Starting phenix.real_space_refine on Tue Nov 18 16:56:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fo1_4287/11_2025/6fo1_4287.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fo1_4287/11_2025/6fo1_4287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6fo1_4287/11_2025/6fo1_4287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fo1_4287/11_2025/6fo1_4287.map" model { file = "/net/cci-nas-00/data/ceres_data/6fo1_4287/11_2025/6fo1_4287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fo1_4287/11_2025/6fo1_4287.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 73 5.16 5 C 9803 2.51 5 N 2729 2.21 5 O 3028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15645 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2469 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 312} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2389 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2416 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 308} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2377 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 300} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2392 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2400 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1040 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 116} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.04, per 1000 atoms: 0.26 Number of scatterers: 15645 At special positions: 0 Unit cell: (129.32, 135.68, 100.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 12 15.00 O 3028 8.00 N 2729 7.00 C 9803 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 586.6 milliseconds 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3748 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 25 sheets defined 57.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.894A pdb=" N SER A 17 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 75 through 87 removed outlier: 3.504A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 107 through 118 removed outlier: 3.574A pdb=" N ASN A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 247 removed outlier: 3.686A pdb=" N ASN A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.773A pdb=" N TYR A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.586A pdb=" N PHE A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 320 " --> pdb=" O HIS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.644A pdb=" N ILE A 377 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.598A pdb=" N ILE A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.769A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 420 removed outlier: 3.515A pdb=" N ASN A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 436 removed outlier: 3.839A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 removed outlier: 4.434A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 removed outlier: 4.034A pdb=" N ILE B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.624A pdb=" N GLU B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.896A pdb=" N ASN B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 290 removed outlier: 3.679A pdb=" N GLU B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.534A pdb=" N PHE B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.854A pdb=" N GLN B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.611A pdb=" N LEU B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 4.102A pdb=" N SER B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 removed outlier: 3.554A pdb=" N ASN B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.685A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'C' and resid 14 through 19 removed outlier: 4.076A pdb=" N SER C 17 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 75 through 88 removed outlier: 3.508A pdb=" N ALA C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.598A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 246 removed outlier: 3.544A pdb=" N ASP C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.597A pdb=" N GLU C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.540A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.586A pdb=" N ILE C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.564A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.933A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 439 through 451 removed outlier: 4.196A pdb=" N LYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 65 removed outlier: 3.650A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.690A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.636A pdb=" N ALA D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 253 removed outlier: 4.011A pdb=" N ILE D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 287 removed outlier: 3.624A pdb=" N ARG D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 4.261A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 removed outlier: 3.867A pdb=" N ASP D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.569A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 414 removed outlier: 3.780A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 452 removed outlier: 4.110A pdb=" N GLU D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR D 446 " --> pdb=" O TYR D 442 