014 0.001 PHE D 80 TYR 0.011 0.001 TYR D 292 ARG 0.002 0.000 ARG C 127 *********************** 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 269 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 211 time to evaluate : 1.655 Fit side-chains REVERT: A 121 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8183 (mm) REVERT: A 135 MET cc_start: 0.8879 (mtm) cc_final: 0.8595 (mtm) REVERT: B 86 MET cc_start: 0.8902 (mtp) cc_final: 0.8579 (mtt) REVERT: B 147 ASP cc_start: 0.8230 (m-30) cc_final: 0.8001 (m-30) REVERT: B 233 MET cc_start: 0.6178 (mtt) cc_final: 0.5905 (mtt) REVERT: B 319 SER cc_start: 0.8102 (OUTLIER) cc_final: 0.7770 (p) REVERT: B 332 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7998 (mp) REVERT: B 373 TYR cc_start: 0.8226 (t80) cc_final: 0.7972 (t80) REVERT: C 27 GLN cc_start: 0.7730 (mp10) cc_final: 0.7221 (mp10) REVERT: C 59 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7946 (mm) REVERT: C 85 MET cc_start: 0.7768 (mtt) cc_final: 0.7537 (mtm) REVERT: C 86 MET cc_start: 0.8781 (mtp) cc_final: 0.8471 (mtt) REVERT: D 82 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8759 (mm) REVERT: E 82 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8762 (mm) REVERT: E 372 ASP cc_start: 0.8107 (p0) cc_final: 0.7171 (m-30) REVERT: F 319 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.7925 (p) REVERT: F 372 ASP cc_start: 0.7787 (p0) cc_final: 0.7216 (m-30) outliers start: 58 outliers final: 44 residues processed: 254 average time/residue: 0.3142 time to fit residues: 114.7189 Evaluate side-chains 259 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 208 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 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 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 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 267 VAL 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 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 22 optimal weight: 0.0970 chunk 115 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 202 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2070 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= 0.164 Angle : 0.479 8.337 23064 Z= 0.244 Chirality : 0.039 0.181 2574 Planarity : 0.005 0.054 2988 Dihedral : 3.809 22.929 2303 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.05 % Allowed : 17.47 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.18), residues: 2052 helix: 1.70 (0.14), residues: 1278 sheet: 0.85 (0.72), residues: 60 loop : -0.22 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 56 HIS 0.002 0.001 HIS F 94 PHE 0.012 0.001 PHE A 139 TYR 0.011 0.001 TYR D 291 ARG 0.004 0.000 ARG A 73 *********************** 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 267 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 214 time to evaluate : 2.076 Fit side-chains REVERT: A 121 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8063 (mm) REVERT: A 135 MET cc_start: 0.8861 (mtm) cc_final: 0.8483 (mtm) REVERT: B 86 MET cc_start: 0.8827 (mtp) cc_final: 0.8483 (mtt) REVERT: B 147 ASP cc_start: 0.8214 (m-30) cc_final: 0.7979 (m-30) REVERT: B 372 ASP cc_start: 0.7859 (p0) cc_final: 0.6936 (m-30) REVERT: B 373 TYR cc_start: 0.8195 (t80) cc_final: 0.7884 (t80) REVERT: C 27 GLN cc_start: 0.7700 (mp10) cc_final: 0.7183 (mp10) REVERT: C 59 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7898 (mm) REVERT: C 86 MET cc_start: 0.8739 (mtp) cc_final: 0.8416 (mtt) REVERT: D 82 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8778 (mm) REVERT: D 258 MET cc_start: 0.6287 (mpp) cc_final: 0.5853 (ptp) REVERT: E 319 SER cc_start: 0.8182 (OUTLIER) cc_final: 0.7859 (p) REVERT: E 372 ASP cc_start: 0.8139 (p0) cc_final: 0.7194 (m-30) REVERT: F 319 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7945 (p) REVERT: F 372 ASP cc_start: 0.7751 (p0) cc_final: 0.7287 (m-30) outliers start: 53 outliers final: 41 residues processed: 254 average time/residue: 0.3282 time to fit residues: 119.6548 Evaluate side-chains 257 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 211 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 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 331 ASP Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 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 234 