Starting phenix.real_space_refine on Sat Sep 28 07:01:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/09_2024/6okr_20102.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/09_2024/6okr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/09_2024/6okr_20102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/09_2024/6okr_20102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/09_2024/6okr_20102.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6okr_20102/09_2024/6okr_20102.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 10.33, per 1000 atoms: 0.55 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: 4.36 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.40 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: 6.09 Time building geometry restraints manager: 5.10 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: 0.00 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 41.010 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- 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= 0.470 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 : 9.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.003 TRP G 503 HIS 0.006 0.003 HIS A 314 PHE 0.032 0.006 PHE B 580 TYR 0.020 0.002 TYR F 261 ARG 0.003 0.000 ARG B 458 *********************** 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 fitting. rotamer outliers: 12 poor density : 472 time to evaluate : 2.112 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: 0.8969 (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: 0.8695 (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: 0.8712 (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: 0.3068 time to fit residues: 221.4998 Evaluate side-chains 376 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 371 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 2.9990 chunk 180 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 GLN D 501 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18893 Z= 0.163 Angle : 0.654 6.315 25585 Z= 0.356 Chirality : 0.046 0.162 2919 Planarity : 0.005 0.058 3339 Dihedral : 6.900 41.888 2555 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 0.29 % Allowed : 4.23 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.14), residues: 2366 helix: -3.45 (0.18), residues: 378 sheet: -1.98 (0.20), residues: 518 loop : -3.35 (0.13), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 245 HIS 0.002 0.001 HIS F 314 PHE 0.024 0.003 PHE C 566 TYR 0.014 0.001 TYR D 396 ARG 0.002 0.000 ARG G 607 *********************** 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 531 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 525 time to evaluate : 2.373 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: symmetry clash REVERT: A 533 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8188 (tppp) REVERT: A 552 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8711 (tm-30) REVERT: B 269 ASP cc_start: 0.9056 (p0) cc_final: 0.8797 (p0) REVERT: B 283 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8395 (mmpt) REVERT: B 403 MET cc_start: 0.8427 (mtp) cc_final: 0.8115 (mtm) REVERT: B 533 LYS cc_start: 0.9035 (tttm) cc_final: 0.8609 (tttm) REVERT: C 533 LYS cc_start: 0.8816 (tttt) cc_final: 0.8175 (tttt) REVERT: C 549 GLU cc_start: 0.8636 (tt0) cc_final: 0.8153 (pt0) REVERT: C 565 TYR cc_start: 0.6983 (m-80) cc_final: 0.6645 (m-10) REVERT: C 614 LYS cc_start: 0.9332 (tptt) cc_final: 0.9069 (mmtp) REVERT: D 311 THR cc_start: 0.7634 (p) cc_final: 0.7399 (p) REVERT: D 432 ASN cc_start: 0.7744 (p0) cc_final: 0.7037 (p0) REVERT: D 482 GLN cc_start: 0.7576 (pt0) cc_final: 0.7327 (pt0) REVERT: D 533 LYS cc_start: 0.8940 (tttt) cc_final: 0.8281 (ttpt) REVERT: D 549 GLU cc_start: 0.8741 (tt0) cc_final: 0.8186 (pt0) REVERT: E 389 ILE cc_start: 0.9152 (tt) cc_final: 0.8932 (mt) REVERT: E 431 ASN cc_start: 0.7304 (m-40) cc_final: 0.6821 (m-40) REVERT: E 533 LYS cc_start: 