Starting phenix.real_space_refine on Thu Mar 5 02:44:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6okr_20102/03_2026/6okr_20102.cif Found real_map, /net/cci-nas-00/data/ceres_data/6okr_20102/03_2026/6okr_20102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6okr_20102/03_2026/6okr_20102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6okr_20102/03_2026/6okr_20102.map" model { file = "/net/cci-nas-00/data/ceres_data/6okr_20102/03_2026/6okr_20102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6okr_20102/03_2026/6okr_20102.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 11620 2.51 5 N 3031 2.21 5 O 3927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18613 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "B" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "C" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "D" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "F" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "G" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2659 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Time building chain proxies: 4.18, per 1000 atoms: 0.22 Number of scatterers: 18613 At special positions: 0 Unit cell: (143.51, 143.51, 105.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 3927 8.00 N 3031 7.00 C 11620 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: 1.33 Conformation dependent library (CDL) restraints added in 763.3 milliseconds 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4480 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 42 sheets defined 19.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.686A pdb=" N PHE A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 251' Processing helix chain 'A' and resid 272 through 279 removed outlier: 3.852A pdb=" N GLY A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.674A pdb=" N ARG A 290 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 4.401A pdb=" N LYS A 468 " --> pdb=" O TYR A 464 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 512 removed outlier: 3.701A pdb=" N SER A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 4.100A pdb=" N GLU A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.951A pdb=" N LYS A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.961A pdb=" N VAL A 603 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 3.701A pdb=" N PHE B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 251' Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.787A pdb=" N GLY B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.613A pdb=" N ARG B 290 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP B 291 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 473 removed outlier: 4.369A pdb=" N LYS B 468 " --> pdb=" O TYR B 464 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 removed outlier: 4.269A pdb=" N ASP B 505 " --> pdb=" O SER B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.669A pdb=" N SER B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 removed outlier: 4.221A pdb=" N GLU B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 removed outlier: 3.830A pdb=" N LYS B 587 " --> pdb=" O ASN B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.947A pdb=" N VAL B 603 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 removed outlier: 3.680A pdb=" N PHE C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 246 through 251' Processing helix chain 'C' and resid 272 through 279 removed outlier: 3.904A pdb=" N GLY C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.645A pdb=" N ARG C 290 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 473 removed outlier: 4.389A pdb=" N LYS C 468 " --> pdb=" O TYR C 464 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 512 removed outlier: 3.651A pdb=" N SER C 512 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 removed outlier: 4.035A pdb=" N GLU C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 592 removed outlier: 3.765A pdb=" N LYS C 587 " --> pdb=" O ASN C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.999A pdb=" N VAL C 603 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 removed outlier: 3.799A pdb=" N ALA D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 251' Processing helix chain 'D' and resid 272 through 279 removed outlier: 3.827A pdb=" N GLY D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.691A pdb=" N ARG D 290 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 473 removed outlier: 4.388A pdb=" N LYS D 468 " --> pdb=" O TYR D 464 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 512 removed outlier: 3.674A pdb=" N SER D 512 " --> pdb=" O SER D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 removed outlier: 4.089A pdb=" N GLU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 555 " --> pdb=" O ILE D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 592 removed outlier: 3.968A pdb=" N LYS D 587 " --> pdb=" O ASN D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 removed outlier: 4.038A pdb=" N VAL D 603 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.885A pdb=" N ALA E 250 " --> pdb=" O ASP E 247 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 247 through 251' Processing helix chain 'E' and resid 272 through 279 removed outlier: 3.921A pdb=" N GLY E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.613A pdb=" N ARG E 290 " --> pdb=" O THR E 287 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP E 291 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 473 removed outlier: 4.385A pdb=" N LYS E 468 " --> pdb=" O TYR E 464 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA E 472 " --> pdb=" O LYS E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 512 removed outlier: 3.719A pdb=" N SER E 512 " --> pdb=" O SER E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 555 removed outlier: 4.229A pdb=" N GLU E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E 555 " --> pdb=" O ILE E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 592 removed outlier: 3.805A pdb=" N LYS E 587 " --> pdb=" O ASN E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 removed outlier: 4.020A pdb=" N VAL E 603 " --> pdb=" O ILE E 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.765A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 247 through 251' Processing helix chain 'F' and resid 272 through 279 removed outlier: 3.833A pdb=" N GLY F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 291 removed outlier: 3.654A pdb=" N ARG F 290 " --> pdb=" O THR F 287 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP F 291 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 473 removed outlier: 4.408A pdb=" N LYS F 468 " --> pdb=" O TYR F 464 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA F 472 " --> pdb=" O LYS F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 512 removed outlier: 3.669A pdb=" N SER F 512 " --> pdb=" O SER F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 555 removed outlier: 4.256A pdb=" N GLU F 552 " --> pdb=" O GLY F 548 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE F 555 " --> pdb=" O