Starting phenix.real_space_refine on Sat Jul 4 06:27:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mdr_48178/07_2026/9mdr_48178.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mdr_48178/07_2026/9mdr_48178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mdr_48178/07_2026/9mdr_48178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mdr_48178/07_2026/9mdr_48178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mdr_48178/07_2026/9mdr_48178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mdr_48178/07_2026/9mdr_48178.map" } resolution = 3.33 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= 0.004 sd= 0.097 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 Ca 14 9.91 5 S 35 5.16 5 C 11529 2.51 5 N 2989 2.21 5 O 3822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s 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: 18389 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2625 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2616 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 336, 2616 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 1 bond proxies already assigned to first conformer: 2647 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.62, per 1000 atoms: 0.14 Number of scatterers: 18389 At special positions: 0 Unit cell: (139.32, 141.04, 96.32, 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) Ca 14 19.99 S 35 16.00 O 3822 8.00 N 2989 7.00 C 11529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4410 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 56 sheets defined 23.2% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.747A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.878A pdb=" N ASP A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 473 removed outlier: 3.748A pdb=" N ALA A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 513 removed outlier: 3.788A pdb=" N SER A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 593 removed outlier: 3.695A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.553A pdb=" N ASN A 602 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.748A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 253 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.878A pdb=" N ASP B 291 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 473 removed outlier: 3.748A pdb=" N ALA B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 513 removed outlier: 3.789A pdb=" N SER B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 593 removed outlier: 3.695A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.553A pdb=" N ASN B 602 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.747A pdb=" N ALA C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.878A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 473 removed outlier: 3.747A pdb=" N ALA C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 513 removed outlier: 3.789A pdb=" N SER C 512 " --> pdb=" O SER C 508 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 593 removed outlier: 3.696A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.553A pdb=" N ASN C 602 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.746A pdb=" N ALA D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY D 253 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.878A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 473 removed outlier: 3.748A pdb=" N ALA D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 513 removed outlier: 3.788A pdb=" N SER D 512 " --> pdb=" O SER D 508 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 556 Processing helix chain 'D' and resid 581 through 593 removed outlier: 3.695A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 removed outlier: 3.553A pdb=" N ASN D 602 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.747A pdb=" N ALA E 250 " --> pdb=" O ASP E 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY E 253 " --> pdb=" O ALA E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.878A pdb=" N ASP E 291 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 473 removed outlier: 3.747A pdb=" N ALA E 472 " --> pdb=" O LYS E 468 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 513 removed outlier: 3.788A pdb=" N SER E 512 " --> pdb=" O SER E 508 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE E 513 " --> pdb=" O GLN E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 593 removed outlier: 3.695A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.553A pdb=" N ASN E 602 " --> pdb=" O LYS E 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.747A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 291 removed outlier: 3.879A pdb=" N ASP F 291 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 473 removed outlier: 3.747A pdb=" N ALA F 472 " --> pdb=" O LYS F 468 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY F 473 " --> pdb=" O LYS F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 513 removed outlier: 3.788A pdb=" N SER F 512 " --> pdb=" O