0.8822 (ttpt) cc_final: 0.7912 (ttpt) REVERT: E 552 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8843 (tm-30) REVERT: F 235 TYR cc_start: 0.9029 (p90) cc_final: 0.8641 (p90) REVERT: F 463 ASN cc_start: 0.6419 (t0) cc_final: 0.6161 (t0) REVERT: F 533 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8066 (tppp) REVERT: F 552 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8738 (tm-30) REVERT: F 614 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8809 (mmtm) REVERT: G 269 ASP cc_start: 0.9019 (p0) cc_final: 0.8647 (p0) REVERT: G 283 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8352 (mmtt) REVERT: G 311 THR cc_start: 0.7591 (p) cc_final: 0.7333 (p) REVERT: G 533 LYS cc_start: 0.8865 (ttpp) cc_final: 0.7987 (tppp) REVERT: G 552 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8766 (tm-30) outliers start: 6 outliers final: 2 residues processed: 526 average time/residue: 0.3255 time to fit residues: 262.8974 Evaluate side-chains 393 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 391 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 214 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 382 ASN C 486 ASN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 486 ASN F 450 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18893 Z= 0.288 Angle : 0.702 8.066 25585 Z= 0.383 Chirality : 0.048 0.168 2919 Planarity : 0.005 0.047 3339 Dihedral : 6.854 39.727 2555 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.33 % Favored : 85.67 % Rotamer: Outliers : 0.19 % Allowed : 3.90 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.15), residues: 2366 helix: -2.88 (0.22), residues: 378 sheet: -1.85 (0.21), residues: 490 loop : -3.17 (0.14), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 503 HIS 0.003 0.001 HIS A 314 PHE 0.032 0.004 PHE E 249 TYR 0.016 0.001 TYR G 526 ARG 0.008 0.001 ARG E 529 *********************** 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 473 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 469 time to evaluate : 2.440 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 311 THR cc_start: 0.7789 (p) cc_final: 0.7556 (p) REVERT: A 533 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8027 (tppp) REVERT: A 552 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8793 (tm-30) REVERT: B 283 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8508 (mmpt) REVERT: B 403 MET cc_start: 0.8456 (mtp) cc_final: 0.8091 (mtm) REVERT: B 509 GLN cc_start: 0.9413 (tt0) cc_final: 0.9199 (tt0) REVERT: B 533 LYS cc_start: 0.9010 (tttm) cc_final: 0.8500 (tttm) REVERT: B 612 LEU cc_start: 0.9161 (tp) cc_final: 0.8920 (tt) REVERT: C 288 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7797 (mt-10) REVERT: C 499 GLU cc_start: 0.7372 (pp20) cc_final: 0.6986 (pp20) REVERT: C 520 ASP cc_start: 0.8612 (p0) cc_final: 0.7608 (t70) REVERT: C 533 LYS cc_start: 0.8814 (tttt) cc_final: 0.8108 (ttpt) REVERT: C 549 GLU cc_start: 0.8744 (tt0) cc_final: 0.8300 (pt0) REVERT: C 609 MET cc_start: 0.8840 (ppp) cc_final: 0.8596 (ppp) REVERT: D 246 GLU cc_start: 0.6456 (pm20) cc_final: 0.5977 (pm20) REVERT: D 311 THR cc_start: 0.7736 (p) cc_final: 0.7532 (p) REVERT: D 432 ASN cc_start: 0.7890 (p0) cc_final: 0.7223 (p0) REVERT: D 529 ARG cc_start: 0.7708 (mmt90) cc_final: 0.7468 (mmt90) REVERT: D 533 LYS cc_start: 0.8991 (tttt) cc_final: 0.8176 (ttpt) REVERT: D 609 MET cc_start: 0.8812 (ppp) cc_final: 0.8377 (ppp) REVERT: E 431 ASN cc_start: 0.7491 (m-40) cc_final: 0.6729 (m-40) REVERT: E 533 LYS cc_start: 0.8785 (ttpt) cc_final: 0.7768 (ttpp) REVERT: F 311 THR cc_start: 0.7902 (p) cc_final: 0.7671 (p) REVERT: F 533 LYS cc_start: 0.8658 (ttpp) cc_final: 0.7971 (tppp) REVERT: F 609 MET cc_start: 0.8816 (ppp) cc_final: 0.8344 (ppp) REVERT: F 610 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.7903 (p0) REVERT: G 283 LYS cc_start: 0.8680 (mmtp) cc_final: 0.8475 (mmtt) REVERT: G 311 THR cc_start: 0.7773 (p) cc_final: 0.7515 (p) REVERT: G 499 GLU cc_start: 0.7542 (pp20) cc_final: 0.7136 (pp20) REVERT: G 533 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8141 (ttpp) outliers start: 4 outliers final: 0 residues processed: 471 average time/residue: 0.3101 time to fit residues: 224.0756 Evaluate side-chains 367 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 366 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 112 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 145 optimal weight: 6.9990 chunk 217 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 overall best weight: 2.2562 ------------------------------------------------------------------------------- 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 450 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** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN F 450 ASN G 425 GLN G 509 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2290 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= 0.217 Angle : 0.652 7.546 25585 Z= 0.356 Chirality : 0.047 0.187 2919 Planarity : 0.005 0.047 3339 Dihedral : 6.567 39.235 2555 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 0.19 % Allowed : 3.22 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.15), residues: 2366 helix: -2.60 (0.23), residues: 378 sheet: -1.68 (0.21), residues: 483 loop : -3.02 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 245 HIS 0.003 0.001 HIS A 314 PHE 0.022 0.003 PHE A 566 TYR 0.024 0.001 TYR G 526 ARG 0.006 0.001 ARG E 529 *********************** 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 492 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 488 time to evaluate : 2.430 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: symmetry clash revert: symmetry clash REVERT: A 237 ILE cc_start: 0.9412 (mp) cc_final: 0.9060 (mt) REVERT: A 288 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8213 (mt-10) REVERT: A 311 THR cc_start: 0.7736 (p) cc_final: 0.7516 (p) REVERT: A 533 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8050 (tppp) REVERT: A 609 MET cc_start: 0.8629 (ppp) cc_final: 0.8331 (ppp) REVERT: B 283 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8452 (mmpt) REVERT: B 533 LYS cc_start: 0.8974 (tttm) cc_final: 0.8435 (tttm) REVERT: B 609 MET cc_start: 0.8683 (ppp) cc_final: 0.8439 (ppp) REVERT: C 288 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7812 (mt-10) REVERT: C 499 GLU cc_start: 0.7423 (pp20) cc_final: 0.7065 (pp20) REVERT: C 533 LYS cc_start: 0.8849 (tttt) cc_final: 0.8143 (ttpt) REVERT: C 609 MET cc_start: 0.8788 (ppp) cc_final: 0.8556 (ppp) REVERT: D 311 THR cc_start: 0.7792 (p) cc_final: 0.7552 (p) REVERT: D 426 GLU cc_start: 0.7689 (pt0) cc_final: 0.7433 (pt0) REVERT: D 432 ASN cc_start: 0.7831 (p0) cc_final: 0.7168 (p0) REVERT: D 529 ARG cc_start: 0.7695 (mmt90) cc_final: 0.7362 (mmt90) REVERT: D 533 LYS cc_start: 0.8966 (tttt) cc_final: 0.8113 (ttpt) REVERT: D 609 MET cc_start: 0.8674 (ppp) cc_final: 0.8448 (ppp) REVERT: E 533 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8000 (ttpt) REVERT: F 533 LYS cc_start: 0.8645 (ttpp) cc_final: 0.7947 (tppp) REVERT: F 610 ASN cc_start: 0.8387 (p0) cc_final: 0.8142 (p0) REVERT: G 269 ASP cc_start: 0.9130 (p0) cc_final: 0.8918 (p0) REVERT: G 311 THR cc_start: 0.7909 (p) cc_final: 0.7660 (p) REVERT: G 533 LYS cc_start: 0.8761 (ttpp) cc_final: 0.8302 (ttpp) outliers start: 4 outliers final: 2 residues processed: 488 average time/residue: 0.2934 time to fit residues: 220.7521 Evaluate side-chains 386 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 384 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 196 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN B 382 ASN B 501 ASN C 390 ASN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN G 252 GLN G 425 GLN G 450 ASN G 509 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18893 Z= 0.225 Angle : 0.653 8.059 25585 