Starting phenix.real_space_refine on Thu Jul 2 17:26:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eyi_50054/07_2026/9eyi_50054.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eyi_50054/07_2026/9eyi_50054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eyi_50054/07_2026/9eyi_50054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eyi_50054/07_2026/9eyi_50054.map" model { file = "/net/cci-nas-00/data/ceres_data/9eyi_50054/07_2026/9eyi_50054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eyi_50054/07_2026/9eyi_50054.cif" } resolution = 2.75 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= 1.000 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 8 5.49 5 S 27 5.16 5 C 6129 2.51 5 N 1614 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9453 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3594 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 469} Chain breaks: 4 Unresolved non-hydrogen bonds: 399 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 8, 'GLU:plan': 25, 'ASP:plan': 6, 'GLN:plan1': 7, 'TYR:plan': 5, 'ARG:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 250 Chain: "B" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3416 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 15, 'TRANS': 456} Chain breaks: 6 Unresolved non-hydrogen bonds: 451 Unresolved non-hydrogen angles: 567 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 4, 'ASN:plan1': 11, 'GLU:plan': 24, 'ASP:plan': 8, 'TYR:plan': 5, 'GLN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 275 Chain: "C" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2265 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 1, 'GLU:plan': 16, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {'A3P': 1} Classifications: {'RNA': 3, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna2p_pur': 3} Link IDs: {'rna2p': 2, None: 1} Not linked: pdbres=" A D 3 " pdbres="A3P D 4 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {'A3P': 1} Classifications: {'RNA': 3, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna2p_pur': 3} Link IDs: {'rna2p': 2, None: 1} Not linked: pdbres=" A E 3 " pdbres="A3P E 4 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 1.74, per 1000 atoms: 0.18 Number of scatterers: 9453 At special positions: 0 Unit cell: (72.6, 126.5, 117.7, 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 27 16.00 P 8 15.00 O 1675 8.00 N 1614 7.00 C 6129 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 283.4 milliseconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 13 sheets defined 45.7% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.553A pdb=" N GLN A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 49 through 64 removed outlier: 3.594A pdb=" N LYS A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.874A pdb=" N LEU A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.708A pdb=" N SER A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.905A pdb=" N ALA A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.596A pdb=" N VAL A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 208 through 218 Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.871A pdb=" N LYS A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.531A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.918A pdb=" N LEU A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 433 through 451 removed outlier: 3.578A pdb=" N LEU A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 475 Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.777A pdb=" N ALA B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.939A pdb=" N LYS B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 280 through 291 removed outlier: 3.649A pdb=" N TRP B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.532A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.679A pdb=" N GLN B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 433 through 451 removed outlier: 3.541A pdb=" N LEU B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 475 Processing helix chain 'B' and resid 501 through 505 removed outlier: 4.138A pdb=" N LEU B 504 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 231 through 250 removed outlier: 3.761A pdb=" N LYS C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 291 through 303 removed outlier: 4.209A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.512A pdb=" N GLN C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 433 through 451 removed outlier: 3.522A pdb=" N ARG C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 450 " --> pdb=" O THR C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 4.137A pdb=" N ASN A 141 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 121 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 6.724A pdb=" N ALA A 175 " --> pdb=" O VAL A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 274 removed outlier: 7.935A pdb=" N ILE A 271 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE A 226 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY A 273 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR A 228 