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 450 " --> pdb=" O TYR D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 65 removed outlier: 3.576A pdb=" N ARG E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 114 through 126 Processing helix chain 'E' and resid 244 through 248 removed outlier: 3.524A pdb=" N ASP E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 244 through 248' Processing helix chain 'E' and resid 269 through 286 removed outlier: 3.769A pdb=" N ARG E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU E 285 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 314 removed outlier: 3.880A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 removed outlier: 3.637A pdb=" N ASP E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 378 removed outlier: 3.596A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 414 removed outlier: 3.536A pdb=" N ILE E 403 " --> pdb=" O LEU E 399 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN E 404 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 417 No H-bonds generated for 'chain 'E' and resid 415 through 417' Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 453 removed outlier: 3.518A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE E 450 " --> pdb=" O TYR E 446 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU E 451 " --> pdb=" O GLN E 447 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN E 453 " --> pdb=" O ALA E 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 65 removed outlier: 3.701A pdb=" N GLU F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.595A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 126 Processing helix chain 'F' and resid 244 through 253 removed outlier: 3.563A pdb=" N VAL F 249 " --> pdb=" O HIS F 245 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE F 250 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.678A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 317 removed outlier: 3.574A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.649A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 378 removed outlier: 3.664A pdb=" N ILE F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.509A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 432 removed outlier: 3.684A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 451 Processing helix chain 'G' and resid 549 through 560 Processing helix chain 'G' and resid 561 through 565 removed outlier: 6.253A pdb=" N ASP G 564 " --> pdb=" O SER G 561 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET G 565 " --> pdb=" O SER G 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 561 through 565' Processing helix chain 'G' and resid 566 through 573 Processing helix chain 'G' and resid 576 through 583 removed outlier: 3.820A pdb=" N LYS G 580 " --> pdb=" O SER G 576 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE G 582 " --> pdb=" O TYR G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 587 through 603 removed outlier: 3.743A pdb=" N GLN G 593 " --> pdb=" O ASP G 589 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE G 594 " --> pdb=" O VAL G 590 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS G 596 " --> pdb=" O ASN G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 607 through 620 removed outlier: 3.609A pdb=" N ARG G 617 " --> pdb=" O GLU G 613 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 631 removed outlier: 4.465A pdb=" N ALA G 627 " --> pdb=" O ARG G 623 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL G 628 " --> pdb=" O PHE G 624 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET G 629 " --> pdb=" O ASP G 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 649 removed outlier: 3.607A pdb=" N ILE G 638 " --> pdb=" O THR G 634 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP G 647 " --> pdb=" O PHE G 643 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS G 648 " --> pdb=" O ASN G 644 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 662 removed outlier: 3.570A pdb=" N GLU G 657 " --> pdb=" O ASP G 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.579A pdb=" N LEU A 39 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.365A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 386 removed outlier: 7.411A pdb=" N ASN A 385 " --> pdb=" O ILE A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 437 through 438 removed outlier: 4.097A pdb=" N ILE F 356 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR F 359 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA F 76 " --> pdb=" O THR F 359 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR F 328 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.550A pdb=" N LEU B 39 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.290A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 120 through 123 Processing sheet with id=AB1, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.519A pdb=" N ALA C 36 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 69 removed outlier: 4.232A pdb=" N ILE C 360 " --> pdb=" O LEU F 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.226A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU C 299 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ALA C 330 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 301 " --> pdb=" O