Z= 0.356 Chirality : 0.047 0.173 2919 Planarity : 0.004 0.048 3339 Dihedral : 6.497 39.499 2555 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.40 % Favored : 86.60 % Rotamer: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.15), residues: 2366 helix: -2.38 (0.24), residues: 378 sheet: -1.66 (0.21), residues: 483 loop : -2.96 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 503 HIS 0.003 0.001 HIS C 314 PHE 0.017 0.003 PHE B 249 TYR 0.011 0.001 TYR A 274 ARG 0.007 0.001 ARG E 529 *********************** 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 485 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 483 time to evaluate : 2.262 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 288 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8174 (mt-10) REVERT: A 499 GLU cc_start: 0.7330 (pp20) cc_final: 0.6949 (pp20) REVERT: A 529 ARG cc_start: 0.7777 (mpt-90) cc_final: 0.7464 (mpt-90) REVERT: A 533 LYS cc_start: 0.8618 (ttpp) cc_final: 0.7981 (tppp) REVERT: A 565 TYR cc_start: 0.6199 (m-80) cc_final: 0.5890 (m-10) REVERT: B 533 LYS cc_start: 0.9007 (tttm) cc_final: 0.8615 (tttm) REVERT: C 288 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7823 (mt-10) REVERT: C 499 GLU cc_start: 0.7403 (pp20) cc_final: 0.7114 (pp20) REVERT: C 533 LYS cc_start: 0.8838 (tttt) cc_final: 0.8083 (ttpt) REVERT: D 246 GLU cc_start: 0.6606 (pm20) cc_final: 0.6393 (pm20) REVERT: D 311 THR cc_start: 0.7792 (p) cc_final: 0.7572 (p) REVERT: D 432 ASN cc_start: 0.7874 (p0) cc_final: 0.7266 (p0) REVERT: D 499 GLU cc_start: 0.7524 (pp20) cc_final: 0.7033 (pp20) REVERT: D 533 LYS cc_start: 0.8989 (tttt) cc_final: 0.8067 (ttpt) REVERT: D 609 MET cc_start: 0.8787 (ppp) cc_final: 0.8390 (ppp) REVERT: E 389 ILE cc_start: 0.9351 (tt) cc_final: 0.9074 (mt) REVERT: E 533 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8054 (ttpt) REVERT: F 269 ASP cc_start: 0.9001 (p0) cc_final: 0.8657 (p0) REVERT: F 533 LYS cc_start: 0.8650 (ttpp) cc_final: 0.7902 (tppp) REVERT: F 609 MET cc_start: 0.8562 (ppp) cc_final: 0.8307 (ppp) REVERT: F 610 ASN cc_start: 0.8298 (p0) cc_final: 0.8003 (p0) REVERT: G 269 ASP cc_start: 0.9110 (p0) cc_final: 0.8892 (p0) REVERT: G 311 THR cc_start: 0.7965 (p) cc_final: 0.7738 (p) REVERT: G 533 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8321 (ttpp) outliers start: 2 outliers final: 1 residues processed: 483 average time/residue: 0.2899 time to fit residues: 214.4357 Evaluate side-chains 382 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN C 450 ASN D 425 GLN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN G 450 ASN G 509 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18893 Z= 0.173 Angle : 0.627 8.037 25585 Z= 0.339 Chirality : 0.046 0.170 2919 Planarity : 0.004 0.048 3339 Dihedral : 6.235 39.017 2555 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.16), residues: 2366 helix: -2.24 (0.24), residues: 371 sheet: -1.53 (0.21), residues: 483 loop : -2.85 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 245 HIS 0.002 0.001 HIS F 314 PHE 0.022 0.003 PHE A 566 TYR 0.013 0.001 TYR B 565 ARG 0.005 0.001 ARG E 529 *********************** 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 510 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 507 time to evaluate : 2.145 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 499 GLU cc_start: 0.7272 (pp20) cc_final: 0.6962 (pp20) REVERT: A 529 ARG cc_start: 0.7855 (mpt-90) cc_final: 0.7477 (mpt-90) REVERT: A 533 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8091 (tppp) REVERT: A 565 TYR cc_start: 0.6339 (m-80) cc_final: 0.6003 (m-10) REVERT: B 283 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8449 (mmpt) REVERT: B 389 ILE cc_start: 0.9425 (tt) cc_final: 0.9129 (mt) REVERT: B 509 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.9153 (tt0) REVERT: B 533 LYS cc_start: 0.9079 (tttm) cc_final: 0.8675 (tttm) REVERT: C 288 