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N SER A 334 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP A 310 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU A 336 " --> pdb=" O TRP A 310 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR A 312 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N MET A 338 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL A 333 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE A 350 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 335 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 378 removed outlier: 5.125A pdb=" N GLN A 460 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 485 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 498 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS A 484 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N CYS A 496 " --> pdb=" O HIS A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.746A pdb=" N LEU B 121 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N PHE B 146 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 176 removed outlier: 6.789A pdb=" N ALA B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.696A pdb=" N GLU B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 270 through 271 removed outlier: 8.036A pdb=" N ILE B 271 " --> pdb=" O PRO B 224 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 226 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N SER B 334 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP B 310 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU B 336 " --> pdb=" O TRP B 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR B 312 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 333 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE B 350 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 335 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS B 346 " --> pdb=" O GLN B 337 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 373 through 378 removed outlier: 7.828A pdb=" N LEU B 416 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY B 388 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 418 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 390 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ALA B 420 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N TYR B 392 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 456 " --> pdb=" O ASP B 481 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N TYR B 483 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 458 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR B 485 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLN B 460 " --> pdb=" O TYR B 485 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS B 484 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N CYS B 496 " --> pdb=" O HIS B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 270 through 273 removed outlier: 7.803A pdb=" N ILE C 271 " --> pdb=" O PRO C 224 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE C 226 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY C 273 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 228 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER C 334 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP C 310 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C 336 " --> pdb=" O TRP C 310 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR C 312 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N MET C 338 " --> pdb=" O TYR C 312 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 335 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 373 through 379 removed outlier: 4.321A pdb=" N ASN C 414 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 387 " --> pdb=" O HIS C 457 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE C 459 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE C 389 " --> pdb=" O PHE C 459 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N THR C 461 " --> pdb=" O PHE C 389 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 391 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE C 456 " --> pdb=" O ASP C 481 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N TYR C 483 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 458 " --> pdb=" O TYR C 483 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR C 485 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N GLN C 460 " --> pdb=" O TYR C 485 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 498 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS C 484 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N CYS C 496 " --> pdb=" O HIS C 484 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1269 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: 1.21 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1507 1.31 - 1.43: 2677 1.43 - 1.56: 5437 1.56 - 1.69: 14 1.69 - 1.82: 43 Bond restraints: 9678 Sorted by residual: bond pdb=" CA LEU A 319 " pdb=" C LEU A 319 " ideal model delta sigma weight residual 1.523 1.406 0.117 1.41e-02 5.03e+03 6.85e+01 bond pdb=" C GLN C 409 " pdb=" N LEU C 410 " ideal model