ALA C 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 236 through 239 removed outlier: 3.507A pdb=" N ILE C 124 " --> pdb=" O GLN C 236 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB7, first strand: chain 'C' and resid 437 through 438 removed outlier: 4.161A pdb=" N ILE E 356 " --> pdb=" O TYR C 438 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU E 296 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA E 327 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE E 298 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 104 Processing sheet with id=AC1, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC2, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC3, first strand: chain 'E' and resid 242 through 243 Processing sheet with id=AC4, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AC5, first strand: chain 'F' and resid 42 through 43 removed outlier: 3.529A pdb=" N SER F 43 " --> pdb=" O MET F 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 242 through 243 Processing sheet with id=AC7, first strand: chain 'F' and resid 332 through 334 762 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.64 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: 5261 1.34 - 1.46: 2682 1.46 - 1.57: 7759 1.57 - 1.69: 18 1.69 - 1.81: 128 Bond restraints: 15848 Sorted by residual: bond pdb=" CA ASP D 352 " pdb=" C ASP D 352 " ideal model delta sigma weight residual 1.524 1.491 0.034 1.66e-02 3.63e+03 4.11e+00 bond pdb=" CA LEU G 559 " pdb=" C LEU G 559 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.56e-02 4.11e+03 3.15e+00 bond pdb=" C GLU G 574 " pdb=" N PRO G 575 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.44e-02 4.82e+03 2.95e+00 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.458 0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CB PHE G 630 " pdb=" CG PHE G 630 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.25e+00 ... (remaining 15843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 20450 1.69 - 3.38: 799 3.38 - 5.08: 114 5.08 - 6.77: 40 6.77 - 8.46: 6 Bond angle restraints: 21409 Sorted by residual: angle pdb=" C THR C 341 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.75e+01 angle pdb=" N LEU G 559 " pdb=" CA LEU G 559 " pdb=" C LEU G 559 " ideal model delta sigma weight residual 113.02 117.33 -4.31 1.20e+00 6.94e-01 1.29e+01 angle pdb=" C GLU F 378 " pdb=" N ASP F 379 " pdb=" CA ASP F 379 " ideal model delta sigma weight residual 122.46 127.02 -4.56 1.41e+00 5.03e-01 1.05e+01 angle pdb=" N GLN F 41 " pdb=" CA GLN F 41 " pdb=" CB GLN F 41 " ideal model delta sigma weight residual 114.17 110.54 3.63 1.14e+00 7.69e-01 1.01e+01 angle pdb=" C GLY E 418 " pdb=" N THR E 419 " pdb=" CA THR E 419 " ideal model delta sigma weight residual 121.54 127.30 -5.76 1.91e+00 2.74e-01 9.11e+00 ... (remaining 21404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.27: 9551 26.27 - 52.53: 164 52.53 - 78.80: 27 78.80 - 105.06: 1 105.06 - 131.33: 6 Dihedral angle restraints: 9749 sinusoidal: 3963 harmonic: 5786 Sorted by residual: dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 71.33 -131.33 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 65.60 -125.60 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 63.10 -123.11 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 9746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1653 0.039 - 0.077: 659 0.077 - 0.116: 188 0.116 - 0.154: 22 0.154 - 0.193: 6 Chirality restraints: 2528 Sorted by residual: chirality pdb=" CB THR A 402 " pdb=" CA THR A 402 " pdb=" OG1 THR A 402 " pdb=" CG2 THR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA PRO G 575 " pdb=" N PRO G 575 " pdb=" C PRO G 575 " pdb=" CB PRO G 575 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CB THR C 402 " pdb=" CA THR C 402 " pdb=" OG1 THR C 402 " pdb=" CG2 THR C 402 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 2525 not shown) Planarity restraints: 2725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 292 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO E 293 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 293 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 293 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 78 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO D 79 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 79 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 79 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 574 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO G 575 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO G 575 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 575 " 0.021 5.00e-02 4.00e+02 ... (remaining 2722 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 214 2.61 - 3.18: 15831 3.18 - 3.76: 22320 3.76 - 4.33: 34199 4.33 - 4.90: 53763 Nonbonded interactions: 126327 Sorted by model distance: nonbonded pdb=" OD1 ASP B 439 " pdb=" OG SER B 442 " model vdw 2.039 3.040 nonbonded pdb=" OD1 ASP C 439 " pdb=" OG SER C 442 " model vdw 2.050 3.040 nonbonded pdb=" O GLU C 396 " pdb=" OG1 THR C 399 " model vdw 2.081 3.040 nonbonded pdb=" OG SER C 17 " pdb=" O3' ADP C 501 " model vdw 2.087 3.040 nonbonded pdb=" OD1 ASP A 439 " pdb=" OG SER A 442 " model vdw 2.089 3.040 ... (remaining 126322 