SER F 508 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE F 513 " --> pdb=" O GLN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 581 through 593 removed outlier: 3.696A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 removed outlier: 3.553A pdb=" N ASN F 602 " --> pdb=" O LYS F 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.747A pdb=" N ALA G 250 " --> pdb=" O ASP G 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY G 253 " --> pdb=" O ALA G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.878A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 473 removed outlier: 3.748A pdb=" N ALA G 472 " --> pdb=" O LYS G 468 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY G 473 " --> pdb=" O LYS G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 513 removed outlier: 3.788A pdb=" N SER G 512 " --> pdb=" O SER G 508 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 593 removed outlier: 3.695A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 removed outlier: 3.553A pdb=" N ASN G 602 " --> pdb=" O LYS G 599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 311 removed outlier: 4.271A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 311 removed outlier: 4.271A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 406 removed outlier: 6.084A pdb=" N LYS A 405 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN A 431 " --> pdb=" O LYS A 405 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 3.882A pdb=" N SER A 420 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 525 through 531 Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 560 Processing sheet with id=AA9, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 311 removed outlier: 4.271A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 298 through 311 removed outlier: 4.271A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 403 through 406 removed outlier: 6.084A pdb=" N LYS B 405 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN B 431 " --> pdb=" O LYS B 405 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 418 through 423 removed outlier: 3.883A pdb=" N SER B 420 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB6, first strand: chain 'B' and resid 525 through 531 Processing sheet with id=AB7, first strand: chain 'B' and resid 559 through 560 Processing sheet with id=AB8, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AB9, first strand: chain 'C' and resid 298 through 311 removed outlier: 4.270A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 298 through 311 removed outlier: 4.270A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 387 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 403 through 406 removed outlier: 6.085A pdb=" N LYS C 405 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C 431 " --> pdb=" O LYS C 405 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 418 through 423 removed outlier: 3.883A pdb=" N SER C 420 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC5, first strand: chain 'C' and resid 525 through 531 Processing sheet with id=AC6, first strand: chain 'C' and resid 559 through 560 Processing sheet with id=AC7, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AC8, first strand: chain 'D' and resid 298 through 311 removed outlier: 4.270A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 298 through 311 removed outlier: 4.270A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 387 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 403 through 406 removed outlier: 6.084A pdb=" N LYS D 405 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN D 431 " --> pdb=" O LYS D 405 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 418 through 423 removed outlier: 3.883A pdb=" N SER D 420 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD4, first strand: chain 'D' and resid 525 through 531 Processing sheet with id=AD5, first strand: chain 'D' and resid 559 through 560 Processing sheet with id=AD6, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AD7, first strand: chain 'E' and resid 298 through 311 removed outlier: 4.270A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 298 through 311 removed outlier: 4.270A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 387 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 403 through 406 removed outlier: 6.084A pdb=" N LYS E 405 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN E 431 " --> pdb=" O LYS E 405 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 418 through 423 removed outlier: 3.883A pdb=" N SER E 420 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AE3, first strand: chain 'E' and resid 525 through 531 Processing sheet with id=AE4, first strand: chain 'E' and resid 559 through 560 Processing sheet with id=AE5, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AE6, first strand: chain 'F' and resid 298 through 311 removed outlier: 4.270A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 298 through 311 