ILE F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 592 removed outlier: 3.842A pdb=" N LYS F 587 " --> pdb=" O ASN F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 removed outlier: 4.020A pdb=" N VAL F 603 " --> pdb=" O ILE F 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.692A pdb=" N PHE G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA G 250 " --> pdb=" O ASP G 247 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 246 through 251' Processing helix chain 'G' and resid 272 through 279 removed outlier: 3.869A pdb=" N GLY G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.633A pdb=" N ARG G 290 " --> pdb=" O THR G 287 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 473 removed outlier: 4.360A pdb=" N LYS G 468 " --> pdb=" O TYR G 464 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA G 472 " --> pdb=" O LYS G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 512 removed outlier: 3.646A pdb=" N SER G 512 " --> pdb=" O SER G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 555 removed outlier: 4.267A pdb=" N GLU G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 555 " --> pdb=" O ILE G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 592 removed outlier: 3.897A pdb=" N LYS G 587 " --> pdb=" O ASN G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 removed outlier: 3.963A pdb=" N VAL G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 238 removed outlier: 3.823A pdb=" N THR A 236 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 310 removed outlier: 4.557A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 423 removed outlier: 3.829A pdb=" N GLN A 482 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN A 411 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N THR A 480 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 413 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU A 478 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.733A pdb=" N THR A 489 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 497 " --> pdb=" O THR A 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 525 through 530 removed outlier: 6.762A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 238 removed outlier: 3.814A pdb=" N THR B 236 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 300 through 310 removed outlier: 4.539A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 423 removed outlier: 6.487A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 489 through 490 removed outlier: 3.771A pdb=" N THR B 489 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 497 " --> pdb=" O THR B 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 525 through 530 removed outlier: 6.755A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 612 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AB4, first strand: chain 'C' and resid 236 through 238 removed outlier: 3.781A pdb=" N THR C 236 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 300 through 310 removed outlier: 4.545A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 421 through 423 removed outlier: 3.807A pdb=" N GLN C 482 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN C 411 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR C 480 " --> pdb=" O ASN C 411 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C 413 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU C 478 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 489 through 490 removed outlier: 3.795A pdb=" N THR C 489 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 497 " --> pdb=" O THR C 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 525 through 530 removed outlier: 6.734A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AC1, first strand: chain 'D' and resid 236 through 238 removed outlier: 3.782A pdb=" N THR D 236 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 299 through 310 removed outlier: 3.806A pdb=" N ILE D 299 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 421 through 423 removed outlier: 3.818A pdb=" N GLN D 482 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN D 411 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N THR D 480 " --> pdb=" O ASN D 411 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL D 413 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU D 478 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 489 through 490 removed outlier: 3.784A pdb=" N THR D 489 " --> pdb=" O VAL D 497 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 497 " --> pdb=" O THR D 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 525 through 530 removed outlier: 6.755A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AC7, first strand: chain 'E' and resid 236 through 238 removed outlier: 3.825A pdb=" N THR E 236 " --> pdb=" O VAL E 243 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 300 through 310 removed outlier: 4.547A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 421 through 423 removed outlier: 6.406A pdb=" N THR E 407 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL E 483 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 489 through 490 removed outlier: 3.779A pdb=" N THR E 489 " --> pdb=" O VAL E 497 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 497 " --> pdb=" O THR E 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 525 through 530 removed outlier: 6.708A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AD4, first strand: chain 'F' and resid 236 through 238 removed outlier: 3.772A pdb=" N THR F 236 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 299 through 310 removed outlier: 3.807A pdb=" N ILE F 299 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 423 removed outlier: 6.427A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 489 through 490 removed outlier: 3.783A pdb=" N THR F 489 " --> pdb=" O VAL F 497 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 497 " --> pdb=" O THR F 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 525 through 530 removed outlier: 6.839A pdb=" N SER F 516 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ILE F 613 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE F 518 " --> pdb=" O ILE F 613 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 612 " --> pdb=" O ILE F 579 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AE1, first strand: chain 'G' and resid 236 through 238 removed outlier: 3.825A pdb=" N THR G 236 " --> pdb=" O VAL G 243 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 300 through 310 removed outlier: 4.569A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 421 through 423 removed outlier: 6.433A pdb=" N THR G 407 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL G 483 " --> pdb=" O THR G 407 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR G 409 " --> pdb=" O THR G 481 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 489 through 490 removed outlier: 3.767A pdb=" N THR G 489 " --> pdb=" O VAL G 497 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL G 497 " --> pdb=" O THR G 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'G' and resid 525 