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' and (resid 5 through 123 or resid 238 through 248 or (resid 271 throu \ gh 272 and (name N or name CA or name C or name O or name CB )) or resid 273 or \ (resid 274 through 276 and (name N or name CA or name C or name O or name CB )) \ or resid 277 through 452 or resid 501)) selection = (chain 'B' and (resid 5 through 248 or (resid 271 through 272 and (name N or nam \ e CA or name C or name O or name CB )) or resid 273 or (resid 274 through 276 an \ d (name N or name CA or name C or name O or name CB )) or resid 277 through 501) \ ) selection = (chain 'C' and (resid 5 through 123 or resid 238 through 248 or resid 271 throug \ h 501)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 23 through 253 or resid 267 through 269 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 through 451 or \ (resid 452 through 453 and (name N or name CA or name C or name O or name CB )) \ or resid 501)) selection = (chain 'F' and (resid 23 through 252 or (resid 253 through 267 and (name N or na \ me CA or name C or name O or name CB )) or resid 268 through 451 or (resid 452 t \ hrough 453 and (name N or name CA or name C or name O or name CB )) or resid 501 \ )) } 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.270 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.012 0.893 15855 Z= 1.052 Angle : 0.815 8.461 21409 Z= 0.455 Chirality : 0.044 0.193 2528 Planarity : 0.004 0.039 2725 Dihedral : 10.812 131.330 6001 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.16), residues: 1974 helix: -2.86 (0.11), residues: 1067 sheet: -1.50 (0.35), residues: 191 loop : -1.80 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 273 TYR 0.019 0.002 TYR G 569 PHE 0.025 0.003 PHE G 582 TRP 0.014 0.002 TRP E 283 HIS 0.007 0.002 HIS F 245 Details of bonding type rmsd covalent geometry : bond 0.00714 (15848) covalent geometry : angle 0.81520 (21409) hydrogen bonds : bond 0.29724 ( 762) hydrogen bonds : angle 9.77675 ( 2217) Misc. bond : bond 0.47633 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.7794 (m-30) cc_final: 0.7467 (m-30) REVERT: B 94 CYS cc_start: 0.8568 (t) cc_final: 0.8300 (t) REVERT: B 276 ARG cc_start: 0.7970 (mmt90) cc_final: 0.6982 (ttt180) REVERT: C 343 ASP cc_start: 0.7162 (t70) cc_final: 0.6934 (t70) REVERT: C 438 TYR cc_start: 0.8554 (m-80) cc_final: 0.8347 (m-10) REVERT: D 443 MET cc_start: 0.8106 (ttm) cc_final: 0.7882 (ttm) REVERT: E 126 SER cc_start: 0.9119 (m) cc_final: 0.8640 (t) REVERT: E 279 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7974 (tttp) REVERT: E 411 LEU cc_start: 0.9104 (tp) cc_final: 0.8876 (tp) REVERT: F 78 GLN cc_start: 0.7774 (mm110) cc_final: 0.7353 (mm-40) REVERT: F 126 SER cc_start: 0.9359 (m) cc_final: 0.8828 (t) REVERT: F 314 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7665 (ttm-80) REVERT: F 382 MET cc_start: 0.6922 (ttp) cc_final: 0.6714 (ttt) REVERT: G 622 LYS cc_start: 0.7881 (mttm) cc_final: 0.7675 (ttpp) REVERT: G 626 MET cc_start: 0.8754 (mmp) cc_final: 0.8451 (mmt) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.1597 time to fit residues: 91.2369 Evaluate side-chains 226 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 247 ASN A 393 HIS B 18 HIS B 393 HIS B 408 GLN B 450 GLN C 280 ASN C 284 ASN C 316 HIS C 393 HIS C 408 GLN D 25 HIS D 404 GLN E 78 GLN E 251 ASN E 277 ASN E 404 GLN F 25 HIS F 277 ASN ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.083214 restraints weight = 33487.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.085879 restraints weight = 18247.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.087639 restraints weight = 12427.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088784 restraints weight = 9724.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.089494 restraints weight = 8315.751| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15855 Z= 0.167 Angle : 0.721 9.669 21409 Z= 0.357 Chirality : 0.045 0.212 2528 Planarity : 0.005 0.055 2725 Dihedral : 9.354 132.864 2224 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.74 % Allowed : 8.03 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.18), residues: 1974 helix: -0.85 (0.15), residues: 1118 sheet: -0.81 (0.35), residues: 201 loop : -1.39 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 40 TYR 0.024 0.002 TYR E 430 PHE 0.021 0.002 PHE D 450 TRP 0.020 0.002 TRP E 283 HIS 0.007 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00373 (15848) covalent geometry : angle 0.72145 (21409) hydrogen bonds : bond 0.04732 ( 762) hydrogen bonds : angle 5.29312 ( 2217) Misc. bond : bond 0.00046 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 296 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 ARG cc_start: 0.7944 (mmt90) cc_final: 0.6893 (ttt-90) REVERT: C 343 ASP cc_start: 0.6936 (t70) cc_final: 0.6566 (t70) REVERT: D 427 LYS cc_start: 0.8927 (tttt) cc_final: 0.8673 (ttpp) REVERT: E 46 MET cc_start: 0.8544 (mmm) cc_final: 0.8278 (mmm) REVERT: E 399 LEU cc_start: 0.9212 (tp) cc_final: 0.8970 (tt) REVERT: F 126 SER cc_start: 0.9207 (m) cc_final: 0.8794 (t) REVERT: G 630 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: G 636 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7832 (ptpp) outliers start: 29 outliers final: 12 residues processed: 313 average time/residue: 0.1255 time to fit residues: 58.3680 Evaluate side-chains 237 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 630 PHE Chi-restraints excluded: chain G residue 636 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 70 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 GLN B 429 HIS B 450 GLN C 241 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS F 277 ASN ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082805 restraints weight = 33626.