removed outlier: 4.270A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 403 through 406 removed outlier: 6.084A pdb=" N LYS F 405 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN F 431 " --> pdb=" O LYS F 405 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 418 through 423 removed outlier: 3.882A pdb=" N SER F 420 " --> pdb=" O LEU F 412 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AF2, first strand: chain 'F' and resid 525 through 531 Processing sheet with id=AF3, first strand: chain 'F' and resid 559 through 560 Processing sheet with id=AF4, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AF5, first strand: chain 'G' and resid 298 through 311 removed outlier: 4.270A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 298 through 311 removed outlier: 4.270A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA G 387 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 403 through 406 removed outlier: 6.084A pdb=" N LYS G 405 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN G 431 " --> pdb=" O LYS G 405 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 418 through 423 removed outlier: 3.883A pdb=" N SER G 420 " --> pdb=" O LEU G 412 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR G 409 " --> pdb=" O THR G 481 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AG1, first strand: chain 'G' and resid 525 through 531 Processing sheet with id=AG2, first strand: chain 'G' and resid 559 through 560 616 hydrogen bonds defined for protein. 1582 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: 3.24 Time building geometry restraints manager: 1.98 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: 6041 1.34 - 1.46: 3258 1.46 - 1.57: 9321 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 18683 Sorted by residual: bond pdb=" C TYR B 439 " pdb=" N PRO B 440 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.67e+00 bond pdb=" C TYR D 439 " pdb=" N PRO D 440 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.66e+00 bond pdb=" C TYR E 439 " pdb=" N PRO E 440 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.60e+00 bond pdb=" C TYR F 439 " pdb=" N PRO F 440 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.59e+00 bond pdb=" C TYR A 439 " pdb=" N PRO A 440 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.58e+00 ... (remaining 18678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 24524 1.51 - 3.01: 606 3.01 - 4.52: 126 4.52 - 6.02: 35 6.02 - 7.53: 35 Bond angle restraints: 25326 Sorted by residual: angle pdb=" C ASN D 431 " pdb=" N ASN D 432 " pdb=" CA ASN D 432 " ideal model delta sigma weight residual 122.82 128.72 -5.90 1.42e+00 4.96e-01 1.73e+01 angle pdb=" C ASN C 431 " pdb=" N ASN C 432 " pdb=" CA ASN C 432 " ideal model delta sigma weight residual 122.82 128.71 -5.89 1.42e+00 4.96e-01 1.72e+01 angle pdb=" C ASN E 431 " pdb=" N ASN E 432 " pdb=" CA ASN E 432 " ideal model delta sigma weight residual 122.82 128.71 -5.89 1.42e+00 4.96e-01 1.72e+01 angle pdb=" C ASN F 431 " pdb=" N ASN F 432 " pdb=" CA ASN F 432 " ideal model delta sigma weight residual 122.82 128.69 -5.87 1.42e+00 4.96e-01 1.71e+01 angle pdb=" C ASN B 431 " pdb=" N ASN B 432 " pdb=" CA ASN B 432 " ideal model delta sigma weight residual 122.82 128.69 -5.87 1.42e+00 4.96e-01 1.71e+01 ... (remaining 25321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 9558 17.27 - 34.54: 1327 34.54 - 51.81: 462 51.81 - 69.08: 70 69.08 - 86.34: 28 Dihedral angle restraints: 11445 sinusoidal: 4550 harmonic: 6895 Sorted by residual: dihedral pdb=" CA TYR A 439 " pdb=" C TYR A 439 " pdb=" N PRO A 440 " pdb=" CA PRO A 440 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA TYR E 439 " pdb=" C TYR E 439 " pdb=" N PRO E 440 " pdb=" CA PRO E 440 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA TYR D 439 " pdb=" C TYR D 439 " pdb=" N PRO D 440 " pdb=" CA PRO D 440 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 11442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1929 0.039 - 0.079: 668 0.079 - 0.118: 218 0.118 - 0.157: 41 0.157 - 0.197: 21 Chirality restraints: 2877 Sorted by residual: chirality pdb=" CB ILE A 569 " pdb=" CA ILE A 569 " pdb=" CG1 ILE A 569 " pdb=" CG2 ILE A 569 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CB ILE E 569 " pdb=" CA ILE E 569 " pdb=" CG1 ILE E 569 " pdb=" CG2 ILE E 569 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CB ILE B 569 " pdb=" CA ILE B 569 " pdb=" CG1 ILE B 569 " pdb=" CG2 ILE B 569 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 2874 not shown) Planarity restraints: 3297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 269 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO E 270 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO E 270 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 270 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 269 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO G 270 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO G 270 