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 VAL 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 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 128 LEU 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 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16974 Z= 0.244 Angle : 0.527 9.185 23064 Z= 0.269 Chirality : 0.041 0.194 2574 Planarity : 0.005 0.054 2988 Dihedral : 3.940 25.683 2303 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.22 % Allowed : 17.64 % Favored : 79.14 % 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: 1.28 (0.18), residues: 2052 helix: 1.51 (0.14), residues: 1284 sheet: 0.76 (0.70), residues: 60 loop : -0.27 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 345 HIS 0.003 0.001 HIS D 369 PHE 0.016 0.001 PHE D 80 TYR 0.021 0.001 TYR C 292 ARG 0.003 0.000 ARG C 127 *********************** 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 267 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 211 time to evaluate : 1.665 Fit side-chains REVERT: A 121 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 135 MET cc_start: 0.8880 (mtm) cc_final: 0.8626 (mtm) REVERT: A 198 MET cc_start: 0.8905 (mtm) cc_final: 0.8420 (mtp) REVERT: B 86 MET cc_start: 0.8892 (mtp) cc_final: 0.8555 (mtt) REVERT: B 147 ASP cc_start: 0.8234 (m-30) cc_final: 0.7997 (m-30) REVERT: B 258 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5553 (pmm) REVERT: B 319 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7763 (p) REVERT: B 372 ASP cc_start: 0.7843 (p0) cc_final: 0.6899 (m-30) REVERT: B 373 TYR cc_start: 0.8246 (t80) cc_final: 0.7961 (t80) REVERT: C 27 GLN cc_start: 0.7712 (mp10) cc_final: 0.7189 (mp10) REVERT: C 59 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7911 (mm) REVERT: C 86 MET cc_start: 0.8779 (mtp) cc_final: 0.8480 (mtt) REVERT: D 82 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8772 (mm) REVERT: D 258 MET cc_start: 0.6354 (mpp) cc_final: 0.5966 (ptp) REVERT: E 82 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8761 (mm) REVERT: E 319 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7954 (p) REVERT: E 372 ASP cc_start: 0.8141 (p0) cc_final: 0.7185 (m-30) REVERT: F 319 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7810 (p) REVERT: F 372 ASP cc_start: 0.7734 (p0) cc_final: 0.7308 (m-30) outliers start: 56 outliers final: 43 residues processed: 255 average time/residue: 0.3301 time to fit residues: 120.9327 Evaluate side-chains 261 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 210 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 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 353 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 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 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 128 LEU 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 319 SER Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.1980 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 57 optimal weight: 0.0870 chunk 170 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 352 GLN F 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2144 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= 0.137 Angle : 0.468 8.365 23064 Z= 0.238 Chirality : 0.039 0.191 2574 Planarity : 0.005 0.053 2988 Dihedral : 3.725 21.044 2303 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.05 % Allowed : 17.76 % Favored : 79.20 % 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: 1.65 (0.18), residues: 2052 helix: 1.80 (0.14), residues: 1278 sheet: 0.95 (0.72), residues: 60 loop : -0.13 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 56 HIS 0.002 0.000 HIS D 94 PHE 0.013 0.001 PHE A 139 TYR 0.018 0.001 TYR D 292 ARG 0.004 0.000 ARG B 122 *********************** 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 263 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 210 time to evaluate : 2.192 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8851 (mtm) cc_final: 0.8442 (mtm) REVERT: B 86 MET cc_start: 0.8831 (mtp) cc_final: 0.8477 (mtt) REVERT: B 147 ASP cc_start: 0.8177 (m-30) cc_final: 0.7926 (m-30) REVERT: B 319 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7736 (p) REVERT: B 372 ASP cc_start: 0.7763 (p0) cc_final: 0.7038 (m-30) REVERT: B 373 TYR cc_start: 0.8165 (t80) cc_final: 0.7900 (t80) REVERT: C 27 GLN cc_start: 