through 530 removed outlier: 6.779A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 558 through 559 376 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.68 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: 6091 1.34 - 1.46: 3500 1.46 - 1.58: 9239 1.58 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 18893 Sorted by residual: bond pdb=" C LEU B 433 " pdb=" N SER B 434 " ideal model delta sigma weight residual 1.330 1.299 0.032 1.37e-02 5.33e+03 5.32e+00 bond pdb=" C LEU C 433 " pdb=" N SER C 434 " ideal model delta sigma weight residual 1.330 1.301 0.029 1.37e-02 5.33e+03 4.51e+00 bond pdb=" C LEU F 433 " pdb=" N SER F 434 " ideal model delta sigma weight residual 1.331 1.300 0.031 1.48e-02 4.57e+03 4.43e+00 bond pdb=" N ASP C 415 " pdb=" CA ASP C 415 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.96e+00 bond pdb=" N ASP B 415 " pdb=" CA ASP B 415 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.86e+00 ... (remaining 18888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 24173 2.10 - 4.19: 1237 4.19 - 6.29: 114 6.29 - 8.38: 47 8.38 - 10.48: 14 Bond angle restraints: 25585 Sorted by residual: angle pdb=" C LEU C 433 " pdb=" N SER C 434 " pdb=" CA SER C 434 " ideal model delta sigma weight residual 120.60 127.89 -7.29 1.53e+00 4.27e-01 2.27e+01 angle pdb=" C LEU B 433 " pdb=" N SER B 434 " pdb=" CA SER B 434 " ideal model delta sigma weight residual 120.60 127.66 -7.06 1.53e+00 4.27e-01 2.13e+01 angle pdb=" C ASP E 224 " pdb=" N ASN E 225 " pdb=" CA ASN E 225 " ideal model delta sigma weight residual 122.08 128.51 -6.43 1.47e+00 4.63e-01 1.91e+01 angle pdb=" C LEU F 433 " pdb=" N SER F 434 " pdb=" CA SER F 434 " ideal model delta sigma weight residual 121.03 127.94 -6.91 1.60e+00 3.91e-01 1.86e+01 angle pdb=" C ASP C 224 " pdb=" N ASN C 225 " pdb=" CA ASN C 225 " ideal model delta sigma weight residual 122.61 129.33 -6.72 1.56e+00 4.11e-01 1.85e+01 ... (remaining 25580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 10049 17.28 - 34.57: 1158 34.57 - 51.85: 288 51.85 - 69.14: 56 69.14 - 86.42: 13 Dihedral angle restraints: 11564 sinusoidal: 4578 harmonic: 6986 Sorted by residual: dihedral pdb=" CA ILE E 460 " pdb=" C ILE E 460 " pdb=" N ALA E 461 " pdb=" CA ALA E 461 " ideal model delta harmonic sigma weight residual 180.00 -136.42 -43.58 0 5.00e+00 4.00e-02 7.60e+01 dihedral pdb=" CA ILE C 460 " pdb=" C ILE C 460 " pdb=" N ALA C 461 " pdb=" CA ALA C 461 " ideal model delta harmonic sigma weight residual -180.00 -136.44 -43.56 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA ILE B 460 " pdb=" C ILE B 460 " pdb=" N ALA B 461 " pdb=" CA ALA B 461 " ideal model delta harmonic sigma weight residual -180.00 -136.47 -43.53 0 5.00e+00 4.00e-02 7.58e+01 ... (remaining 11561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2057 0.060 - 0.120: 679 0.120 - 0.180: 160 0.180 - 0.240: 18 0.240 - 0.300: 5 Chirality restraints: 2919 Sorted by residual: chirality pdb=" CB THR D 451 " pdb=" CA THR D 451 " pdb=" OG1 THR D 451 " pdb=" CG2 THR D 451 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB THR C 451 " pdb=" CA THR C 451 " pdb=" OG1 THR C 451 " pdb=" CG2 THR C 451 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB THR F 451 " pdb=" CA THR F 451 " pdb=" OG1 THR F 451 " pdb=" CG2 THR F 451 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2916 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 306 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C LYS B 306 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS B 306 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU B 307 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 306 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C LYS C 306 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS C 306 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU C 307 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 306 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C LYS F 306 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS F 306 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU F 307 " -0.018 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4904 2.79 - 3.32: 17213 3.32 - 3.84: 29143 3.84 - 4.37: 32522 4.37 - 4.90: 55312 Nonbonded interactions: 139094 Sorted by model distance: nonbonded pdb=" OG SER A 386 " pdb=" OD1 ASN A 463 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR B 438 " pdb=" O PRO B 440 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR C 438 " pdb=" O PRO C 440 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR F 438 " pdb=" O PRO F 440 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR D 438 " pdb=" O PRO D 440 " model vdw 2.265 3.040 ... (remaining 139089 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: 0.01 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.700 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.007 0.049 18893 Z= 0.333 Angle : 1.044 10.479 25585 Z= 0.582 Chirality : 0.062 0.300 2919 Planarity : 0.008 0.065 3339 Dihedral : 15.822 86.421 7084 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.34 % Favored : 84.66 % Rotamer: Outliers : 0.58 % Allowed : 12.94 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -5.16 (0.13), residues: 2366 helix: -4.30 (0.12), residues: 371 sheet: -2.20 (0.21), residues: 518 loop : -3.87 (0.12), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 458 TYR 0.020 0.002 TYR F 261 PHE 0.032 0.006 PHE B 580 TRP 0.014 0.003 TRP G 503 HIS 0.006 0.003 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00724 (18893) covalent geometry : angle 1.04359 (25585) hydrogen bonds : bond 0.17745 ( 376) hydrogen bonds : angle 8.57720 ( 972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 472 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8748 (tm-30) REVERT: A 565 TYR cc_start: 0.6597 (m-80) cc_final: 0.6328 (m-10) REVERT: B 403 MET cc_start: 0.8547 (mtp) cc_final: 0.8283 (mtm) REVERT: B 432 ASN cc_start: 0.8095 (p0) cc_final: 0.7703 (p0) REVERT: B 509 GLN cc_start: 0.9305 (tt0) cc_final: 0.9103 (tt0) REVERT: B 533 LYS cc_start: 0.8970 (tttm) cc_final: 0.8403 (tttp) REVERT: B 583 ASN cc_start: 0.6175 (t0) cc_final: 0.5949 (t0) REVERT: B 607 ARG cc_start: 0.8615 (ttt180) cc_final: 0.7860 (ttt180) REVERT: C 520 ASP cc_start: 0.8931 (p0) cc_final: 0.8700 (p0) REVERT: C 533 LYS cc_start: 0.8778 (tttt) cc_final: 0.8169 (ttpt) REVERT: C 552 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8694 (tm-30) REVERT: C 565 TYR cc_start: 0.7027 (m-80) cc_final: 0.6638 (m-10) REVERT: D 235 TYR cc_start: 0.8938 (p90) cc_final: 0.8389 (p90) REVERT: D 286 LYS cc_start: 0.8621 (mmmm) cc_final: 0.8322 (mtpt) REVERT: D 432 ASN cc_start: 0.8134 (p0) cc_final: 0.7243 (p0) REVERT: D 533 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8430 (ttpt) REVERT: D 544 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8207 (pm20) REVERT: D 549 GLU cc_start: 0.8781 (tt0) cc_final: 0.8198 (pt0) REVERT: E 431 ASN cc_start: 0.7971 (m-40) cc_final: 0.7006 (m-40) REVERT: E 552 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8851 (tm-30) REVERT: E 607 ARG cc_start: 0.8713 (ttt180) cc_final: 0.8401 (tpt-90) REVERT: F 235 TYR cc_start: 0.9000 (p90) cc_final: 0.8387 (p90) REVERT: F 237 ILE cc_start: 0.9278 (mm) cc_final: 0.9008 (mt) REVERT: F 311 THR cc_start: 0.8013 (p) cc_final: 0.7761 (p) REVERT: F 437 ASP cc_start: 0.8848 (m-30) cc_final: 0.8612 (m-30) REVERT: F 533 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8247 (tppp) REVERT: F 552 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8809 (tm-30) REVERT: G 283 LYS cc_start: 0.8752 (mmtp) cc_final: 0.8546 (mmtt) REVERT: G 533 LYS cc_start: 0.8842 (ttpp) cc_final: 0.8494 (ttmm) REVERT: G 552 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8733 (tm-30) REVERT: G 607 ARG cc_start: 0.8649 (ttt180) cc_final: 0.8352 (tpt-90) outliers start: 12 outliers final: 5 residues processed: 481 average time/residue: 0.1333 time to fit residues: 97.5157 Evaluate side-chains 376 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 371 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 397 ASN A 450 ASN A 475 GLN A 501 ASN B 225 ASN B 312 ASN B 314 HIS B 382 ASN B 397 ASN B 450 ASN B 475 GLN B 486 ASN B 501 ASN C 225 ASN C 312 ASN C 382 ASN C 397 ASN C 475 GLN C 501 ASN C 509 GLN D 475 GLN D 501 ASN E 225 ASN E 312 ASN E 382 ASN E 397 ASN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 GLN E 486 ASN E 501 ASN F 382 ASN F 450 ASN F 475 GLN F 486 ASN F 501 ASN G 382 ASN G 397 ASN G 425 GLN G 450 ASN G 475 GLN G 486 ASN G 501 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120560 restraints weight = 35981.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123849 restraints weight = 20295.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126063 restraints weight = 13735.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127476 restraints weight = 10586.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128385 restraints weight = 8938.276| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18893 Z= 0.141 Angle : 0.669 6.605 25585 Z= 0.366 Chirality : 0.047 0.163 2919 Planarity : 0.005 0.059 3339 Dihedral : 7.011 41.665 2555 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 0.34 % Allowed : 4.62 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -4.43 (0.14), residues: 2366 helix: -3.36 (0.19), residues: 378 sheet: -2.02 (0.20), residues: 518 loop : -3.36 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 607 TYR 0.013 0.001 TYR D 396 PHE 0.025 0.003 PHE B 566 TRP 0.005 0.001 TRP C 503 HIS 0.002 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00303 (18893) covalent geometry : angle 0.66888 (25585) hydrogen bonds : bond 0.04389 ( 376) hydrogen bonds : angle 7.44412 ( 972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 503 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8652 (tm-30) REVERT: A 609 MET cc_start: 0.8649 (ppp) cc_final: 0.8341 (ppp) REVERT: B 269 ASP cc_start: 0.9052 (p0) cc_final: 0.8791 (p0) REVERT: B 403 MET cc_start: 0.8423 (mtp) cc_final: 0.8089 (mtm) REVERT: B 533 LYS cc_start: 0.9015 (tttm) cc_final: 0.8615 (tttm) REVERT: C 533 LYS cc_start: 0.8862 (tttt) cc_final: 0.8243 (ttpt) REVERT: C 549 GLU cc_start: 0.8569 (tt0) cc_final: 0.8308 (pt0) REVERT: C 565 TYR cc_start: 0.6741 (m-80) cc_final: 0.6434 (m-10) REVERT: C 614 LYS cc_start: 0.9384 (tptt) cc_final: 0.9090 (mmtp) REVERT: D 286 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8081 (mtpt) REVERT: D 311 THR cc_start: 0.7729 (p) cc_final: 0.7527 (p) REVERT: D 432 ASN cc_start: 0.7793 (p0) cc_final: 0.7095 (p0) REVERT: D 482 GLN cc_start: 0.7652 (pt0) cc_final: 0.7450 (pt0) REVERT: D 533 LYS cc_start: 0.8988 (tttt) cc_final: 0.8279 (ttpt) REVERT: D 583 ASN cc_start: 0.6430 (t0) cc_final: 0.6223 (t0) REVERT: E 431 ASN cc_start: 0.7382 (m-40) cc_final: 0.6707 (m-40) REVERT: E 533 LYS cc_start: 0.8871 (ttpt) cc_final: 0.7916 (ttpt) REVERT: E 544 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8016 (pm20) REVERT: E 552 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8764 (tm-30) REVERT: F 235 TYR cc_start: 0.8957 (p90) cc_final: 0.8562 (p90) REVERT: F 463 ASN cc_start: 0.6583 (t0) cc_final: 0.6306 (t0) REVERT: F 533 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8175 (tppp) REVERT: F 552 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8612 (tm-30) REVERT: G 269 ASP cc_start: 0.9023 (p0) cc_final: 0.8722 (p0) REVERT: G 283 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8359 (mmtt) REVERT: G 311 THR cc_start: 0.7710 (p) cc_final: 0.7453 (p) REVERT: G 533 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8056 (tppp) REVERT: G 552 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8664 (tm-30) REVERT: G 607 ARG cc_start: 0.8540 (ttt180) cc_final: 0.8329 (ttt180) outliers start: 7 outliers final: 3 residues processed: 505 average time/residue: 0.1265 time to fit residues: 98.1882 Evaluate side-chains 389 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 386 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 52 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 193 optimal weight: 0.8980 chunk 158 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 501 ASN C 486 ASN C 501 ASN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 486 ASN E 501 ASN F 397 ASN F 610 ASN ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN G 450 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115943 restraints weight = 36792.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119208 restraints weight = 20778.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121315 restraints weight = 14060.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122681 restraints weight = 10844.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123558 restraints weight = 9187.581| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 18893 Z= 0.230 Angle : 0.734 7.829 25585 Z= 0.400 Chirality : 0.049 0.181 2919 Planarity : 0.005 0.052 3339 Dihedral : 7.072 39.536 2555 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.10 % Favored : 83.90 % Rotamer: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -4.19 (0.15), residues: 2366 helix: -2.83 (0.22), residues: 378 sheet: -1.89 (0.21), residues: 490 loop : -3.27 (0.14), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 529 TYR 0.014 0.002 TYR E 274 PHE 0.035 0.005 PHE E 249 TRP 0.008 0.002 TRP B 503 HIS 0.004 0.002 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00510 (18893) covalent geometry : angle 0.73370 (25585) hydrogen bonds : bond 0.05123 ( 376) hydrogen bonds : angle 7.28505 ( 972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 461 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8074 (mt-10) REVERT: A 311 THR cc_start: 0.7796 (p) cc_final: 0.7578 (p) REVERT: A 533 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8111 (tppp) REVERT: A 552 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8715 (tm-30) REVERT: B 285 ILE cc_start: 0.8958 (mt) cc_final: 0.8746 (mt) REVERT: B 509 GLN cc_start: 0.9440 (tt0) cc_final: 0.9233 (tt0) REVERT: B 533 LYS cc_start: 0.8976 (tttm) cc_final: 0.8470 (tttm) REVERT: B 565 TYR cc_start: 0.6310 (m-10) cc_final: 0.6098 (m-80) REVERT: B 607 ARG cc_start: 