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7828 (mt-10) REVERT: C 533 LYS cc_start: 0.8843 (tttt) cc_final: 0.8272 (ttpt) REVERT: D 389 ILE cc_start: 0.9352 (tt) cc_final: 0.8927 (mt) REVERT: D 426 GLU cc_start: 0.7905 (pt0) cc_final: 0.7542 (pt0) REVERT: D 432 ASN cc_start: 0.7727 (p0) cc_final: 0.7147 (p0) REVERT: D 499 GLU cc_start: 0.7450 (pp20) cc_final: 0.7017 (pp20) REVERT: D 529 ARG cc_start: 0.7788 (mmt90) cc_final: 0.7428 (mmt90) REVERT: D 533 LYS cc_start: 0.8976 (tttt) cc_final: 0.8084 (ttpt) REVERT: D 609 MET cc_start: 0.8735 (ppp) cc_final: 0.8420 (ppp) REVERT: E 389 ILE cc_start: 0.9314 (tt) cc_final: 0.9099 (mt) REVERT: E 533 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8170 (ttpt) REVERT: E 555 PHE cc_start: 0.7737 (m-10) cc_final: 0.7499 (m-10) REVERT: F 520 ASP cc_start: 0.8783 (p0) cc_final: 0.7856 (t70) REVERT: F 533 LYS cc_start: 0.8642 (ttpp) cc_final: 0.7882 (tppp) REVERT: F 610 ASN cc_start: 0.8321 (p0) cc_final: 0.7962 (p0) REVERT: G 269 ASP cc_start: 0.9066 (p0) cc_final: 0.8845 (p0) REVERT: G 311 THR cc_start: 0.7858 (p) cc_final: 0.7618 (p) REVERT: G 524 GLU cc_start: 0.8071 (tt0) cc_final: 0.7760 (tt0) REVERT: G 533 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8097 (ttpp) REVERT: G 544 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8001 (pm20) outliers start: 3 outliers final: 1 residues processed: 507 average time/residue: 0.2891 time to fit residues: 225.0281 Evaluate side-chains 402 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 400 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 0.0980 chunk 25 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN D 450 ASN E 390 ASN G 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18893 Z= 0.164 Angle : 0.621 8.057 25585 Z= 0.334 Chirality : 0.045 0.168 2919 Planarity : 0.004 0.046 3339 Dihedral : 6.059 38.915 2555 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.10 % Allowed : 1.35 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.16), residues: 2366 helix: -2.14 (0.25), residues: 378 sheet: -1.45 (0.21), residues: 483 loop : -2.66 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 503 HIS 0.002 0.001 HIS F 314 PHE 0.014 0.002 PHE G 566 TYR 0.016 0.001 TYR C 464 ARG 0.005 0.001 ARG E 529 *********************** 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 519 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 517 time to evaluate : 2.444 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 246 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7424 (mt-10) REVERT: A 499 GLU cc_start: 0.7256 (pp20) cc_final: 0.6953 (pp20) REVERT: A 529 ARG cc_start: 0.7806 (mpt-90) cc_final: 0.7484 (mpt-90) REVERT: A 533 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8119 (tppp) REVERT: A 565 TYR cc_start: 0.6201 (m-80) cc_final: 0.5920 (m-10) REVERT: A 609 MET cc_start: 0.8361 (ppp) cc_final: 0.8149 (ppp) REVERT: B 283 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8406 (mmpt) REVERT: B 389 ILE cc_start: 0.9433 (tt) cc_final: 0.9151 (mt) REVERT: B 533 LYS cc_start: 0.9076 (tttm) cc_final: 0.8669 (tttm) REVERT: C 533 LYS cc_start: 0.8871 (tttt) cc_final: 0.8130 (ttpt) REVERT: C 555 PHE cc_start: 0.7898 (m-10) cc_final: 0.7672 (m-10) REVERT: D 246 GLU cc_start: 0.6395 (pm20) cc_final: 0.6155 (pm20) REVERT: D 389 ILE cc_start: 0.9349 (tt) cc_final: 0.8969 (mt) REVERT: D 426 GLU cc_start: 0.7731 (pt0) cc_final: 0.7343 (pt0) REVERT: D 432 ASN cc_start: 0.7720 (p0) cc_final: 0.7093 (p0) REVERT: D 499 GLU cc_start: 0.7253 (pp20) cc_final: 0.6863 (pp20) REVERT: D 533 LYS cc_start: 0.8947 (tttt) cc_final: 0.8094 (ttpt) REVERT: D 609 MET cc_start: 0.8628 (ppp) cc_final: 0.8320 (ppp) REVERT: E 389 ILE cc_start: 0.9285 (tt) cc_final: 0.9032 (mt) REVERT: E 533 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8212 (ttpt) REVERT: E 549 GLU cc_start: 0.8748 (tt0) cc_final: 0.8290 (pt0) REVERT: F 520 ASP cc_start: 0.8811 (p0) cc_final: 0.7942 (t70) REVERT: F 533 LYS cc_start: 0.8640 (ttpp) cc_final: 0.7804 (tppp) REVERT: F 609 MET cc_start: 0.8539 (ppp) cc_final: 0.8328 (ppp) REVERT: F 610 ASN cc_start: 0.8357 (p0) cc_final: 0.8005 (p0) REVERT: G 269 ASP cc_start: 0.8918 (p0) cc_final: 0.8708 (p0) REVERT: G 533 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8073 (ttpp) REVERT: G 544 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7924 (pm20) REVERT: G 549 GLU cc_start: 0.8739 (tt0) cc_final: 0.8362 (pt0) outliers start: 2 outliers final: 1 residues processed: 517 average time/residue: 0.3035 time to fit residues: 241.4309 Evaluate side-chains 418 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 180 optimal weight: 0.0030 overall best weight: 2.9996 ------------------------------------------------------------------------------- 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 501 ASN C 501 ASN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN E 509 GLN ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 GLN G 450 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2889 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= 0.270 Angle : 0.689 7.393 25585 Z= 0.372 Chirality : 0.048 0.203 2919 Planarity : 0.004 0.045 3339 Dihedral : 6.404 38.398 2555 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.07 % Favored : 85.93 % Rotamer: Outliers : 0.10 % Allowed : 1.25 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.16), residues: 2366 helix: -2.04 (0.25), residues: 371 sheet: -1.81 (0.23), residues: 427 loop : -2.71 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 503 HIS 0.003 0.001 HIS D 314 PHE 0.026 0.004 PHE C 566 TYR 0.016 0.001 TYR A 274 ARG 0.007 0.001 ARG G 529 *********************** 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 485 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 483 time to evaluate : 2.268 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 311 THR cc_start: 0.7798 (p) cc_final: 0.7586 (p) REVERT: A 499 GLU cc_start: 0.7385 (pp20) cc_final: 0.7069 (pp20) REVERT: A 529 ARG cc_start: 0.7840 (mpt-90) cc_final: 0.7459 (mpt-90) REVERT: A 533 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8112 (tppp) REVERT: A 565 TYR cc_start: 0.6251 (m-80) cc_final: 0.5919 (m-10) REVERT: A 609 MET cc_start: 0.8490 (ppp) cc_final: 0.8271 (ppp) REVERT: B 533 LYS cc_start: 0.9019 (tttm) cc_final: 0.8623 (tttm) REVERT: C 246 GLU cc_start: 0.6658 (pm20) cc_final: 0.6400 (pm20) REVERT: C 520 ASP cc_start: 0.8703 (p0) cc_final: 0.7890 (t70) REVERT: C 533 LYS cc_start: 0.8871 (tttt) cc_final: 0.8132 (ttpt) REVERT: D 246 GLU cc_start: 0.6320 (pm20) cc_final: 0.6059 (pm20) REVERT: D 311 THR cc_start: 0.7869 (p) cc_final: 0.7654 (p) REVERT: D 426 GLU cc_start: 0.7804 (pt0) cc_final: 0.7434 (pt0) REVERT: D 432 ASN cc_start: 0.7942 (p0) cc_final: 0.7307 (p0) REVERT: D 499 GLU cc_start: 0.7562 (pp20) cc_final: 0.7064 (pp20) REVERT: D 533 LYS cc_start: 0.8953 (tttt) cc_final: 0.8626 (ttpt) REVERT: D 609 MET cc_start: 0.8615 (ppp) cc_final: 0.8310 (ppp) REVERT: E 533 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8167 (ttpt) REVERT: E 552 GLU cc_start: 0.9020 (pp20) cc_final: 0.8776 (pp20) REVERT: F 520 ASP cc_start: 0.8711 (p0) cc_final: 0.7793 (t70) REVERT: F 533 LYS cc_start: 0.8693 (ttpp) cc_final: 0.7953 (tppp) REVERT: F 609 MET cc_start: 0.8511 (ppp) cc_final: 0.8255 (ppp) REVERT: F 610 ASN cc_start: 0.8341 (p0) cc_final: 0.7942 (p0) REVERT: G 288 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 311 THR cc_start: 0.8017 (p) cc_final: 0.7814 (p) REVERT: G 533 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8000 (ttpp) REVERT: G 544 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8085 (pm20) outliers start: 2 outliers final: 1 residues processed: 483 average time/residue: 0.2882 time to fit residues: 212.7674 Evaluate side-chains 386 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 