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 270 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 269 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO D 270 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 270 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 270 " -0.021 5.00e-02 4.00e+02 ... (remaining 3294 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6158 2.84 - 3.35: 14674 3.35 - 3.87: 28938 3.87 - 4.38: 32386 4.38 - 4.90: 60103 Nonbonded interactions: 142259 Sorted by model distance: nonbonded pdb=" OD1 ASP C 540 " pdb=" OG1 THR C 542 " model vdw 2.322 3.040 nonbonded pdb=" OD1 ASP E 540 " pdb=" OG1 THR E 542 " model vdw 2.322 3.040 nonbonded pdb=" OD1 ASP B 540 " pdb=" OG1 THR B 542 " model vdw 2.322 3.040 nonbonded pdb=" OD1 ASP D 540 " pdb=" OG1 THR D 542 " model vdw 2.322 3.040 nonbonded pdb=" OD1 ASP G 540 " pdb=" OG1 THR G 542 " model vdw 2.322 3.040 ... (remaining 142254 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.50 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: 2.530 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18683 Z= 0.129 Angle : 0.641 7.531 25326 Z= 0.346 Chirality : 0.046 0.197 2877 Planarity : 0.004 0.037 3297 Dihedral : 18.003 86.344 7035 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.39 % Allowed : 29.25 % Favored : 70.36 % 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: -1.58 (0.16), residues: 2331 helix: -1.62 (0.22), residues: 406 sheet: 0.59 (0.22), residues: 581 loop : -1.68 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 394 TYR 0.008 0.001 TYR B 230 PHE 0.009 0.001 PHE F 487 TRP 0.005 0.001 TRP E 503 HIS 0.001 0.001 HIS G 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (18683) covalent geometry : angle 0.64079 / 0.35 (25326) hydrogen bonds : bond 0.16600 / 11.35 ( 560) hydrogen bonds : angle 7.57666 / 5.29 ( 1582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.624 Fit side-chains REVERT: B 252 GLN cc_start: 0.8124 (mt0) cc_final: 0.7908 (mt0) REVERT: D 565 TYR cc_start: 0.7866 (m-80) cc_final: 0.7225 (m-80) REVERT: E 565 TYR cc_start: 0.7698 (m-80) cc_final: 0.7021 (m-80) outliers start: 8 outliers final: 7 residues processed: 205 average time/residue: 0.1199 time to fit residues: 39.9454 Evaluate side-chains 206 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 199 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain G residue 379 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.0030 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN A 501 ASN B 454 GLN B 501 ASN C 475 GLN C 501 ASN D 454 GLN D 501 ASN E 501 ASN F 501 ASN G 501 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114088 restraints weight = 38834.045| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.06 r_work: 0.3215 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18683 Z= 0.125 Angle : 0.529 5.942 25326 Z= 0.284 Chirality : 0.043 0.172 2877 Planarity : 0.004 0.033 3297 Dihedral : 4.347 32.351 2548 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.06 % Allowed : 27.11 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.16), residues: 2331 helix: -0.86 (0.24), residues: 420 sheet: 0.72 (0.22), residues: 574 loop : -1.62 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 394 TYR 0.013 0.001 TYR F 230 PHE 0.009 0.001 PHE C 487 TRP 0.005 0.001 TRP E 503 HIS 0.001 0.001 HIS D 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (18683) covalent geometry : angle 0.52872 / 0.28 (25326) hydrogen bonds : bond 0.03008 / 1.91 ( 560) hydrogen bonds : angle 5.62174 / 3.89 ( 1582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 0.601 Fit side-chains REVERT: C 586 ASN cc_start: 0.8581 (m-40) cc_final: 0.8061 (m110) REVERT: E 565 TYR cc_start: 0.8019 (m-80) cc_final: 0.7563 (m-80) outliers start: 63 outliers final: 39 residues processed: 263 average time/residue: 0.1001 time to fit residues: 43.4572 Evaluate side-chains 231 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 496 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 110 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 228 optimal weight: 0.0970 chunk 170 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 208 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 0.0370 overall best weight: 1.1058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 314 HIS B 454 GLN D 454 GLN F 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113468 restraints weight = 63487.814| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.26 r_work: 0.3133 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18683 Z= 0.125 Angle : 0.528 6.155 25326 Z= 0.283 Chirality : 0.043 0.175 2877 Planarity : 0.004 0.038 3297 Dihedral : 4.046 14.181 2534 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.96 % Allowed : 27.36 % Favored : 69.68 % 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: -1.15 (0.17), residues: 2331 helix: -0.52 (0.26), residues: 420 sheet: 0.69 (0.22), residues: 574 loop : -1.57 