0.8526 (ttt180) cc_final: 0.8222 (tpt-90) REVERT: B 609 MET cc_start: 0.8769 (ppp) cc_final: 0.8376 (ppp) REVERT: C 246 GLU cc_start: 0.6416 (pm20) cc_final: 0.6081 (pm20) REVERT: C 288 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 499 GLU cc_start: 0.7480 (pp20) cc_final: 0.7086 (pp20) REVERT: C 520 ASP cc_start: 0.8604 (p0) cc_final: 0.7641 (t70) REVERT: C 533 LYS cc_start: 0.8840 (tttt) cc_final: 0.8115 (ttpt) REVERT: C 607 ARG cc_start: 0.8607 (ttt180) cc_final: 0.8399 (ttt-90) REVERT: C 609 MET cc_start: 0.8877 (ppp) cc_final: 0.8607 (ppp) REVERT: D 246 GLU cc_start: 0.6310 (pm20) cc_final: 0.5983 (pm20) REVERT: D 286 LYS cc_start: 0.8466 (mmmm) cc_final: 0.8177 (mtpt) REVERT: D 311 THR cc_start: 0.7877 (p) cc_final: 0.7669 (p) REVERT: D 432 ASN cc_start: 0.7936 (p0) cc_final: 0.7331 (p0) REVERT: D 533 LYS cc_start: 0.8993 (tttt) cc_final: 0.8151 (ttpt) REVERT: D 609 MET cc_start: 0.8825 (ppp) cc_final: 0.8437 (ppp) REVERT: E 533 LYS cc_start: 0.8765 (ttpt) cc_final: 0.7768 (ttpt) REVERT: F 275 GLU cc_start: 0.8468 (tt0) cc_final: 0.8245 (tt0) REVERT: F 311 THR cc_start: 0.7930 (p) cc_final: 0.7695 (p) REVERT: F 533 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8034 (tppp) REVERT: F 609 MET cc_start: 0.8852 (ppp) cc_final: 0.8371 (ppp) REVERT: F 610 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.7856 (p0) REVERT: G 269 ASP cc_start: 0.9037 (p0) cc_final: 0.8834 (p0) REVERT: G 283 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8473 (mmtt) REVERT: G 311 THR cc_start: 0.7887 (p) cc_final: 0.7680 (p) REVERT: G 499 GLU cc_start: 0.7528 (pp20) cc_final: 0.7082 (pp20) REVERT: G 533 LYS cc_start: 0.8805 (ttpp) cc_final: 0.8120 (tppp) outliers start: 2 outliers final: 0 residues processed: 462 average time/residue: 0.1295 time to fit residues: 90.5701 Evaluate side-chains 361 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 123 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 26 optimal weight: 0.0270 chunk 202 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 overall best weight: 3.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 486 ASN A 501 ASN B 382 ASN B 450 ASN C 450 ASN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN E 392 ASN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN F 450 ASN G 425 GLN G 463 ASN G 509 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117288 restraints weight = 36674.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120488 restraints weight = 20581.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122676 restraints weight = 13872.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124089 restraints weight = 10664.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124997 restraints weight = 8981.783| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18893 Z= 0.192 Angle : 0.692 8.722 25585 Z= 0.378 Chirality : 0.048 0.182 2919 Planarity : 0.005 0.049 3339 Dihedral : 6.824 40.178 2555 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Rotamer: Outliers : 0.29 % Allowed : 4.09 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.15), residues: 2366 helix: -2.48 (0.24), residues: 378 sheet: -1.72 (0.21), residues: 483 loop : -3.19 (0.14), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 529 TYR 0.018 0.001 TYR B 526 PHE 0.024 0.004 PHE A 566 TRP 0.006 0.001 TRP B 503 HIS 0.003 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00427 (18893) covalent geometry : angle 0.69179 (25585) hydrogen bonds : bond 0.04492 ( 376) hydrogen bonds : angle 6.98021 ( 972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 481 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 THR cc_start: 0.7739 (p) cc_final: 0.7509 (p) REVERT: A 529 ARG cc_start: 0.7855 (mpt-90) cc_final: 0.7571 (mmt90) REVERT: A 533 LYS cc_start: 0.8642 (ttpp) cc_final: 0.8160 (tppp) REVERT: A 552 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8878 (tm-30) REVERT: A 565 TYR cc_start: 0.5978 (m-80) cc_final: 0.5661 (m-80) REVERT: A 609 MET cc_start: 0.8668 (ppp) cc_final: 0.8447 (ppp) REVERT: B 533 LYS cc_start: 0.9002 (tttm) cc_final: 0.8569 (tttm) REVERT: B 609 MET cc_start: 0.8624 (ppp) cc_final: 0.8419 (ppp) REVERT: C 499 GLU cc_start: 0.7477 (pp20) cc_final: 0.7096 (pp20) REVERT: C 533 LYS cc_start: 0.8860 (tttt) cc_final: 0.8091 (ttpt) REVERT: C 549 GLU cc_start: 0.8690 (tt0) cc_final: 0.8436 (pt0) REVERT: C 609 MET cc_start: 0.8821 (ppp) cc_final: 0.8582 (ppp) REVERT: D 246 GLU cc_start: 0.6410 (pm20) cc_final: 0.6007 (pm20) REVERT: D 311 THR cc_start: 0.7792 (p) cc_final: 0.7553 (p) REVERT: D 432 ASN cc_start: 0.7880 (p0) cc_final: 0.7260 (p0) REVERT: D 529 ARG cc_start: 0.7845 (mmt90) cc_final: 0.7485 (mmt90) REVERT: D 533 LYS cc_start: 0.9002 (tttt) cc_final: 0.8093 (ttpt) REVERT: D 609 MET cc_start: 0.8722 (ppp) cc_final: 0.8397 (ppp) REVERT: D 612 LEU cc_start: 0.9122 (tt) cc_final: 0.8873 (tt) REVERT: D 614 LYS cc_start: 0.9256 (mmtm) cc_final: 0.9046 (mmtp) REVERT: E 533 LYS cc_start: 0.8777 (ttpt) cc_final: 0.7850 (ttpt) REVERT: E 544 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8278 (pm20) REVERT: F 275 GLU cc_start: 0.8500 (tt0) cc_final: 0.8281 (tt0) REVERT: F 533 LYS cc_start: 0.8705 (ttpp) cc_final: 0.8000 (tppp) REVERT: F 610 ASN cc_start: 0.8408 (p0) cc_final: 0.8097 (p0) REVERT: G 283 LYS cc_start: 0.8669 (mmtp) cc_final: 0.8431 (mmtt) REVERT: G 311 THR cc_start: 0.7917 (p) cc_final: 0.7696 (p) REVERT: G 499 GLU cc_start: 0.7583 (pp20) cc_final: 0.7161 (pp20) REVERT: G 533 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8297 (ttpp) outliers start: 6 outliers final: 0 residues processed: 481 average time/residue: 0.1342 time to fit residues: 98.2541 Evaluate side-chains 383 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 58 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 463 ASN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN D 463 ASN F 450 ASN F 463 ASN G 425 GLN G 450 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119762 restraints weight = 36217.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122953 restraints weight = 20396.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125076 restraints weight = 13830.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126442 restraints weight = 10657.