0.7681 (mp10) cc_final: 0.7155 (mp10) REVERT: C 59 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7914 (mm) REVERT: C 86 MET cc_start: 0.8675 (mtp) cc_final: 0.8352 (mtt) REVERT: D 82 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8797 (mm) REVERT: D 258 MET cc_start: 0.6244 (mpp) cc_final: 0.5889 (ptp) REVERT: E 82 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8708 (mm) REVERT: E 319 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7912 (p) REVERT: E 372 ASP cc_start: 0.8014 (p0) cc_final: 0.7163 (m-30) REVERT: F 319 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7923 (p) REVERT: F 372 ASP cc_start: 0.7650 (p0) cc_final: 0.7365 (m-30) outliers start: 53 outliers final: 41 residues processed: 251 average time/residue: 0.3306 time to fit residues: 119.9242 Evaluate side-chains 250 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 353 LEU 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 164 MET 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 128 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 128 optimal weight: 0.0070 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 overall best weight: 2.5404 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16974 Z= 0.382 Angle : 0.609 9.689 23064 Z= 0.312 Chirality : 0.044 0.211 2574 Planarity : 0.005 0.053 2988 Dihedral : 4.177 29.825 2303 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.93 % Allowed : 17.76 % Favored : 79.31 % 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: 0.94 (0.18), residues: 2052 helix: 1.22 (0.14), residues: 1284 sheet: 0.54 (0.68), residues: 60 loop : -0.36 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 345 HIS 0.004 0.001 HIS B 185 PHE 0.020 0.002 PHE D 80 TYR 0.022 0.002 TYR D 292 ARG 0.005 0.001 ARG B 341 ********************** 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 255 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 204 time to evaluate : 1.891 Fit side-chains REVERT: B 147 ASP cc_start: 0.8250 (m-30) cc_final: 0.7995 (m-30) REVERT: B 319 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7832 (p) REVERT: B 372 ASP cc_start: 0.7874 (p0) cc_final: 0.7039 (m-30) REVERT: B 373 TYR cc_start: 0.8246 (t80) cc_final: 0.8005 (t80) REVERT: C 27 GLN cc_start: 0.7737 (mp10) cc_final: 0.7209 (mp10) REVERT: C 59 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7944 (mm) REVERT: D 82 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8797 (mm) REVERT: D 258 MET cc_start: 0.6505 (mpp) cc_final: 0.6175 (ptp) REVERT: E 82 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8812 (mm) REVERT: E 319 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.7987 (p) REVERT: E 372 ASP cc_start: 0.8152 (p0) cc_final: 0.7207 (m-30) REVERT: F 187 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: F 319 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7790 (p) REVERT: F 372 ASP cc_start: 0.7665 (p0) cc_final: 0.7309 (m-30) outliers start: 51 outliers final: 39 residues processed: 245 average time/residue: 0.3128 time to fit residues: 111.7383 Evaluate side-chains 249 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 203 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 353 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 193 SER 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 128 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 376 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.184726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.136091 restraints weight = 15582.236| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.02 r_work: 0.3033 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16974 Z= 0.211 Angle : 0.520 8.837 23064 Z= 0.265 Chirality : 0.041 0.205 2574 Planarity : 0.005 0.053 2988 Dihedral : 4.021 28.306 2303 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.93 % Allowed : 17.64 % Favored : 79.43 % 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: 1.21 (0.18), residues: 2052 helix: 1.46 (0.14), residues: 1278 sheet: 0.63 (0.69), residues: 60 loop : -0.30 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 56 HIS 0.002 0.001 HIS D 369 PHE 0.013 0.001 PHE D 80 TYR 0.021 0.001 TYR D 292 ARG 0.005 0.000 ARG B 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3303.15 seconds wall clock time: 60 minutes 12.16 seconds (3612.16 seconds total)