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 394 TYR 0.011 0.001 TYR D 230 PHE 0.008 0.001 PHE E 555 TRP 0.005 0.001 TRP B 503 HIS 0.001 0.000 HIS G 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (18683) covalent geometry : angle 0.52762 / 0.28 (25326) hydrogen bonds : bond 0.02919 / 1.85 ( 560) hydrogen bonds : angle 5.39498 / 3.73 ( 1582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 205 time to evaluate : 0.729 Fit side-chains REVERT: B 568 ASP cc_start: 0.8259 (m-30) cc_final: 0.8053 (m-30) REVERT: E 313 GLU cc_start: 0.8015 (pp20) cc_final: 0.7754 (pp20) REVERT: E 565 TYR cc_start: 0.8077 (m-80) cc_final: 0.7644 (m-80) outliers start: 61 outliers final: 49 residues processed: 255 average time/residue: 0.1033 time to fit residues: 43.2199 Evaluate side-chains 230 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 502 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 37 optimal weight: 0.0270 chunk 10 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 overall best weight: 2.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 HIS A 454 GLN B 454 GLN C 314 HIS D 265 ASN D 314 HIS E 314 HIS F 314 HIS F 454 GLN G 314 HIS G 432 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104170 restraints weight = 58194.575| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 4.07 r_work: 0.2991 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18683 Z= 0.203 Angle : 0.616 6.824 25326 Z= 0.332 Chirality : 0.046 0.185 2877 Planarity : 0.004 0.044 3297 Dihedral : 4.414 14.973 2534 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.26 % Allowed : 28.23 % Favored : 68.51 % 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: -1.30 (0.16), residues: 2331 helix: -0.63 (0.25), residues: 420 sheet: 0.58 (0.21), residues: 574 loop : -1.67 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 394 TYR 0.016 0.002 TYR F 230 PHE 0.016 0.002 PHE B 555 TRP 0.005 0.001 TRP A 503 HIS 0.001 0.000 HIS G 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (18683) covalent geometry : angle 0.61645 / 0.33 (25326) hydrogen bonds : bond 0.03575 / 2.25 ( 560) hydrogen bonds : angle 5.66531 / 3.93 ( 1582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 197 time to evaluate : 0.576 Fit side-chains REVERT: B 568 ASP cc_start: 0.8346 (m-30) cc_final: 0.8120 (m-30) REVERT: C 606 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8036 (mt-10) REVERT: E 313 GLU cc_start: 0.7868 (pp20) cc_final: 0.7580 (pp20) REVERT: E 565 TYR cc_start: 0.7936 (m-80) cc_final: 0.7445 (m-80) REVERT: E 606 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8049 (mt-10) REVERT: G 606 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7831 (mm-30) outliers start: 67 outliers final: 57 residues processed: 248 average time/residue: 0.1072 time to fit residues: 43.2495 Evaluate side-chains 239 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain G residue 468 LYS Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 502 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 7 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 chunk 184 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN B 454 GLN D 432 ASN F 432 ASN F 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110200 restraints weight = 39241.907| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.20 r_work: 0.3154 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18683 Z= 0.109 Angle : 0.511 6.338 25326 Z= 0.277 Chirality : 0.043 0.206 2877 Planarity : 0.004 0.039 3297 Dihedral : 4.024 14.117 2534 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.43 % Allowed : 29.35 % Favored : 68.22 % 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: -1.13 (0.17), residues: 2331 helix: -0.37 (0.26), residues: 420 sheet: 0.65 (0.22), residues: 574 loop : -1.58 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 394 TYR 0.009 0.001 TYR G 230 PHE 0.006 0.001 PHE G 487 TRP 0.004 0.001 TRP A 503 HIS 0.000 0.000 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (18683) covalent geometry : angle 0.51149 / 0.28 (25326) hydrogen bonds : bond 0.02674 / 1.68 ( 560) hydrogen bonds : angle 5.26381 / 3.64 ( 1582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.783 Fit side-chains REVERT: B 568 ASP cc_start: 0.8286 (m-30) cc_final: 0.8066 (m-30) REVERT: D 445 SER cc_start: 0.8631 (m) cc_final: 0.8420 (m) REVERT: E 313 GLU cc_start: 0.7989 (pp20) cc_final: 0.7634 (pp20) REVERT: E 565 TYR cc_start: 0.7988 (m-80) cc_final: 0.7563 (m-80) outliers start: 50 outliers final: 40 residues processed: 244 average time/residue: 0.1205 time to fit residues: 48.4268 Evaluate side-chains 236 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain G residue 496 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 96 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 102 optimal weight: 0.0980 chunk 50 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 216 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN B 454 GLN C 432 ASN D 265 ASN F 