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127306 restraints weight = 8986.084| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18893 Z= 0.147 Angle : 0.655 8.020 25585 Z= 0.357 Chirality : 0.047 0.176 2919 Planarity : 0.005 0.050 3339 Dihedral : 6.570 39.971 2555 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.95 % Favored : 86.05 % Rotamer: Outliers : 0.19 % Allowed : 2.26 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.15), residues: 2366 helix: -2.32 (0.24), residues: 378 sheet: -1.66 (0.21), residues: 483 loop : -3.04 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 529 TYR 0.016 0.001 TYR D 565 PHE 0.018 0.003 PHE F 566 TRP 0.005 0.001 TRP B 503 HIS 0.003 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00327 (18893) covalent geometry : angle 0.65492 (25585) hydrogen bonds : bond 0.03992 ( 376) hydrogen bonds : angle 6.75430 ( 972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 483 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8192 (tppp) REVERT: A 552 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8820 (tm-30) REVERT: A 565 TYR cc_start: 0.6240 (m-80) cc_final: 0.5869 (m-10) REVERT: A 609 MET cc_start: 0.8588 (ppp) cc_final: 0.8370 (ppp) REVERT: B 533 LYS cc_start: 0.9040 (tttm) cc_final: 0.8631 (tttm) REVERT: C 499 GLU cc_start: 0.7446 (pp20) cc_final: 0.7125 (pp20) REVERT: C 533 LYS cc_start: 0.8911 (tttt) cc_final: 0.8178 (ttpt) REVERT: C 549 GLU cc_start: 0.8566 (tt0) cc_final: 0.8322 (pt0) REVERT: D 246 GLU cc_start: 0.6192 (pm20) cc_final: 0.5837 (pm20) REVERT: D 311 THR cc_start: 0.7786 (p) cc_final: 0.7562 (p) REVERT: D 432 ASN cc_start: 0.7837 (p0) cc_final: 0.7218 (p0) REVERT: D 499 GLU cc_start: 0.7514 (pp20) cc_final: 0.7028 (pp20) REVERT: D 529 ARG cc_start: 0.7455 (mpt-90) cc_final: 0.7131 (mmt90) REVERT: D 533 LYS cc_start: 0.8999 (tttt) cc_final: 0.8071 (ttpt) REVERT: D 609 MET cc_start: 0.8810 (ppp) cc_final: 0.8461 (ppp) REVERT: D 612 LEU cc_start: 0.9185 (tt) cc_final: 0.8885 (tt) REVERT: D 614 LYS cc_start: 0.9257 (mmtm) cc_final: 0.9057 (mmtp) REVERT: E 533 LYS cc_start: 0.8776 (ttpt) cc_final: 0.7999 (ttpt) REVERT: F 269 ASP cc_start: 0.9066 (p0) cc_final: 0.8713 (p0) REVERT: F 275 GLU cc_start: 0.8292 (tt0) cc_final: 0.8025 (tt0) REVERT: F 533 LYS cc_start: 0.8666 (ttpp) cc_final: 0.7902 (tppp) REVERT: F 609 MET cc_start: 0.8552 (ppp) cc_final: 0.8324 (ppp) REVERT: F 610 ASN cc_start: 0.8352 (p0) cc_final: 0.7988 (p0) REVERT: G 269 ASP cc_start: 0.9161 (p0) cc_final: 0.8784 (p0) REVERT: G 283 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8385 (mmtt) REVERT: G 533 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8321 (ttpp) outliers start: 4 outliers final: 2 residues processed: 483 average time/residue: 0.1247 time to fit residues: 93.0075 Evaluate side-chains 392 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 390 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 0.0980 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN C 450 ASN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN D 501 ASN E 509 GLN ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN F 501 ASN G 425 GLN G 450 ASN G 501 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114867 restraints weight = 36588.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118092 restraints weight = 20510.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120207 restraints weight = 13893.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121593 restraints weight = 10684.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122464 restraints weight = 9023.319| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 18893 Z= 0.253 Angle : 0.753 8.345 25585 Z= 0.410 Chirality : 0.050 0.188 2919 Planarity : 0.005 0.063 3339 Dihedral : 7.011 39.469 2555 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.93 % Favored : 84.07 % Rotamer: Outliers : 0.14 % Allowed : 2.74 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.15), residues: 2366 helix: -2.11 (0.25), residues: 378 sheet: -1.92 (0.23), residues: 413 loop : -3.15 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 529 TYR 0.018 0.002 TYR A 274 PHE 0.037 0.005 PHE B 566 TRP 0.010 0.002 TRP C 503 HIS 0.004 0.002 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00566 (18893) covalent geometry : angle 0.75326 (25585) hydrogen bonds : bond 0.04933 ( 376) hydrogen bonds : angle 7.10343 ( 972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 456 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 THR cc_start: 0.7741 (p) cc_final: 0.7507 (p) REVERT: A 499 GLU cc_start: 0.7515 (pp20) cc_final: 0.7098 (pp20) REVERT: A 533 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8024 (tppp) REVERT: A 552 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8802 (tm-30) REVERT: A 565 TYR cc_start: 0.6196 (m-80) cc_final: 0.5780 (m-10) REVERT: B 509 GLN cc_start: 0.9450 (tt0) cc_final: 0.9249 (tt0) REVERT: B 533 LYS cc_start: 0.8983 (tttm) cc_final: 0.8370 (tttp) REVERT: B 609 MET cc_start: 0.8593 (ppp) cc_final: 0.8358 (ppp) REVERT: B 612 LEU cc_start: 0.9156 (tp) cc_final: 0.8925 (tt) REVERT: C 533 LYS cc_start: 0.8932 (tttt) cc_final: 0.8196 (ttpt) REVERT: C 549 GLU cc_start: 0.8687 (tt0) cc_final: 0.8279 (pt0) REVERT: C 609 MET cc_start: 0.8760 (ppp) cc_final: 0.8505 (ppp) REVERT: D 246 GLU cc_start: 0.6162 (pm20) cc_final: 0.5499 (pm20) REVERT: D 311 THR cc_start: 0.7912 (p) cc_final: 0.7663 (p) REVERT: D 426 GLU cc_start: 0.7929 (pt0) cc_final: 0.7639 (pt0) REVERT: D 432 ASN cc_start: 0.7897 (p0) cc_final: 0.7298 (p0) REVERT: D 499 GLU cc_start: 0.7626 (pp20) cc_final: 0.7066 (pp20) REVERT: D 529 ARG cc_start: 0.7634 (mpt-90) cc_final: 0.7079 (mmt90) REVERT: D 533 LYS cc_start: 0.8993 (tttt) cc_final: 0.8650 (ttpt) REVERT: D 610 ASN cc_start: 0.8510 (p0) cc_final: 0.8267 (p0) REVERT: F 275 GLU cc_start: 0.8424 (tt0) cc_final: 0.8216 (tt0) REVERT: F 533 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8006 (tppp) REVERT: F 609 MET cc_start: 0.8640 (ppp) cc_final: 0.8391 (ppp) REVERT: F 610 ASN cc_start: 0.8411 (p0) cc_final: 0.7974 (p0) REVERT: G 283 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8415 (mmtt) REVERT: G 533 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8365 (ttpp) outliers start: 3 outliers final: 0 residues processed: 456 average time/residue: 0.1244 time to fit residues: 87.2580 Evaluate side-chains 362 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 92 optimal weight: 10.0000 chunk 39 optimal weight: 0.0670 chunk 75 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 overall best weight: 2.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 450 ASN A 463 ASN A 501 ASN B 450 ASN B 501 ASN D 425 GLN D 450 ASN D 463 ASN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN E 501 ASN F 450 ASN F 463 ASN F 501 ASN G 425 GLN G 463 ASN G 501 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118110 restraints weight = 36581.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121348 restraints weight = 20592.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123447 restraints weight = 13890.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124784 restraints weight = 10693.