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085495 restraints weight = 18298.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.087282 restraints weight = 12476.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.088437 restraints weight = 9758.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.089088 restraints weight = 8349.528| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15855 Z= 0.148 Angle : 0.639 9.631 21409 Z= 0.311 Chirality : 0.043 0.182 2528 Planarity : 0.004 0.038 2725 Dihedral : 9.097 137.512 2224 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 2.16 % Allowed : 11.02 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 1974 helix: -0.11 (0.15), residues: 1117 sheet: -0.44 (0.37), residues: 202 loop : -1.05 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.020 0.002 TYR F 430 PHE 0.015 0.001 PHE D 450 TRP 0.015 0.002 TRP E 283 HIS 0.005 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00333 (15848) covalent geometry : angle 0.63888 (21409) hydrogen bonds : bond 0.03936 ( 762) hydrogen bonds : angle 4.70208 ( 2217) Misc. bond : bond 0.00056 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 ARG cc_start: 0.7934 (mmt90) cc_final: 0.6921 (ttt-90) REVERT: C 429 HIS cc_start: 0.7940 (m90) cc_final: 0.7662 (m170) REVERT: D 427 LYS cc_start: 0.8992 (tttt) cc_final: 0.8685 (ttpp) REVERT: E 46 MET cc_start: 0.8563 (mmm) cc_final: 0.8006 (mmm) REVERT: F 126 SER cc_start: 0.9247 (m) cc_final: 0.8804 (t) REVERT: F 382 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.7023 (mtp) REVERT: G 626 MET cc_start: 0.8819 (mmm) cc_final: 0.8574 (mmm) outliers start: 36 outliers final: 21 residues processed: 275 average time/residue: 0.1314 time to fit residues: 53.2851 Evaluate side-chains 242 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 634 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 130 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 144 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 393 HIS B 316 HIS B 450 GLN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS E 78 GLN F 25 HIS ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 568 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.083977 restraints weight = 33463.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086714 restraints weight = 18099.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.088513 restraints weight = 12288.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.089677 restraints weight = 9595.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.090338 restraints weight = 8197.507| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15855 Z= 0.122 Angle : 0.610 11.530 21409 Z= 0.293 Chirality : 0.043 0.194 2528 Planarity : 0.003 0.031 2725 Dihedral : 8.881 142.920 2224 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.50 % Rotamer: Outliers : 2.58 % Allowed : 12.34 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 1974 helix: 0.34 (0.16), residues: 1119 sheet: -0.05 (0.38), residues: 202 loop : -0.78 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 317 TYR 0.017 0.001 TYR F 430 PHE 0.019 0.001 PHE F 450 TRP 0.012 0.001 TRP E 283 HIS 0.011 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00269 (15848) covalent geometry : angle 0.60955 (21409) hydrogen bonds : bond 0.03324 ( 762) hydrogen bonds : angle 4.30287 ( 2217) Misc. bond : bond 0.00049 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 ARG cc_start: 0.7881 (mmt90) cc_final: 0.6936 (ttt-90) REVERT: B 345 THR cc_start: 0.9192 (m) cc_final: 0.8880 (p) REVERT: D 427 LYS cc_start: 0.9047 (tttt) cc_final: 0.8744 (ttpp) REVERT: E 46 MET cc_start: 0.8545 (mmm) cc_final: 0.8017 (mmm) REVERT: F 126 SER cc_start: 0.9222 (m) cc_final: 0.8666 (t) REVERT: G 586 LEU cc_start: 0.8481 (tm) cc_final: 0.8214 (tp) REVERT: G 626 MET cc_start: 0.8844 (mmm) cc_final: 0.8308 (mmt) outliers start: 43 outliers final: 24 residues processed: 291 average time/residue: 0.1267 time to fit residues: 55.6532 Evaluate side-chains 255 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 590 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 179 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 GLN C 429 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN F 25 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.103921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.081670 restraints weight = 33794.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.084350 restraints weight = 18586.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086094 restraints weight = 12713.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.087236 restraints weight = 9996.