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.101539 restraints weight = 50045.191| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.28 r_work: 0.2951 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18683 Z= 0.219 Angle : 0.616 6.960 25326 Z= 0.332 Chirality : 0.047 0.208 2877 Planarity : 0.004 0.038 3297 Dihedral : 4.383 14.816 2534 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.40 % Allowed : 28.96 % Favored : 67.64 % 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: -1.29 (0.16), residues: 2331 helix: -0.54 (0.26), residues: 420 sheet: 0.49 (0.21), residues: 574 loop : -1.64 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 394 TYR 0.016 0.002 TYR A 395 PHE 0.016 0.002 PHE E 555 TRP 0.007 0.001 TRP G 503 HIS 0.001 0.000 HIS C 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (18683) covalent geometry : angle 0.61646 / 0.33 (25326) hydrogen bonds : bond 0.03537 / 2.21 ( 560) hydrogen bonds : angle 5.55196 / 3.85 ( 1582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 190 time to evaluate : 0.753 Fit side-chains REVERT: C 432 ASN cc_start: 0.9399 (OUTLIER) cc_final: 0.9172 (p0) REVERT: E 313 GLU cc_start: 0.8073 (pp20) cc_final: 0.7693 (pp20) REVERT: E 565 TYR cc_start: 0.8108 (m-80) cc_final: 0.7693 (m-80) outliers start: 70 outliers final: 56 residues processed: 245 average time/residue: 0.1192 time to fit residues: 48.2754 Evaluate side-chains 239 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 496 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 44 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 GLN C 432 ASN F 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106074 restraints weight = 46096.199| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.00 r_work: 0.3026 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18683 Z= 0.116 Angle : 0.529 6.542 25326 Z= 0.284 Chirality : 0.043 0.192 2877 Planarity : 0.004 0.033 3297 Dihedral : 4.074 14.380 2534 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.01 % Allowed : 29.20 % Favored : 67.78 % 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: -1.16 (0.17), residues: 2331 helix: -0.32 (0.26), residues: 420 sheet: 0.54 (0.21), residues: 574 loop : -1.57 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 394 TYR 0.009 0.001 TYR F 230 PHE 0.006 0.001 PHE G 487 TRP 0.005 0.001 TRP A 503 HIS 0.000 0.000 HIS E 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (18683) covalent geometry : angle 0.52853 / 0.28 (25326) hydrogen bonds : bond 0.02761 / 1.73 ( 560) hydrogen bonds : angle 5.28062 / 3.65 ( 1582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 199 time to evaluate : 0.806 Fit side-chains REVERT: D 445 SER cc_start: 0.8673 (m) cc_final: 0.8413 (m) REVERT: E 313 GLU cc_start: 0.8009 (pp20) cc_final: 0.7622 (pp20) REVERT: E 565 TYR cc_start: 0.8026 (m-80) cc_final: 0.7616 (m-80) REVERT: G 445 SER cc_start: 0.8619 (m) cc_final: 0.8410 (m) outliers start: 62 outliers final: 55 residues processed: 245 average time/residue: 0.1121 time to fit residues: 45.4181 Evaluate side-chains 243 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 468 LYS Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain G residue 468 LYS Chi-restraints excluded: chain G residue 496 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 77 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 196 optimal weight: 0.0470 chunk 120 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 160 optimal weight: 0.0670 chunk 205 optimal weight: 1.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 GLN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN F 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110902 restraints weight = 46064.223| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.42 r_work: 0.3135 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18683 Z= 0.098 Angle : 0.497 6.087 25326 Z= 0.267 Chirality : 0.043 0.178 2877 Planarity : 0.003 0.031 3297 Dihedral : 3.845 14.124 2534 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.96 % Allowed : 29.30 % Favored : 67.74 % 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: -1.04 (0.17), residues: 2331 helix: -0.17 (0.26), residues: 420 sheet: 0.62 (0.22), residues: 574 loop : -1.52 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 458 TYR 0.007 0.001 TYR F 230 PHE 0.006 0.001 PHE E 555 TRP 0.005 0.001 TRP B 503 HIS 0.001 0.000 HIS G 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (18683) covalent geometry : angle 0.49682 / 0.27 (25326) hydrogen bonds : bond 0.02472 / 1.55 ( 560) hydrogen bonds : angle 4.99388 / 3.44 ( 1582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 0.763 Fit side-chains REVERT: D 445 SER cc_start: 0.8538 (m) cc_final: 0.8296 (m) REVERT: E 565 TYR cc_start: 0.7908 (m-80) cc_final: 0.7478 (m-80) REVERT: G 304 MET cc_start: 0.8293 (tmm) cc_final: 0.7670 (tmm) outliers start: 61 outliers final: 54 residues processed: 261 average time/residue: 0.1207 time to fit residues: 