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125489 restraints weight = 9054.874| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18893 Z= 0.174 Angle : 0.692 8.090 25585 Z= 0.375 Chirality : 0.048 0.171 2919 Planarity : 0.005 0.055 3339 Dihedral : 6.748 39.933 2555 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 0.24 % Allowed : 1.20 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.16), residues: 2366 helix: -1.95 (0.26), residues: 378 sheet: -1.61 (0.21), residues: 483 loop : -3.06 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 529 TYR 0.025 0.001 TYR C 526 PHE 0.028 0.004 PHE C 566 TRP 0.005 0.001 TRP B 503 HIS 0.003 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00389 (18893) covalent geometry : angle 0.69214 (25585) hydrogen bonds : bond 0.04241 ( 376) hydrogen bonds : angle 6.85455 ( 972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 474 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.9028 (p90) cc_final: 0.8540 (p90) REVERT: A 499 GLU cc_start: 0.7412 (pp20) cc_final: 0.7017 (pp20) REVERT: A 533 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8163 (tppp) REVERT: A 552 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8752 (tm-30) REVERT: A 565 TYR cc_start: 0.6163 (m-80) cc_final: 0.5716 (m-10) REVERT: B 285 ILE cc_start: 0.8881 (mt) cc_final: 0.8668 (mt) REVERT: B 612 LEU cc_start: 0.9236 (tp) cc_final: 0.9010 (tt) REVERT: C 520 ASP cc_start: 0.8606 (p0) cc_final: 0.7871 (t70) REVERT: C 524 GLU cc_start: 0.8766 (pt0) cc_final: 0.8508 (pt0) REVERT: C 533 LYS cc_start: 0.8941 (tttt) cc_final: 0.8247 (ttpt) REVERT: C 549 GLU cc_start: 0.8648 (tt0) cc_final: 0.8344 (pt0) REVERT: D 311 THR cc_start: 0.7779 (p) cc_final: 0.7557 (p) REVERT: D 426 GLU cc_start: 0.7873 (pt0) cc_final: 0.7591 (pt0) REVERT: D 432 ASN cc_start: 0.7856 (p0) cc_final: 0.7213 (p0) REVERT: D 499 GLU cc_start: 0.7573 (pp20) cc_final: 0.7067 (pp20) REVERT: D 529 ARG cc_start: 0.7605 (mpt-90) cc_final: 0.7019 (mmt90) REVERT: D 533 LYS cc_start: 0.9003 (tttt) cc_final: 0.8688 (ttpt) REVERT: D 609 MET cc_start: 0.8604 (ppp) cc_final: 0.8386 (ppp) REVERT: D 612 LEU cc_start: 0.9209 (tt) cc_final: 0.8989 (tt) REVERT: F 275 GLU cc_start: 0.8391 (tt0) cc_final: 0.8144 (tt0) REVERT: F 533 LYS cc_start: 0.8758 (ttpp) cc_final: 0.8037 (tppp) REVERT: F 610 ASN cc_start: 0.8445 (p0) cc_final: 0.8055 (p0) REVERT: G 269 ASP cc_start: 0.9017 (p0) cc_final: 0.8628 (p0) REVERT: G 533 LYS cc_start: 0.8820 (ttpp) cc_final: 0.8291 (ttpp) REVERT: G 609 MET cc_start: 0.8744 (ppp) cc_final: 0.8520 (ppp) outliers start: 5 outliers final: 2 residues processed: 474 average time/residue: 0.1234 time to fit residues: 89.8739 Evaluate side-chains 389 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 387 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 62 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 210 optimal weight: 0.3980 chunk 219 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 450 ASN C 450 ASN C 501 ASN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN D 501 ASN F 450 ASN F 463 ASN G 425 GLN G 450 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124059 restraints weight = 36007.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127406 restraints weight = 20443.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129560 restraints weight = 13812.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131015 restraints weight = 10626.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131930 restraints weight = 8975.603| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18893 Z= 0.112 Angle : 0.632 7.497 25585 Z= 0.341 Chirality : 0.045 0.168 2919 Planarity : 0.005 0.068 3339 Dihedral : 6.155 41.142 2555 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 0.24 % Allowed : 1.01 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.16), residues: 2366 helix: -1.90 (0.26), residues: 364 sheet: -1.47 (0.22), residues: 483 loop : -2.80 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 529 TYR 0.021 0.001 TYR A 274 PHE 0.037 0.002 PHE D 566 TRP 0.008 0.001 TRP E 503 HIS 0.002 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00241 (18893) covalent geometry : angle 0.63165 (25585) hydrogen bonds : bond 0.03415 ( 376) hydrogen bonds : angle 6.46260 ( 972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 523 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8997 (p90) cc_final: 0.8633 (p90) REVERT: A 425 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8008 (mm-40) REVERT: A 479 GLU cc_start: 0.7900 (mp0) cc_final: 0.7690 (mm-30) REVERT: A 499 GLU cc_start: 0.7218 (pp20) cc_final: 0.6913 (pp20) REVERT: A 533 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8160 (tppp) REVERT: A 565 TYR cc_start: 0.6292 (m-80) cc_final: 0.5711 (m-80) REVERT: B 533 LYS cc_start: 0.9077 (tttm) cc_final: 0.8683 (tttm) REVERT: C 293 LEU cc_start: 0.8454 (mt) cc_final: 0.8182 (mt) REVERT: C 520 ASP cc_start: 0.8682 (p0) cc_final: 0.7940 (t70) REVERT: C 524 GLU cc_start: 0.8691 (pt0) cc_final: 0.8399 (pt0) REVERT: C 533 LYS cc_start: 0.8943 (tttt) cc_final: 0.8300 (ttpt) REVERT: D 311 THR cc_start: 0.7660 (p) cc_final: 0.7446 (p) REVERT: D 389 ILE cc_start: 0.9344 (tt) cc_final: 0.8968 (mt) REVERT: D 426 GLU cc_start: 0.7982 (pt0) cc_final: 0.7658 (pt0) REVERT: D 432 ASN cc_start: 0.7653 (p0) cc_final: 0.7065 (p0) REVERT: D 499 GLU cc_start: 0.7290 (pp20) cc_final: 0.6867 (pp20) REVERT: D 529 ARG cc_start: 0.7694 (mpt-90) cc_final: 0.7149 (mmt90) REVERT: D 533 LYS cc_start: 0.8938 (tttt) cc_final: 0.8640 (ttpt) REVERT: D 566 PHE cc_start: 0.7048 (t80) cc_final: 0.6797 (t80) REVERT: D 609 MET cc_start: 0.8429 (ppp) cc_final: 0.8195 (ppp) REVERT: F 286 LYS cc_start: 0.8217 (mmmm) cc_final: 0.8005 (mmmm) REVERT: F 533 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8033 (tppp) REVERT: F 610 ASN cc_start: 0.8373 (p0) cc_final: 0.8001 (p0) REVERT: G 431 ASN cc_start: 0.7586 (m-40) cc_final: 0.7322 (m110) REVERT: G 533 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8075 (ttpp) REVERT: G 544 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8010 (pm20) REVERT: G 566 PHE cc_start: 0.6880 (t80) cc_final: 0.6672 (t80) outliers start: 5 outliers final: 1 residues processed: 523 average time/residue: 0.1172 time to fit residues: 95.3711 Evaluate side-chains 419 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 418 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 224 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 450 ASN A 463 ASN B 450 ASN C 450 ASN C 509 GLN D 450 ASN ** E 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN G 425 GLN G 450 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119473 restraints weight = 36512.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122684 restraints weight = 20798.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124845 restraints weight = 14144.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126218 restraints weight = 10960.