delta sigma weight residual 1.332 1.442 -0.110 1.53e-02 4.27e+03 5.17e+01 bond pdb=" O2P A3P D 4 " pdb=" P1 A3P D 4 " ideal model delta sigma weight residual 1.610 1.470 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" O3P A3P E 4 " pdb=" P1 A3P E 4 " ideal model delta sigma weight residual 1.610 1.476 0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" O2P A3P E 4 " pdb=" P1 A3P E 4 " ideal model delta sigma weight residual 1.610 1.478 0.132 2.00e-02 2.50e+03 4.34e+01 ... (remaining 9673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 13157 3.08 - 6.16: 46 6.16 - 9.24: 10 9.24 - 12.31: 5 12.31 - 15.39: 4 Bond angle restraints: 13222 Sorted by residual: angle pdb=" C3' A3P D 4 " pdb=" O3' A3P D 4 " pdb=" P1 A3P D 4 " ideal model delta sigma weight residual 106.84 122.23 -15.39 3.00e+00 1.11e-01 2.63e+01 angle pdb=" N LEU A 321 " pdb=" CA LEU A 321 " pdb=" C LEU A 321 " ideal model delta sigma weight residual 111.28 106.10 5.18 1.09e+00 8.42e-01 2.26e+01 angle pdb=" C5' A3P D 4 " pdb=" O5' A3P D 4 " pdb=" P2 A3P D 4 " ideal model delta sigma weight residual 106.77 120.86 -14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" C5' A3P E 4 " pdb=" O5' A3P E 4 " pdb=" P2 A3P E 4 " ideal model delta sigma weight residual 106.77 120.79 -14.02 3.00e+00 1.11e-01 2.19e+01 angle pdb=" N LEU A 319 " pdb=" CA LEU A 319 " pdb=" C LEU A 319 " ideal model delta sigma weight residual 113.20 107.55 5.65 1.21e+00 6.83e-01 2.18e+01 ... (remaining 13217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5084 17.96 - 35.92: 429 35.92 - 53.88: 131 53.88 - 71.83: 27 71.83 - 89.79: 9 Dihedral angle restraints: 5680 sinusoidal: 2019 harmonic: 3661 Sorted by residual: dihedral pdb=" CA GLN A 460 " pdb=" C GLN A 460 " pdb=" N THR A 461 " pdb=" CA THR A 461 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" C LEU A 319 " pdb=" N LEU A 319 " pdb=" CA LEU A 319 " pdb=" CB LEU A 319 " ideal model delta harmonic sigma weight residual -122.60 -114.29 -8.31 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" CA GLU C 339 " pdb=" C GLU C 339 " pdb=" N PHE C 340 " pdb=" CA PHE C 340 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 5677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1140 0.044 - 0.088: 276 0.088 - 0.133: 104 0.133 - 0.177: 4 0.177 - 0.221: 3 Chirality restraints: 1527 Sorted by residual: chirality pdb=" C2' A3P D 4 " pdb=" C3' A3P D 4 " pdb=" O2' A3P D 4 " pdb=" C1' A3P D 4 " both_signs ideal model delta sigma weight residual False -2.72 -2.50 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE C 350 " pdb=" CA ILE C 350 " pdb=" CG1 ILE C 350 " pdb=" CG2 ILE C 350 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C2' A3P E 4 " pdb=" C3' A3P E 4 " pdb=" O2' A3P E 4 " pdb=" C1' A3P E 4 " both_signs ideal model delta sigma weight residual False -2.72 -2.51 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1524 not shown) Planarity restraints: 1651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 318 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C THR A 318 " 0.050 2.00e-02 2.50e+03 pdb=" O THR A 318 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 319 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 381 " 0.032 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO C 382 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 260 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" CG ASP A 260 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 260 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 260 " 0.010 2.00e-02 2.50e+03 ... (remaining 1648 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1026 2.75 - 3.29: 9241 3.29 - 3.82: 16885 3.82 - 4.36: 20233 4.36 - 4.90: 34056 Nonbonded interactions: 81441 Sorted by model distance: nonbonded pdb=" NE2 GLN B 285 " pdb=" O VAL B 497 " model vdw 2.211 3.120 nonbonded pdb=" OG SER C 395 " pdb=" O1P A3P E 4 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR B 312 " pdb=" OE1 GLN B 320 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR C 312 " pdb=" OE1 GLN C 320 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR C 345 " pdb=" N7 A E 3 " model vdw 2.244 3.120 ... (remaining 81436 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 4 through 23 and (name N or name CA or name C or name O o \ r name CB )) or resid 24 through 26 or (resid 27 through 30 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 62 or resid 66 through \ 85 or (resid 86 through 88 and (name N or name CA or name C or name O or name CB \ )) or resid 89 through 92 or (resid 93 and (name N or name CA or name C or name \ O or name CB )) or resid 94 through 96 or (resid 104 through 107 and (name N or \ name CA or name C or name O or name CB )) or resid 108 through 127 or (resid 12 \ 8 through 130 and (name N or name CA or name C or name O or name CB )) or resid \ 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or re \ sid 133 through 152 or (resid 153 through 154 and (name N or name CA or name C o \ r name O or name CB )) or resid 155 through 165 or (resid 166 through 173 and (n \ ame N or name CA or name C or name O or name