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087863 restraints weight = 8571.361| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15855 Z= 0.184 Angle : 0.638 11.818 21409 Z= 0.310 Chirality : 0.044 0.195 2528 Planarity : 0.003 0.029 2725 Dihedral : 8.945 146.855 2224 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 3.24 % Allowed : 13.60 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.19), residues: 1974 helix: 0.40 (0.16), residues: 1134 sheet: 0.05 (0.38), residues: 200 loop : -0.82 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 317 TYR 0.016 0.002 TYR G 567 PHE 0.013 0.001 PHE G 591 TRP 0.014 0.002 TRP E 283 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00425 (15848) covalent geometry : angle 0.63796 (21409) hydrogen bonds : bond 0.03507 ( 762) hydrogen bonds : angle 4.35848 ( 2217) Misc. bond : bond 0.00042 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 233 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ILE cc_start: 0.8433 (mm) cc_final: 0.8213 (mm) REVERT: B 123 ARG cc_start: 0.4198 (tpm170) cc_final: 0.3945 (tpm170) REVERT: B 276 ARG cc_start: 0.7900 (mmt90) cc_final: 0.6977 (ttt-90) REVERT: B 345 THR cc_start: 0.9213 (m) cc_final: 0.8873 (p) REVERT: D 411 LEU cc_start: 0.9079 (tp) cc_final: 0.8800 (tt) REVERT: E 46 MET cc_start: 0.8588 (mmm) cc_final: 0.8048 (mmm) REVERT: F 126 SER cc_start: 0.9254 (m) cc_final: 0.8736 (t) REVERT: F 283 TRP cc_start: 0.7048 (m-10) cc_final: 0.6773 (m-10) REVERT: G 586 LEU cc_start: 0.8504 (tm) cc_final: 0.8208 (tp) REVERT: G 626 MET cc_start: 0.8850 (mmm) cc_final: 0.7747 (mmm) outliers start: 54 outliers final: 34 residues processed: 267 average time/residue: 0.1246 time to fit residues: 50.4856 Evaluate side-chains 247 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 442 TYR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 599 HIS Chi-restraints excluded: chain G residue 634 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 119 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 108 optimal weight: 8.9990 chunk 150 optimal weight: 0.0670 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 450 GLN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084110 restraints weight = 33432.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.086818 restraints weight = 18193.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.088570 restraints weight = 12373.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.089720 restraints weight = 9719.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.090346 restraints weight = 8325.542| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15855 Z= 0.113 Angle : 0.596 13.232 21409 Z= 0.286 Chirality : 0.042 0.196 2528 Planarity : 0.003 0.032 2725 Dihedral : 8.813 156.865 2224 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 2.52 % Allowed : 14.98 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1974 helix: 0.71 (0.16), residues: 1110 sheet: 0.20 (0.38), residues: 201 loop : -0.60 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 317 TYR 0.014 0.001 TYR F 430 PHE 0.013 0.001 PHE G 591 TRP 0.010 0.001 TRP E 283 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00249 (15848) covalent geometry : angle 0.59585 (21409) hydrogen bonds : bond 0.03060 ( 762) hydrogen bonds : angle 4.08233 ( 2217) Misc. bond : bond 0.00050 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 ARG cc_start: 0.3864 (tpm170) cc_final: 0.3619 (tpm170) REVERT: B 276 ARG cc_start: 0.7917 (mmt90) cc_final: 0.6967 (ttt-90) REVERT: B 345 THR cc_start: 0.9140 (m) cc_final: 0.8852 (p) REVERT: C 385 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7750 (p0) REVERT: D 411 LEU cc_start: 0.9060 (tp) cc_final: 0.8801 (tt) REVERT: E 46 MET cc_start: 0.8521 (mmm) cc_final: 0.8018 (mmm) REVERT: E 274 GLU cc_start: 0.7782 (tp30) cc_final: 0.7561 (tm-30) REVERT: F 84 THR cc_start: 0.9103 (m) cc_final: 0.8664 (p) REVERT: F 126 SER cc_start: 0.9164 (m) cc_final: 0.8550 (t) REVERT: G 567 TYR cc_start: 0.6968 (p90) cc_final: 0.6726 (p90) REVERT: G 626 MET cc_start: 0.8669 (mmm) cc_final: 0.7713 (mmm) outliers start: 42 outliers final: 26 residues processed: 287 average time/residue: 0.1193 time to fit residues: 52.3558 Evaluate side-chains 252 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 599 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 7 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.082550 restraints weight = 33339.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.085199 restraints weight = 18297.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086924 restraints weight = 12528.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088035 restraints weight = 9863.