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127126 restraints weight = 9313.768| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18893 Z= 0.176 Angle : 0.682 8.129 25585 Z= 0.368 Chirality : 0.047 0.171 2919 Planarity : 0.005 0.063 3339 Dihedral : 6.389 40.176 2555 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.44 % Favored : 86.56 % Rotamer: Outliers : 0.29 % Allowed : 0.58 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.16), residues: 2366 helix: -1.83 (0.25), residues: 371 sheet: -1.49 (0.22), residues: 483 loop : -2.78 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 529 TYR 0.028 0.001 TYR C 464 PHE 0.040 0.004 PHE D 566 TRP 0.009 0.001 TRP G 503 HIS 0.003 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00393 (18893) covalent geometry : angle 0.68214 (25585) hydrogen bonds : bond 0.04178 ( 376) hydrogen bonds : angle 6.58146 ( 972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 468 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.9047 (p90) cc_final: 0.8553 (p90) REVERT: A 499 GLU cc_start: 0.7342 (pp20) cc_final: 0.7006 (pp20) REVERT: A 533 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8159 (tppp) REVERT: A 565 TYR cc_start: 0.6329 (m-80) cc_final: 0.5739 (m-80) REVERT: B 533 LYS cc_start: 0.9081 (tttm) cc_final: 0.8660 (tttm) REVERT: C 246 GLU cc_start: 0.6670 (pm20) cc_final: 0.6399 (pm20) REVERT: C 520 ASP cc_start: 0.8630 (p0) cc_final: 0.7848 (t70) REVERT: C 524 GLU cc_start: 0.8739 (pt0) cc_final: 0.8390 (pt0) REVERT: C 533 LYS cc_start: 0.9012 (tttt) cc_final: 0.8353 (ttpt) REVERT: D 311 THR cc_start: 0.7710 (p) cc_final: 0.7483 (p) REVERT: D 426 GLU cc_start: 0.7967 (pt0) cc_final: 0.7662 (pt0) REVERT: D 432 ASN cc_start: 0.7818 (p0) cc_final: 0.7269 (p0) REVERT: D 499 GLU cc_start: 0.7528 (pp20) cc_final: 0.7038 (pp20) REVERT: D 533 LYS cc_start: 0.9031 (tttt) cc_final: 0.8704 (ttpt) REVERT: D 566 PHE cc_start: 0.7117 (t80) cc_final: 0.6848 (t80) REVERT: D 610 ASN cc_start: 0.8402 (p0) cc_final: 0.8058 (p0) REVERT: E 426 GLU cc_start: 0.8019 (pt0) cc_final: 0.7749 (pt0) REVERT: F 286 LYS cc_start: 0.8301 (mmmm) cc_final: 0.8073 (mmmm) REVERT: F 533 LYS cc_start: 0.8753 (ttpp) cc_final: 0.8006 (tppp) REVERT: F 610 ASN cc_start: 0.8407 (p0) cc_final: 0.7943 (p0) REVERT: G 288 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8152 (mt-10) REVERT: G 311 THR cc_start: 0.7845 (p) cc_final: 0.7635 (p) REVERT: G 431 ASN cc_start: 0.7791 (m-40) cc_final: 0.7467 (m110) REVERT: G 533 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8126 (ttpp) outliers start: 6 outliers final: 2 residues processed: 468 average time/residue: 0.1187 time to fit residues: 86.5954 Evaluate side-chains 394 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 392 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 174 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 141 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 450 ASN B 509 GLN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN F 450 ASN G 425 GLN G 450 ASN G 463 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121822 restraints weight = 36246.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125065 restraints weight = 20818.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127207 restraints weight = 14181.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128587 restraints weight = 11022.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.129353 restraints weight = 9383.476| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18893 Z= 0.137 Angle : 0.658 7.606 25585 Z= 0.355 Chirality : 0.046 0.173 2919 Planarity : 0.005 0.058 3339 Dihedral : 6.272 39.826 2555 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 0.24 % Allowed : 0.48 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.16), residues: 2366 helix: -1.86 (0.25), residues: 371 sheet: -1.47 (0.22), residues: 483 loop : -2.74 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 528 TYR 0.019 0.001 TYR A 526 PHE 0.039 0.003 PHE D 566 TRP 0.004 0.001 TRP B 503 HIS 0.002 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00303 (18893) covalent geometry : angle 0.65821 (25585) hydrogen bonds : bond 0.03753 ( 376) hydrogen bonds : angle 6.46471 ( 972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 487 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8185 (mm-40) REVERT: A 499 GLU cc_start: 0.7285 (pp20) cc_final: 0.6966 (pp20) REVERT: A 533 LYS cc_start: 0.8636 (ttpp) cc_final: 0.8169 (tppp) REVERT: A 565 TYR cc_start: 0.6326 (m-80) cc_final: 0.5711 (m-80) REVERT: B 533 LYS cc_start: 0.9089 (tttm) cc_final: 0.8658 (tttm) REVERT: C 246 GLU cc_start: 0.6615 (pm20) cc_final: 0.6409 (pm20) REVERT: C 293 LEU cc_start: 0.8418 (mt) cc_final: 0.8167 (mt) REVERT: C 520 ASP cc_start: 0.8669 (p0) cc_final: 0.7919 (t70) REVERT: C 533 LYS cc_start: 0.8992 (tttt) cc_final: 0.8357 (ttpt) REVERT: D 311 THR cc_start: 0.7636 (p) cc_final: 0.7407 (p) REVERT: D 426 GLU cc_start: 0.8109 (pt0) cc_final: 0.7777 (pt0) REVERT: D 432 ASN cc_start: 0.7672 (p0) cc_final: 0.7097 (p0) REVERT: D 499 GLU cc_start: 0.7351 (pp20) cc_final: 0.6868 (pp20) REVERT: D 529 ARG cc_start: 0.7839 (mpt-90) cc_final: 0.7322 (mmt90) REVERT: D 533 LYS cc_start: 0.8979 (tttt) cc_final: 0.8671 (ttpt) REVERT: D 566 PHE cc_start: 0.7140 (t80) cc_final: 0.6876 (t80) REVERT: D 610 ASN cc_start: 0.8325 (p0) cc_final: 0.8058 (p0) REVERT: E 246 GLU cc_start: 0.6073 (pm20) cc_final: 0.5694 (pm20) REVERT: E 426 GLU cc_start: 0.7910 (pt0) cc_final: 0.7598 (pt0) REVERT: E 533 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8062 (ptmt) REVERT: E 555 PHE cc_start: 0.7749 (m-10) cc_final: 0.7423 (m-10) REVERT: F 285 ILE cc_start: 0.8962 (mt) cc_final: 0.8759 (mt) REVERT: F 286 LYS cc_start: 0.8117 (mmmm) cc_final: 0.7900 (mmmm) REVERT: F 533 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8012 (tppp) REVERT: G 269 ASP cc_start: 0.8834 (p0) cc_final: 0.8599 (p0) REVERT: G 288 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7994 (mt-10) REVERT: G 311 THR cc_start: 0.7743 (p) cc_final: 0.7533 (p) REVERT: G 431 ASN cc_start: 0.7687 (m-40) cc_final: 0.7401 (m110) REVERT: G 533 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8094 (ttpp) REVERT: G 544 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8042 (pm20) REVERT: G 566 PHE cc_start: 0.6984 (t80) cc_final: 0.6775 (t80) outliers start: 5 outliers final: 2 residues processed: 487 average time/residue: 0.1218 time to fit residues: 92.2751 Evaluate side-chains 401 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 399 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN C 382 ASN C 450 ASN C 509 GLN D 450 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 GLN F 450 ASN G 425 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.147476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120523 restraints weight = 36548.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123749 restraints weight = 20846.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125880 restraints weight = 14246.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127248 restraints weight = 11064.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128120 restraints weight = 9421.876| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18893 Z= 0.158 Angle : 0.675 7.820 25585 Z= 0.365 Chirality : 0.047 0.171 2919 Planarity : 0.004 0.056 3339 Dihedral : 6.333 39.515 2555 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.16), residues: 2366 helix: -1.88 (0.25), residues: 371 sheet: -1.49 (0.22), residues: 483 loop : -2.70 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 529 TYR 0.019 0.001 TYR A 526 PHE 0.039 0.004 PHE D 566 TRP 0.008 0.001 TRP A 245 HIS 0.003 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00351 (18893) covalent geometry : angle 0.67540 (25585) hydrogen bonds : bond 0.04035 ( 376) hydrogen bonds : angle 6.51951 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.47 seconds wall clock time: 48 minutes 45.43 seconds (2925.43 seconds total)