CB )) or resid 174 through 182 or ( \ resid 183 and (name N or name CA or name C or name O or name CB )) or resid 184 \ through 189 or resid 201 through 212 or (resid 213 through 214 and (name N or na \ me CA or name C or name O or name CB )) or resid 215 through 230 or (resid 231 a \ nd (name N or name CA or name C or name O or name CB )) or resid 232 through 235 \ or (resid 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 275 or (resid 276 and (name N or name CA or name C or name O or nam \ e CB )) or resid 277 through 293 or (resid 294 and (name N or name CA or name C \ or name O or name CB )) or resid 295 through 300 or (resid 301 and (name N or na \ me CA or name C or name O or name CB )) or resid 302 through 303 or (resid 304 a \ nd (name N or name CA or name C or name O or name CB )) or resid 305 through 339 \ or (resid 340 through 342 and (name N or name CA or name C or name O or name CB \ )) or resid 343 or (resid 344 and (name N or name CA or name C or name O or nam \ e CB )) or resid 345 through 366 or (resid 367 through 369 and (name N or name C \ A or name C or name O or name CB )) or resid 370 or (resid 371 and (name N or na \ me CA or name C or name O or name CB )) or resid 372 through 375 or (resid 376 a \ nd (name N or name CA or name C or name O or name CB )) or resid 377 through 380 \ or (resid 381 and (name N or name CA or name C or name O or name CB )) or resid \ 382 through 395 or (resid 396 and (name N or name CA or name C or name O or nam \ e CB )) or resid 397 through 421 or (resid 422 and (name N or name CA or name C \ or name O or name CB )) or (resid 426 and (name N or name CA or name C or name O \ or name CB )) or resid 427 or (resid 428 and (name N or name CA or name C or na \ me O or name CB )) or resid 429 through 430 or (resid 431 and (name N or name CA \ or name C or name O or name CB )) or resid 432 through 486 or (resid 487 throug \ h 489 and (name N or name CA or name C or name O or name CB )) or resid 492 thro \ ugh 503 or (resid 504 through 505 and (name N or name CA or name C or name O or \ name CB )))) selection = (chain 'B' and (resid 4 through 13 or resid 18 through 39 or (resid 40 through 4 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 49 through 6 \ 7 or (resid 68 through 73 and (name N or name CA or name C or name O or name CB \ )) or resid 74 through 106 or (resid 107 and (name N or name CA or name C or nam \ e O or name CB )) or resid 108 through 146 or (resid 147 through 149 and (name N \ or name CA or name C or name O or name CB )) or resid 150 through 166 or resid \ 171 through 296 or (resid 297 and (name N or name CA or name C or name O or name \ CB )) or resid 298 through 338 or (resid 339 through 342 and (name N or name CA \ or name C or name O or name CB )) or resid 343 through 368 or (resid 369 and (n \ ame N or name CA or name C or name O or name CB )) or resid 370 through 505)) } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.005 0.140 9680 Z= 0.308 Angle : 0.633 15.392 13222 Z= 0.308 Chirality : 0.044 0.221 1527 Planarity : 0.003 0.050 1651 Dihedral : 15.674 89.791 3304 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.15 % Allowed : 19.59 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.12 (0.25), residues: 1220 helix: 1.43 (0.24), residues: 484 sheet: -0.45 (0.34), residues: 258 loop : -0.97 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 421 TYR 0.010 0.001 TYR A 436 PHE 0.016 0.001 PHE B 498 TRP 0.005 0.001 TRP B 215 HIS 0.006 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.30 ( 9678) covalent geometry : angle 0.63302 / 0.31 (13222) hydrogen bonds : bond 0.20921 / 15.12 ( 444) hydrogen bonds : angle 7.54243 / 5.47 ( 1269) Misc. bond : bond 0.04829 / 2.43 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7938 (mp10) outliers start: 18 outliers final: 14 residues processed: 103 average time/residue: 0.3679 time to fit residues: 41.1786 Evaluate side-chains 96 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 285 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.116370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094017 restraints weight = 19707.287| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.29 r_work: 0.3367 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9680 Z= 0.206 Angle : 0.595 8.498 13222 Z= 0.310 Chirality : 0.045 0.205 1527 Planarity : 0.004 0.034 1651 Dihedral : 10.406 77.329 1459 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.87 % Allowed : 18.88 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.09 (0.25), residues: 1220 helix: 1.36 (0.24), residues: 509 sheet: -0.53 (0.33), residues: 267 loop : -1.02 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 331 TYR 0.015 0.002 TYR A 436 PHE 0.019 0.001 PHE B 498 TRP 0.008 0.001 TRP B 215 HIS 0.005 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 ( 9678) covalent geometry : angle 0.59541 / 0.31 (13222) hydrogen bonds : bond 0.05222 / 3.68 ( 444) hydrogen bonds : angle 5.72347 / 4.17 ( 1269) Misc. bond : bond 0.00849 / 0.43 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8473 (mm-40) REVERT: B 205 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7868 (mpp80) REVERT: B 237 ARG cc_start: 0.7743 (ptp90) cc_final: 0.7510 (ptp90) REVERT: B 240 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7892 (tmtt) REVERT: B 285 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7918 (mp-120) outliers start: 24 outliers final: 10 residues processed: 110 average time/residue: 0.3171 time to fit residues: 38.4501 Evaluate side-chains 97 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 285 GLN Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 470 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 0.0670 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.117456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.095539 restraints weight = 19489.066| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.24 r_work: 0.3388 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9680 Z= 0.147 Angle : 0.538 7.959 13222 Z= 0.278 Chirality : 0.044 0.211 1527 Planarity : 0.003 0.031 1651 Dihedral : 10.132 71.242 1444 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.94 % Allowed : 18.40 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.25), residues: 1220 helix: 1.52 (0.24), residues: 510 sheet: -0.46 (0.34), residues: 257 loop : -1.08 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 448 TYR 0.013 0.001 TYR A 436 PHE 0.017 0.001 PHE B 498 TRP 0.006 0.001 TRP C 433 HIS 0.006 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 9678) covalent geometry : angle 0.53767 / 0.28 (13222) hydrogen bonds : bond 0.04288 / 3.03 ( 444) hydrogen bonds : angle 5.29027 / 3.86 ( 1269) Misc. bond : bond 0.00085 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8399 (mm110) REVERT: B 205 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7854 (mpp80) REVERT: B 237 ARG cc_start: 0.7634 (ptp90) cc_final: 0.7431 (ptp90) REVERT: B 240 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7869 (ttpp) REVERT: B 268 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.7490 (t0) REVERT: C 455 ARG cc_start: 0.8501 (tpp-160) cc_final: 0.8185 (tpp-160) outliers start: 33 outliers final: 14 residues processed: 115 average time/residue: 0.3365 time to fit residues: 42.6372 Evaluate side-chains 98 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.118211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097687 restraints weight = 20088.901| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.18 r_work: 0.3409 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9680 Z= 0.170 Angle : 0.550 7.042 13222 Z= 0.282 Chirality : 0.044 0.196 1527 Planarity : 0.003 0.032 1651 Dihedral : 9.856 70.052 1441 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.35 % Allowed : 19.59 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.20 (0.25), residues: 1220 helix: 1.53 (0.24), residues: 511 sheet: -0.45 (0.34), residues: 257 loop : -1.09 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 448 TYR 0.013 0.001 TYR A 436 PHE 0.017 0.001 PHE B 498 TRP 0.007 0.001 TRP B 284 HIS 0.006 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 9678) covalent geometry : angle 0.55040 / 0.28 (13222) hydrogen bonds : bond 0.03998 / 2.81 ( 444) hydrogen bonds : angle 5.20794 / 3.79 ( 1269) Misc. bond : bond 0.00225 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: B 49 ASN cc_start: 0.8066 (t0) cc_final: 0.7716 (t0) REVERT: B 205 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7865 (mpp80) REVERT: B 240 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7880 (tmtt) REVERT: B 268 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.7617 (t0) REVERT: C 407 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: C 455 ARG cc_start: 0.8417 (tpp-160) cc_final: 0.8151 (tpp-160) outliers start: 28 outliers final: 14 residues processed: 110 average time/residue: 0.3644 time to fit residues: 44.1462 Evaluate side-chains 97 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.119238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098702 restraints weight = 19866.327| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.17 r_work: 0.3428 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9680 Z= 0.129 Angle : 0.533 11.707 13222 Z= 0.271 Chirality : 0.043 0.185 1527 Planarity : 0.003 0.033 1651 Dihedral : 9.608 69.307 1438 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.58 % Allowed : 19.47 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1220 helix: 1.62 (0.24), residues: 512 sheet: -0.38 (0.34), residues: 251 loop : -1.09 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 237 TYR 0.013 0.001 TYR A 436 PHE 0.016 0.001 PHE B 498 TRP 0.005 0.001 TRP C 252 HIS 0.005 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9678) covalent geometry : angle 0.53291 / 0.27 (13222) hydrogen bonds : bond 0.03631 / 2.56 ( 444) hydrogen bonds : angle 5.04402 / 3.67 ( 1269) Misc. bond : bond 0.00074 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 49 ASN cc_start: 0.8060 (t0) cc_final: 0.7654 (t0) REVERT: B 205 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7822 (mpp80) REVERT: B 237 ARG cc_start: 0.7794 (ptp90) cc_final: 0.7483 (ptp90) REVERT: B 240 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7869 (ttpp) REVERT: B 268 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7632 (t0) REVERT: C 455 ARG cc_start: 0.8398 (tpp-160) cc_final: 0.8062 (tpp-160) outliers start: 30 outliers final: 14 residues processed: 116 average time/residue: 0.3680 time to fit residues: 46.9772 Evaluate side-chains 101 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 0.0060 chunk 0 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 3 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN C 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.119307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098721 restraints weight = 19834.053| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.18 r_work: 0.3432 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9680 Z= 0.129 Angle : 0.541 13.491 13222 Z= 0.273 Chirality : 0.043 0.192 1527 Planarity : 0.003 0.032 1651 Dihedral : 9.521 68.985 1438 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.46 % Allowed : 20.31 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1220 helix: 1.61 (0.24), residues: 514 sheet: -0.42 (0.35), residues: 247 loop : -1.05 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.014 0.001 TYR A 436 PHE 0.015 0.001 PHE B 498 TRP 0.005 0.001 TRP B 284 HIS 0.005 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9678) covalent geometry : angle 0.54107 / 0.27 (13222) hydrogen bonds : bond 0.03511 / 2.48 ( 444) hydrogen bonds : angle 4.98230 / 3.62 ( 1269) Misc. bond : bond 0.00121 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: B 49 ASN cc_start: 0.8081 (t0) cc_final: 0.7672 (t0) REVERT: B 237 ARG cc_start: 0.7773 (ptp90) cc_final: 0.7472 (ptp90) REVERT: B 240 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7803 (ttpp) REVERT: B 268 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8040 (t0) REVERT: C 407 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: C 455 ARG cc_start: 0.8353 (tpp-160) cc_final: 0.7998 (tpp-160) outliers start: 29 outliers final: 12 residues processed: 114 average time/residue: 0.3488 time to fit residues: 44.0897 Evaluate side-chains 97 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 116 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.119689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.099089 restraints weight = 19792.102| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.16 r_work: 0.3440 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9680 Z= 0.123 Angle : 0.537 13.645 13222 Z= 0.271 Chirality : 0.043 0.154 1527 Planarity : 0.003 0.032 1651 Dihedral : 9.312 68.531 1434 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.99 % Allowed : 21.03 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.25), residues: 1220 helix: 1.56 (0.23), residues: 522 sheet: -0.41 (0.34), residues: 258 loop : -1.10 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.014 0.001 TYR C 312 PHE 0.013 0.001 PHE B 498 TRP 0.011 0.001 TRP C 252 HIS 0.005 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9678) covalent geometry : angle 0.53701 / 0.27 (13222) hydrogen bonds : bond 0.03382 / 2.39 ( 444) hydrogen bonds : angle 4.88710 / 3.56 ( 1269) Misc. bond : bond 0.00098 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8603 (mt-10) REVERT: B 49 ASN cc_start: 0.8171 (t0) cc_final: 0.7793 (t0) REVERT: B 237 ARG cc_start: 0.7807 (ptp90) cc_final: 0.7524 (ptp90) REVERT: B 268 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7990 (t0) REVERT: B 285 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7631 (mp-120) REVERT: C 407 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: C 455 ARG cc_start: 0.8334 (tpp-160) cc_final: 0.7987 (tpp-160) outliers start: 25 outliers final: 13 residues processed: 112 average time/residue: 0.3369 time to fit residues: 41.8592 Evaluate side-chains 101 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 285 GLN Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.119381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098810 restraints weight = 19752.076| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.17 r_work: 0.3432 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9680 Z= 0.145 Angle : 0.546 13.700 13222 Z= 0.276 Chirality : 0.043 0.155 1527 Planarity : 0.004 0.070 1651 Dihedral : 9.247 69.236 1434 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.75 % Allowed : 21.27 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.30 (0.25), residues: 1220 helix: 1.57 (0.23), residues: 523 sheet: -0.36 (0.34), residues: 256 loop : -1.09 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 421 TYR 0.014 0.001 TYR C 451 PHE 0.026 0.001 PHE B 498 TRP 0.016 0.001 TRP C 252 HIS 0.006 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 9678) covalent geometry : angle 0.54644 / 0.28 (13222) hydrogen bonds : bond 0.03438 / 2.44 ( 444) hydrogen bonds : angle 4.89934 / 3.56 ( 1269) Misc. bond : bond 0.00140 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: B 49 ASN cc_start: 0.8174 (t0) cc_final: 0.7792 (t0) REVERT: B 237 ARG cc_start: 0.7755 (ptp90) cc_final: 0.7435 (ptp90) REVERT: B 240 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7801 (ttpp) REVERT: B 268 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7944 (t0) REVERT: C 407 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: C 455 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7973 (tpp-160) outliers start: 23 outliers final: 12 residues processed: 107 average time/residue: 0.3302 time to fit residues: 39.0312 Evaluate side-chains 96 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.119743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.099331 restraints weight = 19751.349| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.16 r_work: 0.3441 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9680 Z= 0.130 Angle : 0.541 13.715 13222 Z= 0.273 Chirality : 0.043 0.154 1527 Planarity : 0.004 0.066 1651 Dihedral : 9.117 68.886 1434 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.39 % Allowed : 21.98 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.35 (0.25), residues: 1220 helix: 1.62 (0.23), residues: 524 sheet: -0.32 (0.34), residues: 259 loop : -1.09 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 421 TYR 0.013 0.001 TYR A 436 PHE 0.016 0.001 PHE B 498 TRP 0.016 0.001 TRP C 252 HIS 0.005 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9678) covalent geometry : angle 0.54052 / 0.27 (13222) hydrogen bonds : bond 0.03337 / 2.37 ( 444) hydrogen bonds : angle 4.83990 / 3.52 ( 1269) Misc. bond : bond 0.00113 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 132 SER cc_start: 0.8924 (p) cc_final: 0.8702 (p) REVERT: A 409 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: B 49 ASN cc_start: 0.8177 (t0) cc_final: 0.7792 (t0) REVERT: B 237 ARG cc_start: 0.7770 (ptp90) cc_final: 0.7462 (ptp90) REVERT: B 268 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7929 (t0) REVERT: C 339 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8545 (tm-30) REVERT: C 407 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7561 (pp30) REVERT: C 455 ARG cc_start: 0.8319 (tpp-160) cc_final: 0.7717 (tpm170) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.3601 time to fit residues: 41.9338 Evaluate side-chains 103 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 0.0870 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.120665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100163 restraints weight = 19557.729| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.17 r_work: 0.3459 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9680 Z= 0.112 Angle : 0.538 13.754 13222 Z= 0.271 Chirality : 0.043 0.152 1527 Planarity : 0.004 0.063 1651 Dihedral : 8.944 67.723 1434 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.27 % Allowed : 22.22 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.40 (0.25), residues: 1220 helix: 1.69 (0.23), residues: 524 sheet: -0.32 (0.34), residues: 259 loop : -1.09 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.014 0.001 TYR C 451 PHE 0.018 0.001 PHE B 498 TRP 0.022 0.001 TRP C 252 HIS 0.006 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 9678) covalent geometry : angle 0.53839 / 0.27 (13222) hydrogen bonds : bond 0.03138 / 2.23 ( 444) hydrogen bonds : angle 4.76253 / 3.46 ( 1269) Misc. bond : bond 0.00074 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: B 49 ASN cc_start: 0.8124 (t0) cc_final: 0.7747 (t0) REVERT: B 237 ARG cc_start: 0.7761 (ptp90) cc_final: 0.7453 (ptp90) REVERT: B 268 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7792 (t0) REVERT: C 339 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8558 (tm-30) REVERT: C 455 ARG cc_start: 0.8304 (tpp-160) cc_final: 0.7990 (tpp-160) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 0.3601 time to fit residues: 40.5759 Evaluate side-chains 99 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 4.9990 chunk 12 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.0970 chunk 83 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.121348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.101088 restraints weight = 19517.543| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.16 r_work: 0.3477 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9680 Z= 0.103 Angle : 0.540 13.496 13222 Z= 0.270 Chirality : 0.042 0.150 1527 Planarity : 0.004 0.063 1651 Dihedral : 8.840 66.851 1434 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.91 % Allowed : 23.18 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.45 (0.25), residues: 1220 helix: 1.75 (0.23), residues: 524 sheet: -0.29 (0.34), residues: 259 loop : -1.08 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 205 TYR 0.013 0.001 TYR C 451 PHE 0.017 0.001 PHE B 498 TRP 0.021 0.001 TRP C 252 HIS 0.007 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 9678) covalent geometry : angle 0.54009 / 0.27 (13222) hydrogen bonds : bond 0.03056 / 2.18 ( 444) hydrogen bonds : angle 4.70969 / 3.42 ( 1269) Misc. bond : bond 0.00052 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2545.32 seconds wall clock time: 44 minutes 6.37 seconds (2646.37 seconds total)