385 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.5980 chunk 219 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 213 optimal weight: 0.4980 chunk 128 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 382 ASN C 450 ASN D 463 ASN E 432 ASN E 450 ASN F 463 ASN G 425 GLN G 450 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18893 Z= 0.207 Angle : 0.659 8.039 25585 Z= 0.354 Chirality : 0.047 0.256 2919 Planarity : 0.004 0.048 3339 Dihedral : 6.300 39.343 2555 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 0.19 % Allowed : 0.43 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.16), residues: 2366 helix: -1.96 (0.25), residues: 371 sheet: -1.49 (0.21), residues: 497 loop : -2.66 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 503 HIS 0.002 0.001 HIS D 314 PHE 0.014 0.003 PHE B 566 TYR 0.019 0.001 TYR C 526 ARG 0.006 0.001 ARG G 529 *********************** 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 495 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 491 time to evaluate : 2.166 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 246 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7408 (mt-10) REVERT: A 311 THR cc_start: 0.7744 (p) cc_final: 0.7523 (p) REVERT: A 499 GLU cc_start: 0.7308 (pp20) cc_final: 0.7014 (pp20) REVERT: A 529 ARG cc_start: 0.7803 (mpt-90) cc_final: 0.7419 (mpt-90) REVERT: A 533 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8192 (tppp) REVERT: A 565 TYR cc_start: 0.6277 (m-80) cc_final: 0.5921 (m-10) REVERT: A 609 MET cc_start: 0.8443 (ppp) cc_final: 0.8190 (ppp) REVERT: B 533 LYS cc_start: 0.9054 (tttm) cc_final: 0.8636 (tttm) REVERT: C 246 GLU cc_start: 0.6569 (pm20) cc_final: 0.6312 (pm20) REVERT: C 520 ASP cc_start: 0.8688 (p0) cc_final: 0.7826 (t70) REVERT: C 524 GLU cc_start: 0.8433 (pt0) cc_final: 0.8171 (pt0) REVERT: C 533 LYS cc_start: 0.8860 (tttt) cc_final: 0.8280 (ttpt) REVERT: D 246 GLU cc_start: 0.6291 (pm20) cc_final: 0.5968 (pm20) REVERT: D 311 THR cc_start: 0.7976 (p) cc_final: 0.7775 (p) REVERT: D 426 GLU cc_start: 0.7854 (pt0) cc_final: 0.7470 (pt0) REVERT: D 432 ASN cc_start: 0.7848 (p0) cc_final: 0.7290 (p0) REVERT: D 499 GLU cc_start: 0.7353 (pp20) cc_final: 0.6864 (pp20) REVERT: D 533 LYS cc_start: 0.8947 (tttt) cc_final: 0.8622 (ttpt) REVERT: D 609 MET cc_start: 0.8625 (ppp) cc_final: 0.8366 (ppp) REVERT: E 246 GLU cc_start: 0.6503 (pm20) cc_final: 0.6200 (pm20) REVERT: E 533 LYS cc_start: 0.8955 (ttpt) cc_final: 0.8249 (ttpt) REVERT: E 552 GLU cc_start: 0.9054 (pp20) cc_final: 0.8734 (pp20) REVERT: E 555 PHE cc_start: 0.8164 (m-10) cc_final: 0.7921 (m-10) REVERT: F 533 LYS cc_start: 0.8661 (ttpp) cc_final: 0.7898 (tppp) REVERT: F 609 MET cc_start: 0.8577 (ppp) cc_final: 0.8325 (ppp) REVERT: F 610 ASN cc_start: 0.8385 (p0) cc_final: 0.7945 (p0) REVERT: G 288 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8116 (mt-10) REVERT: G 431 ASN cc_start: 0.7800 (m-40) cc_final: 0.7552 (m110) REVERT: G 533 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8034 (ttpp) REVERT: G 544 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8042 (pm20) outliers start: 4 outliers final: 0 residues processed: 491 average time/residue: 0.3110 time to fit residues: 237.0031 Evaluate side-chains 400 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 145 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN A 501 ASN B 450 ASN C 382 ASN C 501 ASN F 463 ASN G 425 GLN G 450 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18893 Z= 0.157 Angle : 0.624 7.300 25585 Z= 0.333 Chirality : 0.045 0.211 2919 Planarity : 0.004 0.047 3339 Dihedral : 5.914 38.343 2555 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 0.10 % Allowed : 0.24 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.16), residues: 2366 helix: -2.09 (0.25), residues: 364 sheet: -1.40 (0.21), residues: 497 loop : -2.51 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 503 HIS 