51.5594 Evaluate side-chains 251 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 468 LYS Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain G residue 496 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 130 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 134 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN B 454 GLN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104663 restraints weight = 51804.919| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.47 r_work: 0.2988 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18683 Z= 0.146 Angle : 0.558 7.346 25326 Z= 0.297 Chirality : 0.044 0.195 2877 Planarity : 0.003 0.030 3297 Dihedral : 4.047 14.329 2534 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.16 % Allowed : 29.11 % Favored : 67.74 % 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: -1.10 (0.17), residues: 2331 helix: -0.25 (0.26), residues: 420 sheet: 0.54 (0.21), residues: 574 loop : -1.52 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 394 TYR 0.010 0.001 TYR D 230 PHE 0.011 0.001 PHE E 555 TRP 0.006 0.001 TRP G 503 HIS 0.000 0.000 HIS G 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (18683) covalent geometry : angle 0.55787 / 0.30 (25326) hydrogen bonds : bond 0.02972 / 1.86 ( 560) hydrogen bonds : angle 5.18025 / 3.59 ( 1582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.664 Fit side-chains REVERT: A 441 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7940 (mtmm) REVERT: D 445 SER cc_start: 0.8618 (m) cc_final: 0.8350 (m) REVERT: E 565 TYR cc_start: 0.8031 (m-80) cc_final: 0.7610 (m-80) outliers start: 65 outliers final: 60 residues processed: 240 average time/residue: 0.1122 time to fit residues: 44.1419 Evaluate side-chains 244 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 468 LYS Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 145 optimal weight: 0.0050 chunk 42 optimal weight: 0.0570 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.0000 chunk 188 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 226 optimal weight: 0.0050 chunk 6 optimal weight: 0.3980 overall best weight: 0.0930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN B 432 ASN B 454 GLN D 265 ASN E 432 ASN E 610 ASN F 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114678 restraints weight = 36326.359| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.99 r_work: 0.3206 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18683 Z= 0.092 Angle : 0.493 6.679 25326 Z= 0.262 Chirality : 0.042 0.169 2877 Planarity : 0.003 0.033 3297 Dihedral : 3.728 14.222 2534 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.80 % Allowed : 30.52 % Favored : 67.69 % 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: -0.93 (0.17), residues: 2331 helix: -0.03 (0.26), residues: 420 sheet: 0.66 (0.22), residues: 574 loop : -1.44 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 232 TYR 0.014 0.001 TYR D 261 PHE 0.004 0.001 PHE A 281 TRP 0.005 0.001 TRP E 245 HIS 0.001 0.000 HIS G 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (18683) covalent geometry : angle 0.49334 / 0.26 (25326) hydrogen bonds : bond 0.02195 / 1.38 ( 560) hydrogen bonds : angle 4.87846 / 3.36 ( 1582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.592 Fit side-chains REVERT: A 231 GLU cc_start: 0.7529 (tt0) cc_final: 0.7042 (tt0) REVERT: D 445 SER cc_start: 0.8459 (m) cc_final: 0.8220 (m) REVERT: D 505 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7895 (p0) REVERT: E 565 TYR cc_start: 0.7926 (m-80) cc_final: 0.7504 (m-80) outliers start: 37 outliers final: 29 residues processed: 236 average time/residue: 0.1173 time to fit residues: 45.2257 Evaluate side-chains 230 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain G residue 468 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 174 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN B 454 GLN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109126 restraints weight = 37896.918| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.04 r_work: 0.3131 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18683 Z= 0.138 Angle : 0.556 7.693 25326 Z= 0.293 Chirality : 0.044 0.187 2877 Planarity : 0.003 0.029 3297 Dihedral : 3.900 14.202 2534 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.51 % Allowed : 30.81 % Favored : 67.69 % 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: -1.00 (0.17), residues: 2331 helix: -0.11 (0.26), residues: 420 sheet: 0.60 (0.21), residues: 574 loop : -1.47 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.014 0.001 TYR D 261 PHE 0.011 0.001 PHE E 555 TRP 0.007 0.001 TRP E 503 HIS 0.000 0.000 HIS G 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (18683) covalent geometry : angle 0.55610 / 0.29 (25326) hydrogen bonds : bond 0.02814 / 1.76 ( 560) hydrogen bonds : angle 4.98220 / 3.44 ( 1582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4050.80 seconds wall clock time: 70 minutes 28.57 seconds (4228.57 seconds total)