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088796 restraints weight = 8473.511| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15855 Z= 0.157 Angle : 0.632 8.704 21409 Z= 0.303 Chirality : 0.043 0.196 2528 Planarity : 0.003 0.031 2725 Dihedral : 8.829 160.016 2224 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 2.64 % Allowed : 15.64 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1974 helix: 0.68 (0.16), residues: 1124 sheet: 0.22 (0.38), residues: 200 loop : -0.59 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 317 TYR 0.012 0.002 TYR F 430 PHE 0.014 0.001 PHE G 591 TRP 0.013 0.003 TRP F 283 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00365 (15848) covalent geometry : angle 0.63189 (21409) hydrogen bonds : bond 0.03281 ( 762) hydrogen bonds : angle 4.18604 ( 2217) Misc. bond : bond 0.00050 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 359 MET cc_start: 0.8456 (ptp) cc_final: 0.8250 (ptp) REVERT: B 123 ARG cc_start: 0.3960 (tpm170) cc_final: 0.3581 (tpm170) REVERT: B 276 ARG cc_start: 0.7849 (mmt90) cc_final: 0.6886 (tmt170) REVERT: B 345 THR cc_start: 0.9179 (m) cc_final: 0.8868 (p) REVERT: C 317 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7572 (ttp80) REVERT: D 411 LEU cc_start: 0.9075 (tp) cc_final: 0.8782 (tt) REVERT: E 25 HIS cc_start: 0.8150 (m-70) cc_final: 0.7919 (m90) REVERT: E 46 MET cc_start: 0.8574 (mmm) cc_final: 0.8055 (mmm) REVERT: E 124 ARG cc_start: 0.7405 (mtt180) cc_final: 0.7171 (mtt180) REVERT: E 274 GLU cc_start: 0.7810 (tp30) cc_final: 0.7564 (tm-30) REVERT: F 126 SER cc_start: 0.9194 (m) cc_final: 0.8622 (t) REVERT: G 586 LEU cc_start: 0.8391 (tm) cc_final: 0.8078 (tp) outliers start: 44 outliers final: 34 residues processed: 254 average time/residue: 0.1155 time to fit residues: 45.4131 Evaluate side-chains 252 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 442 TYR Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 599 HIS Chi-restraints excluded: chain G residue 611 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 145 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 187 optimal weight: 0.0060 chunk 152 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN C 18 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.083582 restraints weight = 33261.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.086276 restraints weight = 18105.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087996 restraints weight = 12334.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.089119 restraints weight = 9681.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.089752 restraints weight = 8329.562| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15855 Z= 0.124 Angle : 0.620 9.515 21409 Z= 0.295 Chirality : 0.042 0.212 2528 Planarity : 0.003 0.032 2725 Dihedral : 8.771 166.089 2224 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 2.40 % Allowed : 15.76 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1974 helix: 0.78 (0.16), residues: 1119 sheet: 0.31 (0.38), residues: 199 loop : -0.50 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.017 0.001 TYR G 567 PHE 0.012 0.001 PHE G 591 TRP 0.010 0.002 TRP E 283 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00284 (15848) covalent geometry : angle 0.61984 (21409) hydrogen bonds : bond 0.03076 ( 762) hydrogen bonds : angle 4.06101 ( 2217) Misc. bond : bond 0.00046 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 ARG cc_start: 0.4058 (tpm170) cc_final: 0.3825 (tpm170) REVERT: B 276 ARG cc_start: 0.7824 (mmt90) cc_final: 0.6901 (ttt180) REVERT: B 345 THR cc_start: 0.9157 (m) cc_final: 0.8874 (p) REVERT: C 317 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7602 (ttp80) REVERT: C 385 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8151 (p0) REVERT: D 411 LEU cc_start: 0.9071 (tp) cc_final: 0.8735 (tt) REVERT: E 25 HIS cc_start: 0.8198 (m-70) cc_final: 0.7909 (m90) REVERT: E 46 MET cc_start: 0.8556 (mmm) cc_final: 0.8072 (mmm) REVERT: F 84 THR cc_start: 0.9086 (m) cc_final: 0.8652 (p) REVERT: F 126 SER cc_start: 0.9174 (m) cc_final: 0.8526 (t) REVERT: G 586 LEU cc_start: 0.8346 (tm) cc_final: 0.8074 (tp) REVERT: G 638 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7512 (pp) outliers start: 40 outliers final: 32 residues processed: 269 average time/residue: 0.1169 time to fit residues: 48.7535 Evaluate side-chains 255 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 599 HIS Chi-restraints excluded: chain G residue 611 ILE Chi-restraints excluded: chain G residue 638 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 119 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 HIS ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.083069 restraints weight = 33586.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.085748 restraints weight = 18392.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.087492 restraints weight = 12605.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088586 restraints weight = 9925.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.089306 restraints weight = 8541.210| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15855 Z= 0.145 Angle : 0.645 11.302 21409 Z= 0.306 Chirality : 0.043 0.226 2528 Planarity : 0.003 0.035 2725 Dihedral : 8.769 167.514 2224 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 2.28 % Allowed : 16.12 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1974 helix: 0.80 (0.16), residues: 1119 sheet: 0.24 (0.38), residues: 201 loop : -0.48 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.013 0.001 TYR F 430 PHE 0.012 0.001 PHE G 591 TRP 0.046 0.005 TRP E 283 HIS 0.005 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00337 (15848) covalent geometry : angle 0.64531 (21409) hydrogen bonds : bond 0.03161 ( 762) hydrogen bonds : angle 4.09590 ( 2217) Misc. bond : bond 0.00043 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 ARG cc_start: 0.4236 (tpm170) cc_final: 0.3894 (tpm170) REVERT: B 276 ARG cc_start: 0.7816 (mmt90) cc_final: 0.6906 (ttt180) REVERT: B 345 THR cc_start: 0.9163 (m) cc_final: 0.8873 (p) REVERT: C 317 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7609 (ttp80) REVERT: D 411 LEU cc_start: 0.9060 (tp) cc_final: 0.8745 (tt) REVERT: E 46 MET cc_start: 0.8557 (mmm) cc_final: 0.8048 (mmm) REVERT: E 320 MET cc_start: 0.8208 (mtt) cc_final: 0.7946 (mtm) REVERT: F 84 THR cc_start: 0.9122 (m) cc_final: 0.8688 (p) REVERT: F 126 SER cc_start: 0.9181 (m) cc_final: 0.8576 (t) REVERT: F 443 MET cc_start: 0.8395 (mmm) cc_final: 0.8025 (mmm) REVERT: G 586 LEU cc_start: 0.8349 (tm) cc_final: 0.8090 (tp) REVERT: G 638 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7494 (pp) outliers start: 38 outliers final: 35 residues processed: 249 average time/residue: 0.1172 time to fit residues: 44.9336 Evaluate side-chains 252 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 599 HIS Chi-restraints excluded: chain G residue 611 ILE Chi-restraints excluded: chain G residue 638 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 116 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 139 optimal weight: 0.3980 chunk 170 optimal weight: 4.9990 chunk 158 optimal weight: 0.0070 chunk 137 optimal weight: 0.9990 chunk 18 optimal weight: 0.0060 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 HIS B 450 GLN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.084925 restraints weight = 33142.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.087624 restraints weight = 18100.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.089384 restraints weight = 12370.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090478 restraints weight = 9728.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.091166 restraints weight = 8389.066| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15855 Z= 0.113 Angle : 0.649 12.250 21409 Z= 0.307 Chirality : 0.043 0.238 2528 Planarity : 0.003 0.038 2725 Dihedral : 8.680 170.906 2224 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.04 % Allowed : 16.48 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 1974 helix: 0.89 (0.16), residues: 1118 sheet: 0.39 (0.39), residues: 199 loop : -0.39 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.013 0.001 TYR F 430 PHE 0.013 0.001 PHE G 591 TRP 0.076 0.007 TRP E 283 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00252 (15848) covalent geometry : angle 0.64868 (21409) hydrogen bonds : bond 0.02971 ( 762) hydrogen bonds : angle 3.99824 ( 2217) Misc. bond : bond 0.00044 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6513 (m-30) REVERT: B 123 ARG cc_start: 0.4115 (tpm170) cc_final: 0.3828 (tpm170) REVERT: B 276 ARG cc_start: 0.7781 (mmt90) cc_final: 0.6903 (ttt-90) REVERT: B 345 THR cc_start: 0.9117 (m) cc_final: 0.8866 (p) REVERT: C 317 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7562 (ttp80) REVERT: D 411 LEU cc_start: 0.9029 (tp) cc_final: 0.8815 (tt) REVERT: D 443 MET cc_start: 0.7738 (ttp) cc_final: 0.7485 (ttt) REVERT: E 46 MET cc_start: 0.8508 (mmm) cc_final: 0.8018 (mmm) REVERT: E 283 TRP cc_start: 0.7446 (m-90) cc_final: 0.7139 (m-90) REVERT: E 320 MET cc_start: 0.8055 (mtt) cc_final: 0.7775 (mtm) REVERT: F 84 THR cc_start: 0.9081 (m) cc_final: 0.8652 (p) REVERT: F 126 SER cc_start: 0.8981 (m) cc_final: 0.8449 (t) REVERT: F 443 MET cc_start: 0.8248 (mmm) cc_final: 0.7951 (mmm) REVERT: G 586 LEU cc_start: 0.8351 (tm) cc_final: 0.8093 (tp) REVERT: G 626 MET cc_start: 0.8821 (mmm) cc_final: 0.8558 (tpp) REVERT: G 638 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7513 (pp) outliers start: 34 outliers final: 27 residues processed: 260 average time/residue: 0.1248 time to fit residues: 48.7441 Evaluate side-chains 256 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 599 HIS Chi-restraints excluded: chain G residue 611 ILE Chi-restraints excluded: chain G residue 638 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 166 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 138 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 GLN C 85 GLN C 332 ASN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.084013 restraints weight = 33326.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.086657 restraints weight = 18095.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.088394 restraints weight = 12405.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.089493 restraints weight = 9768.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.090147 restraints weight = 8416.438| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15855 Z= 0.135 Angle : 0.664 11.659 21409 Z= 0.316 Chirality : 0.043 0.224 2528 Planarity : 0.004 0.046 2725 Dihedral : 8.680 170.018 2224 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 1.98 % Allowed : 17.26 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1974 helix: 0.90 (0.16), residues: 1118 sheet: 0.42 (0.38), residues: 199 loop : -0.38 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 400 TYR 0.016 0.001 TYR E 401 PHE 0.013 0.001 PHE G 591 TRP 0.082 0.007 TRP E 283 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00313 (15848) covalent geometry : angle 0.66417 (21409) hydrogen bonds : bond 0.03009 ( 762) hydrogen bonds : angle 3.99994 ( 2217) Misc. bond : bond 0.00048 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2626.30 seconds wall clock time: 46 minutes 10.78 seconds (2770.78 seconds total)