0.002 0.001 HIS F 314 PHE 0.026 0.002 PHE C 566 TYR 0.018 0.001 TYR C 526 ARG 0.005 0.000 ARG G 528 ********************** 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 538 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 536 time to evaluate : 2.350 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: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7451 (mt-10) REVERT: A 529 ARG cc_start: 0.7738 (mpt-90) cc_final: 0.7372 (mpt-90) REVERT: A 533 LYS cc_start: 0.8531 (ttpp) cc_final: 0.8062 (tppp) REVERT: A 565 TYR cc_start: 0.6325 (m-80) cc_final: 0.5793 (m-80) REVERT: A 566 PHE cc_start: 0.7707 (t80) cc_final: 0.7418 (t80) REVERT: A 609 MET cc_start: 0.8263 (ppp) cc_final: 0.7949 (ppp) REVERT: B 283 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8507 (mmpt) REVERT: B 288 GLU cc_start: 0.7798 (tp30) cc_final: 0.7562 (tp30) REVERT: B 389 ILE cc_start: 0.9423 (tt) cc_final: 0.9183 (mt) REVERT: B 533 LYS cc_start: 0.9092 (tttm) cc_final: 0.8597 (tttm) REVERT: C 460 ILE cc_start: 0.8597 (mp) cc_final: 0.8260 (mp) REVERT: C 482 GLN cc_start: 0.8535 (pp30) cc_final: 0.7495 (pp30) REVERT: C 520 ASP cc_start: 0.8679 (p0) cc_final: 0.7851 (t70) REVERT: C 524 GLU cc_start: 0.8323 (pt0) cc_final: 0.8023 (pt0) REVERT: D 246 GLU cc_start: 0.6275 (pm20) cc_final: 0.5940 (pm20) REVERT: D 426 GLU cc_start: 0.7930 (pt0) cc_final: 0.7482 (pt0) REVERT: D 432 ASN cc_start: 0.7650 (p0) cc_final: 0.6992 (p0) REVERT: D 499 GLU cc_start: 0.7169 (pp20) cc_final: 0.6750 (pp20) REVERT: D 533 LYS cc_start: 0.9001 (tttt) cc_final: 0.8671 (ttpt) REVERT: D 609 MET cc_start: 0.8537 (ppp) cc_final: 0.8329 (ppp) REVERT: E 389 ILE cc_start: 0.9285 (tt) cc_final: 0.9057 (mt) REVERT: E 533 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8196 (ttpt) REVERT: E 552 GLU cc_start: 0.9097 (pp20) cc_final: 0.8661 (pp20) REVERT: F 275 GLU cc_start: 0.8306 (tt0) cc_final: 0.7941 (pt0) REVERT: F 278 SER cc_start: 0.9533 (p) cc_final: 0.9321 (m) REVERT: F 533 LYS cc_start: 0.8688 (ttpp) cc_final: 0.7970 (tppp) REVERT: F 610 ASN cc_start: 0.8336 (p0) cc_final: 0.7934 (p0) REVERT: F 614 LYS cc_start: 0.9180 (mmtp) cc_final: 0.8925 (mmtp) REVERT: G 431 ASN cc_start: 0.7614 (m-40) cc_final: 0.7141 (m110) REVERT: G 524 GLU cc_start: 0.8264 (tt0) cc_final: 0.8060 (tt0) REVERT: G 533 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8001 (ttpp) REVERT: G 544 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8027 (pm20) outliers start: 2 outliers final: 0 residues processed: 536 average time/residue: 0.2912 time to fit residues: 239.6358 Evaluate side-chains 434 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN B 390 ASN B 509 GLN C 450 ASN C 501 ASN D 450 ASN ** E 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN E 509 GLN ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN G 425 GLN G 450 ASN G 509 GLN G 610 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.147916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120876 restraints weight = 36347.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124076 restraints weight = 20754.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126209 restraints weight = 14185.367| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 18893 Z= 0.276 Angle : 0.703 11.337 25585 Z= 0.377 Chirality : 0.048 0.301 2919 Planarity : 0.004 0.044 3339 Dihedral : 6.267 38.462 2555 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Rotamer: Outliers : 0.19 % Allowed : 0.58 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.16), residues: 2366 helix: -2.06 (0.25), residues: 371 sheet: -1.78 (0.23), residues: 427 loop : -2.60 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 503 HIS 0.003 0.001 HIS D 314 PHE 0.031 0.004 PHE A 566 TYR 0.016 0.001 TYR A 274 ARG 0.006 0.001 ARG G 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4461.82 seconds wall clock time: 81 minutes 25.36 seconds (4885.36 seconds total)